Starting phenix.real_space_refine on Wed Jun 25 02:24:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ppq_17808/06_2025/8ppq_17808_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ppq_17808/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ppq_17808/06_2025/8ppq_17808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ppq_17808/06_2025/8ppq_17808.map" model { file = "/net/cci-nas-00/data/ceres_data/8ppq_17808/06_2025/8ppq_17808_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ppq_17808/06_2025/8ppq_17808_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.97, per 1000 atoms: 0.48 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: 6.86 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.88 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: 11.46 Time building geometry restraints manager: 8.59 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 496 or resid 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: 0.850 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: 0.530 Extract box with map and model: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 60.740 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.247 0.031 TRP C 44 HIS 0.043 0.005 HIS B 146 PHE 0.067 0.017 PHE C 220 TYR 0.191 0.035 TYR b 47 ARG 0.027 0.002 ARG c 77 Details of bonding type rmsd link_NAG-ASN : bond 0.01678 ( 3) link_NAG-ASN : angle 7.33469 ( 9) hydrogen bonds : bond 0.20329 ( 558) hydrogen bonds : angle 7.27531 ( 1503) SS BOND : bond 0.02883 ( 24) SS BOND : angle 2.59422 ( 48) covalent geometry : bond 0.01259 (14989) covalent geometry : angle 1.91886 (20335) *********************** 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 : 1.957 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: 0.5183 time to fit residues: 328.9741 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 : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.186660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145349 restraints weight = 65444.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152295 restraints weight = 26950.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156608 restraints weight = 14301.025| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15016 Z= 0.167 Angle : 0.684 12.394 20392 Z= 0.369 Chirality : 0.045 0.240 2357 Planarity : 0.006 0.081 2574 Dihedral : 5.896 65.417 2105 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.45 % Allowed : 8.48 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1899 helix: 1.92 (0.26), residues: 416 sheet: -0.50 (0.21), residues: 594 loop : -1.73 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 44 HIS 0.016 0.002 HIS A 282 PHE 0.029 0.002 PHE c 64 TYR 0.017 0.002 TYR b 47 ARG 0.007 0.001 ARG A 99 Details of bonding type rmsd link_NAG-ASN : bond 0.01044 ( 3) link_NAG-ASN : angle 6.60595 ( 9) hydrogen bonds : bond 0.05688 ( 558) hydrogen bonds : angle 6.19081 ( 1503) SS BOND : bond 0.00480 ( 24) SS BOND : angle 1.40804 ( 48) covalent geometry : bond 0.00380 (14989) covalent geometry : angle 0.66752 (20335) *********************** 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 383 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 360 time to evaluate : 1.994 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: A 1 SER cc_start: 0.8490 (t) cc_final: 0.7895 (p) REVERT: A 82 LEU cc_start: 0.8283 (mt) cc_final: 0.8038 (mt) REVERT: A 98 ASP cc_start: 0.8008 (t0) cc_final: 0.7650 (p0) REVERT: A 116 CYS cc_start: 0.4839 (m) cc_final: 0.4452 (m) REVERT: A 161 LYS cc_start: 0.8467 (mptt) cc_final: 0.8209 (mptt) REVERT: A 187 ARG cc_start: 0.7522 (ttt-90) cc_final: 0.7049 (ttm110) REVERT: A 230 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 285 SER cc_start: 0.6851 (t) cc_final: 0.6498 (p) REVERT: A 294 LEU cc_start: 0.8265 (tp) cc_final: 0.7933 (tp) REVERT: A 471 MET cc_start: 0.2954 (mpp) cc_final: 0.2546 (mpp) REVERT: A 478 MET cc_start: 0.3498 (mmp) cc_final: 0.2828 (mmp) REVERT: B 285 SER cc_start: 0.7647 (t) cc_final: 0.7346 (m) REVERT: B 356 MET cc_start: 0.5257 (ttm) cc_final: 0.4925 (tpt) REVERT: C 24 VAL cc_start: 0.7542 (OUTLIER) cc_final: 0.7285 (p) REVERT: C 42 ASP cc_start: 0.7002 (t70) cc_final: 0.6791 (t0) REVERT: C 66 SER cc_start: 0.8269 (p) cc_final: 0.8053 (t) REVERT: C 211 THR cc_start: 0.6743 (p) cc_final: 0.4997 (m) REVERT: C 234 ASN cc_start: 0.7874 (m-40) cc_final: 0.7629 (m-40) REVERT: C 324 ASP cc_start: 0.7728 (t0) cc_final: 0.7384 (t0) REVERT: C 380 ASP cc_start: 0.7671 (m-30) cc_final: 0.7246 (p0) REVERT: C 392 TRP cc_start: 0.7824 (t-100) cc_final: 0.7594 (t-100) REVERT: b 13 ARG cc_start: 0.6277 (ptm160) cc_final: 0.4982 (ptp-170) REVERT: c 24 ARG cc_start: 0.5450 (mmt180) cc_final: 0.5227 (ptt-90) REVERT: c 43 ASP cc_start: 0.7989 (t0) cc_final: 0.7676 (t0) REVERT: c 59 VAL cc_start: 0.8884 (t) cc_final: 0.8674 (p) REVERT: c 74 GLU cc_start: 0.5261 (pt0) cc_final: 0.5010 (pt0) REVERT: c 119 ARG cc_start: 0.7228 (ttt180) cc_final: 0.6887 (ttm110) outliers start: 23 outliers final: 18 residues processed: 368 average time/residue: 0.5256 time to fit residues: 291.9403 Evaluate side-chains 352 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 333 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 163 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.189377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147221 restraints weight = 68351.