Starting phenix.real_space_refine on Thu Feb 5 21:49:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nrz_49742/02_2026/9nrz_49742.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nrz_49742/02_2026/9nrz_49742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nrz_49742/02_2026/9nrz_49742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nrz_49742/02_2026/9nrz_49742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nrz_49742/02_2026/9nrz_49742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nrz_49742/02_2026/9nrz_49742.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 12589 2.51 5 N 3420 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19971 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3043 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 28, 'TRANS': 369} Chain: "G" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3043 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 28, 'TRANS': 369} Chain: "J" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2676 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 23, 'TRANS': 316} Chain breaks: 1 Chain: "N" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2648 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 23, 'TRANS': 312} Chain breaks: 1 Chain: "O" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3043 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 28, 'TRANS': 369} Chain: "Q" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2662 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 23, 'TRANS': 314} Chain breaks: 1 Chain: "X" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 952 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "Y" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 952 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "Z" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 952 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Time building chain proxies: 5.02, per 1000 atoms: 0.25 Number of scatterers: 19971 At special positions: 0 Unit cell: (171.902, 164.428, 143.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 3836 8.00 N 3420 7.00 C 12589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.04 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.07 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.04 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.04 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 123 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 27 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 104 " distance=2.04 Simple disulfide: pdb=" SG CYS J 151 " - pdb=" SG CYS J 266 " distance=2.03 Simple disulfide: pdb=" SG CYS J 200 " - pdb=" SG CYS J 226 " distance=2.04 Simple disulfide: pdb=" SG CYS J 202 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 90 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 266 " distance=2.03 Simple disulfide: pdb=" SG CYS N 200 " - pdb=" SG CYS N 226 " distance=2.03 Simple disulfide: pdb=" SG CYS N 202 " - pdb=" SG CYS N 220 " distance=2.03 Simple disulfide: pdb=" SG CYS O 62 " - pdb=" SG CYS O 94 " distance=2.03 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 259 " - pdb=" SG CYS O 271 " distance=2.04 Simple disulfide: pdb=" SG CYS O 301 " - pdb=" SG CYS O 376 " distance=2.03 Simple disulfide: pdb=" SG CYS O 306 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 328 " - pdb=" SG CYS O 370 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 123 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 27 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 90 " - pdb=" SG CYS Q 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 151 " - pdb=" SG CYS Q 266 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 200 " - pdb=" SG CYS Q 226 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 202 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 67 sheets defined 5.6% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.678A pdb=" N LEU B 115 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA B 116 " --> pdb=" O ASP B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 116' Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.869A pdb=" N GLN B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.730A pdb=" N GLY B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 259' Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.523A pdb=" N LEU B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'G' and resid 112 through 115 removed outlier: 4.585A pdb=" N LEU G 115 " --> pdb=" O ASP G 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 115' Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 289 through 293 Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 8 through 12 removed outlier: 3.639A pdb=" N LEU J 11 " --> pdb=" O GLU J 8 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR J 12 " --> pdb=" O TYR J 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 8 through 12' Processing helix chain 'J' and resid 222 through 226 Processing helix chain 'N' and resid 3 through 11 removed outlier: 5.367A pdb=" N GLU N 8 " --> pdb=" O GLU N 4 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TYR N 9 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU N 11 " --> pdb=" O ASN N 7 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 246 removed outlier: 3.726A pdb=" N GLN O 242 " --> pdb=" O SER O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 254 Processing helix chain 'O' and resid 283 through 287 removed outlier: 3.765A pdb=" N LEU O 286 " --> pdb=" O PRO O 283