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154398 restraints weight = 27936.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.158984 restraints weight = 14905.635| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15016 Z= 0.121 Angle : 0.572 6.383 20392 Z= 0.308 Chirality : 0.044 0.167 2357 Planarity : 0.004 0.075 2574 Dihedral : 5.509 58.947 2105 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.20 % Allowed : 11.39 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 1899 helix: 2.19 (0.27), residues: 416 sheet: -0.52 (0.21), residues: 567 loop : -1.57 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 44 HIS 0.011 0.001 HIS B 323 PHE 0.017 0.001 PHE c 64 TYR 0.016 0.002 TYR b 47 ARG 0.007 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00907 ( 3) link_NAG-ASN : angle 4.63810 ( 9) hydrogen bonds : bond 0.04473 ( 558) hydrogen bonds : angle 5.69757 ( 1503) SS BOND : bond 0.00393 ( 24) SS BOND : angle 1.38428 ( 48) covalent geometry : bond 0.00263 (14989) covalent geometry : angle 0.56030 (20335) *********************** 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 363 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 344 time to evaluate : 2.182 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: A 1 SER cc_start: 0.8232 (t) cc_final: 0.7678 (p) REVERT: A 58 GLU cc_start: 0.6654 (tt0) cc_final: 0.6298 (tt0) REVERT: A 82 LEU cc_start: 0.8216 (mt) cc_final: 0.7965 (mt) REVERT: A 95 ASP cc_start: 0.8182 (t70) cc_final: 0.7837 (t0) REVERT: A 116 CYS cc_start: 0.4922 (m) cc_final: 0.4614 (m) REVERT: A 161 LYS cc_start: 0.8404 (mptt) cc_final: 0.8186 (mptt) REVERT: A 164 SER cc_start: 0.8581 (p) cc_final: 0.8345 (p) REVERT: A 187 ARG cc_start: 0.7545 (ttt-90) cc_final: 0.7168 (ttm110) REVERT: A 230 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7756 (mm-30) REVERT: A 285 SER cc_start: 0.6871 (t) cc_final: 0.6470 (p) REVERT: A 294 LEU cc_start: 0.8319 (tp) cc_final: 0.7986 (tp) REVERT: A 471 MET cc_start: 0.2881 (mpp) cc_final: 0.2441 (mpp) REVERT: B 20 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7335 (mtp180) REVERT: B 203 ASP cc_start: 0.7654 (t0) cc_final: 0.7412 (t0) REVERT: B 285 SER cc_start: 0.7496 (t) cc_final: 0.7233 (m) REVERT: B 356 MET cc_start: 0.5194 (ttm) cc_final: 0.4921 (tpt) REVERT: C 24 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7412 (p) REVERT: C 66 SER cc_start: 0.8189 (p) cc_final: 0.7982 (t) REVERT: C 211 THR cc_start: 0.6576 (p) cc_final: 0.4847 (m) REVERT: C 234 ASN cc_start: 0.7764 (m-40) cc_final: 0.7528 (m-40) REVERT: C 324 ASP cc_start: 0.7782 (t0) cc_final: 0.7427 (t0) REVERT: C 356 MET cc_start: 0.2203 (ttp) cc_final: 0.1890 (ttm) REVERT: C 380 ASP cc_start: 0.7675 (m-30) cc_final: 0.7411 (p0) REVERT: C 392 TRP cc_start: 0.7819 (t-100) cc_final: 0.7414 (t-100) REVERT: b 13 ARG cc_start: 0.6412 (ptm160) cc_final: 0.5017 (ptp-170) REVERT: c 13 ARG cc_start: 0.7126 (ptp-170) cc_final: 0.5813 (ptp-170) REVERT: c 24 ARG cc_start: 0.5514 (mmt180) cc_final: 0.5286 (ptt-90) REVERT: c 43 ASP cc_start: 0.8004 (t0) cc_final: 0.7702 (t0) REVERT: c 74 GLU cc_start: 0.5352 (pt0) cc_final: 0.4830 (pt0) REVERT: c 119 ARG cc_start: 0.7249 (ttt180) cc_final: 0.6893 (ttm110) REVERT: c 121 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6715 (mp0) outliers start: 19 outliers final: 15 residues processed: 352 average time/residue: 0.5422 time to fit residues: 289.6005 Evaluate side-chains 352 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 335 time to evaluate : 2.242 ------------------------------------------------------------------------------- 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 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 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 1 THR Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 121 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 4 optimal weight: 0.8980 chunk 152 optimal weight: 0.0000 chunk 18 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 50 GLN ** 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 = 0.4206 r_free = 0.4206 target = 0.186097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.146808 restraints weight = 62901.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153581 restraints weight = 25463.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157816 restraints weight = 13358.424| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15016 Z= 0.138 Angle : 0.565 6.487 20392 Z= 0.303 Chirality : 0.043 0.165 2357 Planarity : 0.003 0.055 2574 Dihedral : 5.375 53.997 2105 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.83 % Allowed : 11.95 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 1899 helix: 2.55 (0.27), residues: 401 sheet: -0.40 (0.21), residues: 581 loop : -1.65 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 227 HIS 0.009 0.001 HIS A 323 PHE 0.020 0.001 PHE c 64 TYR 0.019 0.002 TYR b 47 ARG 0.005 0.000 ARG A 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00894 ( 3) link_NAG-ASN : angle 4.36577 ( 9) hydrogen bonds : bond 0.04168 ( 558) hydrogen bonds : angle 5.51144 ( 1503) SS BOND : bond 0.00442 ( 24) SS BOND : angle 1.56783 ( 48) covalent geometry : bond 0.00300 (14989) covalent geometry : angle 0.55256 (20335) *********************** 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 370 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 341 time to evaluate : 2.328 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: A 1 SER cc_start: 0.8270 (t) cc_final: 0.7717 (p) REVERT: A 82 LEU cc_start: 0.8305 (mt) cc_final: 0.8089 (mt) REVERT: A 95 ASP cc_start: 0.8172 (t70) cc_final: 0.7752 (t0) REVERT: A 98 ASP cc_start: 0.7982 (t0) cc_final: 0.7469 (p0) REVERT: A 116 CYS cc_start: 0.4893 (m) cc_final: 0.4540 (m) REVERT: A 146 HIS cc_start: 0.6516 (OUTLIER) cc_final: 0.6250 (t-90) REVERT: A 161 LYS cc_start: 0.8412 (mptt) cc_final: 0.8160 (mptt) REVERT: A 164 SER cc_start: 0.8607 (p) cc_final: 0.8371 (p) REVERT: A 187 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.7111 (ttm110) REVERT: A 230 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 248 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6736 (m170) REVERT: A 294 LEU cc_start: 0.8327 (tp) cc_final: 0.7976 (tp) REVERT: A 471 MET cc_start: 0.2974 (mpp) cc_final: 0.2739 (mpp) REVERT: B 20 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7371 (mtp180) REVERT: B 203 ASP cc_start: 0.7809 (t0) cc_final: 0.7571 (t0) REVERT: B 285 SER cc_start: 0.7607 (t) cc_final: 0.7280 (m) REVERT: B 356 MET cc_start: 0.5093 (ttm) cc_final: 0.4877 (tpt) REVERT: C 24 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7359 (p) REVERT: C 144 GLU cc_start: 0.6835 (mp0) cc_final: 0.6542 (mp0) REVERT: C 211 THR cc_start: 0.6535 (p) cc_final: 0.4857 (m) REVERT: C 234 ASN cc_start: 0.7753 (m-40) cc_final: 0.7470 (m-40) REVERT: C 324 ASP cc_start: 0.7803 (t0) cc_final: 0.7461 (t0) REVERT: C 356 MET cc_start: 0.2089 (ttp) cc_final: 0.1801 (ttm) REVERT: C 380 ASP cc_start: 0.7703 (m-30) cc_final: 0.7429 (p0) REVERT: C 392 TRP cc_start: 0.7857 (t-100) cc_final: 0.7429 (t-100) REVERT: b 13 ARG cc_start: 0.6551 (ptm160) cc_final: 0.5240 (ptp-170) REVERT: c 24 ARG cc_start: 0.5484 (mmt180) cc_final: 0.5048 (ptt-90) REVERT: c 43 ASP cc_start: 0.8068 (t0) cc_final: 0.7801 (t0) REVERT: c 119 ARG cc_start: 0.7217 (ttt180) cc_final: 0.6899 (ttm110) REVERT: c 121 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6680 (mp0) outliers start: 29 outliers final: 24 residues processed: 355 average time/residue: 0.5209 time to fit residues: 283.6203 Evaluate side-chains 361 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 333 time to evaluate : 2.288 ------------------------------------------------------------------------------- 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 248 HIS 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 66 SER 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 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 112 SER Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 157 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 17 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 144 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.185595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146278 restraints weight = 63163.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.153105 restraints weight = 25639.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.157321 restraints weight = 13443.376| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 15016 Z= 0.146 Angle : 0.570 7.430 20392 Z= 0.305 Chirality : 0.043 0.216 2357 Planarity : 0.004 0.057 2574 Dihedral : 5.257 48.276 2105 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.96 % Allowed : 12.90 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.19), residues: 1899 helix: 2.59 (0.27), residues: 401 sheet: -0.43 (0.21), residues: 551 loop : -1.62 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 227 HIS 0.009 0.001 HIS A 323 PHE 0.030 0.001 PHE B 371 TYR 0.020 0.002 TYR b 47 ARG 0.004 0.000 ARG A 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00920 ( 3) link_NAG-ASN : angle 4.21502 ( 9) hydrogen bonds : bond 0.04020 ( 558) hydrogen bonds : angle 5.38227 ( 1503) SS BOND : bond 0.00431 ( 24) SS BOND : angle 1.78998 ( 48) covalent geometry : bond 0.00334 (14989) covalent geometry : angle 0.55715 (20335) *********************** 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 369 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 338 time to evaluate : 2.362 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: 0.8327 (t) cc_final: 0.7788 (p) REVERT: A 59 TYR cc_start: 0.6729 (m-80) cc_final: 0.6444 (m-80) REVERT: A 82 LEU cc_start: 0.8320 (mt) cc_final: 0.8078 (mt) REVERT: A 98 ASP cc_start: 0.8044 (t0) cc_final: 0.7469 (p0) REVERT: A 116 CYS cc_start: 0.4842 (m) cc_final: 0.4508 (m) REVERT: A 146 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.6404 (t-90) REVERT: A 161 LYS cc_start: 0.8480 (mptt) cc_final: 0.8256 (mptt) REVERT: A 164 SER cc_start: 0.8589 (p) cc_final: 0.8359 (p) REVERT: A 187 ARG cc_start: 0.7420 (ttt-90) cc_final: 0.7164 (ttm110) REVERT: A 223 LEU cc_start: 0.7750 (tp) cc_final: 0.7465 (tp) REVERT: A 230 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 248 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.6667 (m170) REVERT: A 294 LEU cc_start: 0.8311 (tp) cc_final: 0.7944 (tp) REVERT: A 471 MET cc_start: 0.3027 (mpp) cc_final: 0.2784 (mpp) REVERT: B 20 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7336 (mtp180) REVERT: B 203 ASP cc_start: 0.7850 (t0) cc_final: 0.7615 (t0) REVERT: B 285 SER cc_start: 0.7602 (t) cc_final: 0.7305 (m) REVERT: C 24 VAL cc_start: 0.7586 (OUTLIER) cc_final: 0.7334 (p) REVERT: C 92 CYS cc_start: 0.5350 (m) cc_final: 0.5024 (m) REVERT: C 144 GLU cc_start: 0.6843 (mp0) cc_final: 0.6513 (mp0) REVERT: C 211 THR cc_start: 0.6534 (p) cc_final: 0.4848 (m) REVERT: C 234 ASN cc_start: 0.7795 (m-40) cc_final: 0.7481 (m-40) REVERT: C 324 ASP cc_start: 0.7787 (t0) cc_final: 0.7454 (t0) REVERT: C 356 MET cc_start: 0.1997 (ttp) cc_final: 0.1715 (ttm) REVERT: C 380 ASP cc_start: 0.7762 (m-30) cc_final: 0.7432 (p0) REVERT: C 392 TRP cc_start: 0.7891 (t-100) cc_final: 0.7436 (t-100) REVERT: a 60 ASP cc_start: 0.7252 (t0) cc_final: 0.6986 (t0) REVERT: b 13 ARG cc_start: 0.6663 (ptm160) cc_final: 0.5397 (ptp-170) REVERT: c 24 ARG cc_start: 0.5543 (mmt180) cc_final: 0.5030 (ptt-90) REVERT: c 43 ASP cc_start: 0.8005 (t0) cc_final: 0.7778 (t0) REVERT: c 57 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7003 (mm-30) REVERT: c 119 ARG cc_start: 0.7204 (ttt180) cc_final: 0.6900 (ttm110) outliers start: 31 outliers final: 24 residues processed: 351 average time/residue: 0.5446 time to fit residues: 294.1030 Evaluate side-chains 363 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 336 time to evaluate : 2.266 ------------------------------------------------------------------------------- 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 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 23 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 SER 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 46 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4173 r_free = 0.4173 target = 0.182472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143478 restraints weight = 62754.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.150125 restraints weight = 25463.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.154222 restraints weight = 13384.334| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 15016 Z= 0.219 Angle : 0.623 11.249 20392 Z= 0.335 Chirality : 0.044 0.242 2357 Planarity : 0.004 0.057 2574 Dihedral : 5.468 49.271 2105 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.34 % Allowed : 14.55 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1899 helix: 2.19 (0.27), residues: 416 sheet: -0.61 (0.21), residues: 581 loop : -1.88 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 227 HIS 0.012 0.002 HIS B 282 PHE 0.025 0.002 PHE B 371 TYR 0.031 0.003 TYR b 47 ARG 0.006 0.001 ARG B 99 Details of bonding type rmsd link_NAG-ASN : bond 0.01107 ( 3) link_NAG-ASN : angle 4.01917 ( 9) hydrogen bonds : bond 0.04394 ( 558) hydrogen bonds : angle 5.44376 ( 1503) SS BOND : bond 0.00774 ( 24) SS BOND : angle 1.71728 ( 48) covalent geometry : bond 0.00487 (14989) covalent geometry : angle 0.61219 (20335) *********************** 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 371 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 334 time to evaluate : 2.093 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: 0.8530 (t) cc_final: 0.8077 (p) REVERT: A 59 TYR cc_start: 0.7095 (m-80) cc_final: 0.6893 (m-80) REVERT: A 82 LEU cc_start: 0.8349 (mt) cc_final: 0.8144 (mt) REVERT: A 116 CYS cc_start: 0.4769 (m) cc_final: 0.4415 (m) REVERT: A 146 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6741 (t-90) REVERT: A 161 LYS cc_start: 0.8525 (mptt) cc_final: 0.8256 (mptt) REVERT: A 164 SER cc_start: 0.8605 (p) cc_final: 0.8361 (p) REVERT: A 187 ARG cc_start: 0.7582 (ttt-90) cc_final: 0.7215 (ttm110) REVERT: A 230 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 285 SER cc_start: 0.7073 (t) cc_final: 0.6624 (p) REVERT: A 294 LEU cc_start: 0.8402 (tp) cc_final: 0.8007 (tp) REVERT: A 471 MET cc_start: 0.3042 (mpp) cc_final: 0.2777 (mpp) REVERT: B 20 ARG cc_start: 0.7929 (mtp85) cc_final: 0.7307 (mtp180) REVERT: B 203 ASP cc_start: 0.7825 (t0) cc_final: 0.7601 (t0) REVERT: B 285 SER cc_start: 0.7727 (t) cc_final: 0.7426 (m) REVERT: B 374 MET cc_start: 0.5508 (mmm) cc_final: 0.5290 (mmm) REVERT: C 24 VAL cc_start: 0.7619 (OUTLIER) cc_final: 0.7348 (p) REVERT: C 92 CYS cc_start: 0.5365 (m) cc_final: 0.5039 (m) REVERT: C 211 THR cc_start: 0.6612 (p) cc_final: 0.4964 (m) REVERT: C 234 ASN cc_start: 0.7802 (m-40) cc_final: 0.7466 (m-40) REVERT: C 324 ASP cc_start: 0.7862 (t0) cc_final: 0.7501 (t0) REVERT: C 333 SER cc_start: 0.7861 (m) cc_final: 0.7458 (p) REVERT: C 356 MET cc_start: 0.1699 (ttp) cc_final: 0.1414 (ttm) REVERT: C 380 ASP cc_start: 0.7807 (m-30) cc_final: 0.7459 (p0) REVERT: b 13 ARG cc_start: 0.6904 (ptm160) cc_final: 0.5826 (ptp-170) REVERT: c 24 ARG cc_start: 0.5602 (mmt180) cc_final: 0.5005 (ptt-90) REVERT: c 43 ASP cc_start: 0.7994 (t0) cc_final: 0.7767 (t0) REVERT: c 57 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7112 (mm-30) REVERT: c 119 ARG cc_start: 0.7222 (ttt180) cc_final: 0.6913 (ttm110) outliers start: 37 outliers final: 32 residues processed: 350 average time/residue: 0.5219 time to fit residues: 280.0614 Evaluate side-chains 365 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 331 time to evaluate : 2.532 ------------------------------------------------------------------------------- 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 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 23 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 66 SER 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 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 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 61 VAL 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 46 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 170 optimal weight: 0.0170 chunk 175 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.184964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145511 restraints weight = 62826.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152361 restraints weight = 25442.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156541 restraints weight = 13385.402| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15016 Z= 0.118 Angle : 0.555 9.108 20392 Z= 0.295 Chirality : 0.043 0.204 2357 Planarity : 0.003 0.043 2574 Dihedral : 5.122 46.410 2105 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.64 % Allowed : 15.88 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1899 helix: 2.67 (0.27), residues: 401 sheet: -0.54 (0.20), residues: 590 loop : -1.67 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 44 HIS 0.007 0.001 HIS A 323 PHE 0.018 0.001 PHE c 64 TYR 0.016 0.002 TYR b 47 ARG 0.006 0.000 ARG A 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00908 ( 3) link_NAG-ASN : angle 4.29616 ( 9) hydrogen bonds : bond 0.03719 ( 558) hydrogen bonds : angle 5.25927 ( 1503) SS BOND : bond 0.00447 ( 24) SS BOND : angle 1.62148 ( 48) covalent geometry : bond 0.00269 (14989) covalent geometry : angle 0.54268 (20335) *********************** 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 359 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 333 time to evaluate : 2.210 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: 0.8436 (t) cc_final: 0.7697 (p) REVERT: A 59 TYR cc_start: 0.6995 (m-80) cc_final: 0.6754 (m-80) REVERT: A 82 LEU cc_start: 0.8310 (mt) cc_final: 0.8107 (mt) REVERT: A 95 ASP cc_start: 0.8228 (t70) cc_final: 0.7856 (t0) REVERT: A 116 CYS cc_start: 0.4790 (m) cc_final: 0.4440 (m) REVERT: A 146 HIS cc_start: 0.6941 (OUTLIER) cc_final: 0.5594 (t-90) REVERT: A 161 LYS cc_start: 0.8462 (mptt) cc_final: 0.8251 (mptt) REVERT: A 164 SER cc_start: 0.8537 (p) cc_final: 0.8303 (p) REVERT: A 187 ARG cc_start: 0.7502 (ttt-90) cc_final: 0.7185 (ttm110) REVERT: A 230 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 294 LEU cc_start: 0.8357 (tp) cc_final: 0.7947 (tp) REVERT: A 471 MET cc_start: 0.3032 (mpp) cc_final: 0.2739 (mpp) REVERT: B 20 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7249 (mtp180) REVERT: B 203 ASP cc_start: 0.7849 (t0) cc_final: 0.7640 (t0) REVERT: B 285 SER cc_start: 0.7677 (t) cc_final: 0.7376 (m) REVERT: C 24 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7341 (p) REVERT: C 92 CYS cc_start: 0.5274 (m) cc_final: 0.4962 (m) REVERT: C 211 THR cc_start: 0.6536 (p) cc_final: 0.4868 (m) REVERT: C 234 ASN cc_start: 0.7778 (m-40) cc_final: 0.7447 (m-40) REVERT: C 324 ASP cc_start: 0.7857 (t0) cc_final: 0.7526 (t0) REVERT: C 333 SER cc_start: 0.7763 (m) cc_final: 0.7320 (p) REVERT: C 356 MET cc_start: 0.1731 (ttp) cc_final: 0.1436 (ttm) REVERT: C 380 ASP cc_start: 0.7770 (m-30) cc_final: 0.7474 (p0) REVERT: b 13 ARG cc_start: 0.6642 (ptm160) cc_final: 0.5552 (ptp-170) REVERT: c 24 ARG cc_start: 0.5632 (mmt180) cc_final: 0.5018 (ptt-90) REVERT: c 43 ASP cc_start: 0.7997 (t0) cc_final: 0.7779 (t0) REVERT: c 57 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7144 (mm-30) REVERT: c 119 ARG cc_start: 0.7214 (ttt180) cc_final: 0.6886 (ttm110) outliers start: 26 outliers final: 20 residues processed: 344 average time/residue: 0.5361 time to fit residues: 285.0270 Evaluate side-chains 351 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 329 time to evaluate : 2.558 ------------------------------------------------------------------------------- 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 299 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 333 SER 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 478 MET 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 31 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 188 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.180747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141509 restraints weight = 62861.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.148138 restraints weight = 25648.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152303 restraints weight = 13620.052| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 15016 Z= 0.255 Angle : 0.645 8.689 20392 Z= 0.345 Chirality : 0.045 0.220 2357 Planarity : 0.004 0.053 2574 Dihedral : 5.444 50.154 2105 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 2.59 % Allowed : 15.69 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 1899 helix: 2.17 (0.27), residues: 416 sheet: -0.67 (0.21), residues: 581 loop : -2.02 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 44 HIS 0.013 0.002 HIS B 282 PHE 0.026 0.002 PHE A 220 TYR 0.032 0.003 TYR B 49 ARG 0.007 0.001 ARG c 88 Details of bonding type rmsd link_NAG-ASN : bond 0.01149 ( 3) link_NAG-ASN : angle 4.05289 ( 9) hydrogen bonds : bond 0.04441 ( 558) hydrogen bonds : angle 5.40869 ( 1503) SS BOND : bond 0.00642 ( 24) SS BOND : angle 1.81288 ( 48) covalent geometry : bond 0.00564 (14989) covalent geometry : angle 0.63462 (20335) *********************** 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 367 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 2.561 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: 0.8550 (t) cc_final: 0.8141 (p) REVERT: A 41 MET cc_start: 0.7013 (mtt) cc_final: 0.6752 (mtt) REVERT: A 82 LEU cc_start: 0.8419 (mt) cc_final: 0.8211 (mt) REVERT: A 116 CYS cc_start: 0.4784 (m) cc_final: 0.4461 (m) REVERT: A 161 LYS cc_start: 0.8512 (mptt) cc_final: 0.8243 (mptt) REVERT: A 164 SER cc_start: 0.8609 (p) cc_final: 0.8361 (p) REVERT: A 187 ARG cc_start: 0.7563 (ttt-90) cc_final: 0.7197 (ttm110) REVERT: A 230 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7967 (mm-30) REVERT: A 294 LEU cc_start: 0.8411 (tp) cc_final: 0.8045 (tp) REVERT: A 471 MET cc_start: 0.3053 (mpp) cc_final: 0.2773 (mpp) REVERT: B 20 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7266 (mtp180) REVERT: B 285 SER cc_start: 0.7800 (t) cc_final: 0.7460 (m) REVERT: C 24 VAL cc_start: 0.7605 (OUTLIER) cc_final: 0.7335 (p) REVERT: C 92 CYS cc_start: 0.5460 (m) cc_final: 0.5169 (m) REVERT: C 211 THR cc_start: 0.6519 (p) cc_final: 0.4910 (m) REVERT: C 234 ASN cc_start: 0.7804 (m-40) cc_final: 0.7466 (m-40) REVERT: C 324 ASP cc_start: 0.7903 (t0) cc_final: 0.7527 (t0) REVERT: C 333 SER cc_start: 0.7924 (m) cc_final: 0.7526 (p) REVERT: C 356 MET cc_start: 0.1718 (ttp) cc_final: 0.1415 (ttm) REVERT: C 380 ASP cc_start: 0.7866 (m-30) cc_final: 0.7494 (p0) REVERT: b 13 ARG cc_start: 0.6948 (ptm160) cc_final: 0.5997 (ptp-170) REVERT: c 24 ARG cc_start: 0.5640 (mmt180) cc_final: 0.4961 (ptt-90) REVERT: c 43 ASP cc_start: 0.7993 (t0) cc_final: 0.7770 (t0) REVERT: c 57 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7356 (mm-30) REVERT: c 119 ARG cc_start: 0.7228 (ttt180) cc_final: 0.6916 (ttm110) outliers start: 41 outliers final: 35 residues processed: 343 average time/residue: 0.6577 time to fit residues: 346.1040 Evaluate side-chains 363 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 327 time to evaluate : 4.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 90 THR 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 248 HIS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 SER 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 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 27 LEU Chi-restraints excluded: chain C residue 60 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 61 VAL 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 22 optimal weight: 0.6980 chunk 141 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 135 optimal weight: 0.0060 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.184771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.145387 restraints weight = 62406.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152175 restraints weight = 25359.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156360 restraints weight = 13436.378| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15016 Z= 0.112 Angle : 0.561 8.426 20392 Z= 0.297 Chirality : 0.043 0.198 2357 Planarity : 0.003 0.037 2574 Dihedral : 5.051 46.504 2105 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.45 % Allowed : 17.27 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1899 helix: 2.69 (0.27), residues: 401 sheet: -0.53 (0.21), residues: 557 loop : -1.66 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 44 HIS 0.006 0.001 HIS A 323 PHE 0.017 0.001 PHE c 64 TYR 0.014 0.001 TYR b 47 ARG 0.006 0.000 ARG A 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00902 ( 3) link_NAG-ASN : angle 4.36800 ( 9) hydrogen bonds : bond 0.03593 ( 558) hydrogen bonds : angle 5.18215 ( 1503) SS BOND : bond 0.00381 ( 24) SS BOND : angle 1.56745 ( 48) covalent geometry : bond 0.00258 (14989) covalent geometry : angle 0.54942 (20335) *********************** 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 359 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 336 time to evaluate : 2.232 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: 0.8475 (t) cc_final: 0.7918 (p) REVERT: A 95 ASP cc_start: 0.8208 (t70) cc_final: 0.7835 (t0) REVERT: A 116 CYS cc_start: 0.4785 (m) cc_final: 0.4443 (m) REVERT: A 161 LYS cc_start: 0.8478 (mptt) cc_final: 0.8246 (mptt) REVERT: A 164 SER cc_start: 0.8514 (p) cc_final: 0.8269 (p) REVERT: A 187 ARG cc_start: 0.7472 (ttt-90) cc_final: 0.7158 (ttm110) REVERT: A 230 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7945 (mm-30) REVERT: A 294 LEU cc_start: 0.8362 (tp) cc_final: 0.8017 (tp) REVERT: A 471 MET cc_start: 0.2949 (mpp) cc_final: 0.2668 (mpp) REVERT: B 20 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7254 (mtp180) REVERT: B 285 SER cc_start: 0.7767 (t) cc_final: 0.7462 (m) REVERT: C 24 VAL cc_start: 0.7592 (OUTLIER) cc_final: 0.7347 (p) REVERT: C 92 CYS cc_start: 0.5280 (m) cc_final: 0.4963 (m) REVERT: C 211 THR cc_start: 0.6468 (p) cc_final: 0.4782 (m) REVERT: C 234 ASN cc_start: 0.7781 (m-40) cc_final: 0.7451 (m-40) REVERT: C 243 GLU cc_start: 0.7726 (tt0) cc_final: 0.7499 (mt-10) REVERT: C 324 ASP cc_start: 0.7869 (t0) cc_final: 0.7543 (t0) REVERT: C 328 MET cc_start: 0.2208 (tpt) cc_final: 0.1361 (mmm) REVERT: C 333 SER cc_start: 0.7847 (m) cc_final: 0.7455 (p) REVERT: C 356 MET cc_start: 0.1926 (ttp) cc_final: 0.1617 (ttm) REVERT: C 380 ASP cc_start: 0.7842 (m-30) cc_final: 0.7516 (p0) REVERT: b 13 ARG cc_start: 0.6675 (ptm160) cc_final: 0.5604 (ptp-170) REVERT: c 24 ARG cc_start: 0.5675 (mmt180) cc_final: 0.4997 (ptt-90) REVERT: c 43 ASP cc_start: 0.7968 (t0) cc_final: 0.7755 (t0) REVERT: c 57 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7144 (mm-30) REVERT: c 119 ARG cc_start: 0.7194 (ttt180) cc_final: 0.6887 (ttm110) outliers start: 23 outliers final: 20 residues processed: 345 average time/residue: 0.5313 time to fit residues: 280.1352 Evaluate side-chains 355 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 334 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 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 299 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 66 SER 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 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 203 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 ASN ** C 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.182636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143350 restraints weight = 62547.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150077 restraints weight = 25497.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.154285 restraints weight = 13501.044| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15016 Z= 0.184 Angle : 0.601 9.163 20392 Z= 0.319 Chirality : 0.044 0.210 2357 Planarity : 0.004 0.045 2574 Dihedral : 5.166 48.791 2105 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.71 % Allowed : 17.33 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.19), residues: 1899 helix: 2.33 (0.27), residues: 416 sheet: -0.58 (0.21), residues: 581 loop : -1.86 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 44 HIS 0.007 0.002 HIS A 5 PHE 0.018 0.001 PHE c 64 TYR 0.027 0.002 TYR b 47 ARG 0.007 0.001 ARG B 187 Details of bonding type rmsd link_NAG-ASN : bond 0.01003 ( 3) link_NAG-ASN : angle 4.18894 ( 9) hydrogen bonds : bond 0.03962 ( 558) hydrogen bonds : angle 5.22078 ( 1503) SS BOND : bond 0.00491 ( 24) SS BOND : angle 1.65052 ( 48) covalent geometry : bond 0.00412 (14989) covalent geometry : angle 0.58943 (20335) ********************** 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 351 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 324 time to evaluate : 2.885 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: A 116 CYS cc_start: 0.4815 (m) cc_final: 0.4459 (m) REVERT: A 161 LYS cc_start: 0.8557 (mptt) cc_final: 0.8267 (mptt) REVERT: A 164 SER cc_start: 0.8536 (p) cc_final: 0.8296 (p) REVERT: A 187 ARG cc_start: 0.7516 (ttt-90) cc_final: 0.7197 (ttm110) REVERT: A 230 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 294 LEU cc_start: 0.8435 (tp) cc_final: 0.8040 (tp) REVERT: A 471 MET cc_start: 0.3011 (mpp) cc_final: 0.2727 (mpp) REVERT: B 20 ARG cc_start: 0.7971 (mtp85) cc_final: 0.7279 (mtp180) REVERT: B 268 LEU cc_start: 0.8625 (tp) cc_final: 0.8241 (tp) REVERT: B 285 SER cc_start: 0.7834 (t) cc_final: 0.7505 (m) REVERT: B 297 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.5922 (tt) REVERT: B 324 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7358 (t0) REVERT: C 24 VAL cc_start: 0.7614 (OUTLIER) cc_final: 0.7364 (p) REVERT: C 92 CYS cc_start: 0.5327 (m) cc_final: 0.5026 (m) REVERT: C 211 THR cc_start: 0.6578 (p) cc_final: 0.4961 (m) REVERT: C 234 ASN cc_start: 0.7802 (m-40) cc_final: 0.7437 (m-40) REVERT: C 299 MET cc_start: 0.5494 (mtt) cc_final: 0.5276 (mtt) REVERT: C 324 ASP cc_start: 0.7901 (t0) cc_final: 0.7550 (t0) REVERT: C 328 MET cc_start: 0.2303 (tpt) cc_final: 0.1499 (mmm) REVERT: C 333 SER cc_start: 0.7943 (m) cc_final: 0.7558 (p) REVERT: C 356 MET cc_start: 0.1962 (ttp) cc_final: 0.1663 (ttm) REVERT: C 380 ASP cc_start: 0.7833 (m-30) cc_final: 0.7494 (p0) REVERT: b 13 ARG cc_start: 0.6821 (ptm160) cc_final: 0.5829 (ptp-170) REVERT: c 24 ARG cc_start: 0.5712 (mmt180) cc_final: 0.5013 (ptt-90) REVERT: c 43 ASP cc_start: 0.7974 (t0) cc_final: 0.7761 (t0) REVERT: c 57 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7296 (mm-30) REVERT: c 119 ARG cc_start: 0.7198 (ttt180) cc_final: 0.6900 (ttm110) outliers start: 27 outliers final: 23 residues processed: 335 average time/residue: 0.6474 time to fit residues: 335.9923 Evaluate side-chains 346 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 320 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 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 299 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 66 SER 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 297 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 333 SER 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 203 ASP Chi-restraints excluded: chain C residue 285 SER 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 168 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.186583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144701 restraints weight = 67788.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.151582 restraints weight = 28382.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.155930 restraints weight = 15516.763| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15016 Z= 0.174 Angle : 0.593 8.767 20392 Z= 0.315 Chirality : 0.043 0.206 2357 Planarity : 0.004 0.041 2574 Dihedral : 5.187 48.954 2105 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.90 % Allowed : 17.14 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1899 helix: 2.32 (0.27), residues: 416 sheet: -0.65 (0.21), residues: 592 loop : -1.86 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 44 HIS 0.007 0.001 HIS A 5 PHE 0.031 0.002 PHE C 108 TYR 0.023 0.002 TYR b 47 ARG 0.006 0.001 ARG C 2 Details of bonding type rmsd link_NAG-ASN : bond 0.01006 ( 3) link_NAG-ASN : angle 4.17905 ( 9) hydrogen bonds : bond 0.03867 ( 558) hydrogen bonds : angle 5.19610 ( 1503) SS BOND : bond 0.00473 ( 24) SS BOND : angle 1.64195 ( 48) covalent geometry : bond 0.00389 (14989) covalent geometry : angle 0.58164 (20335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9782.44 seconds wall clock time: 170 minutes 22.69 seconds (10222.69 seconds total)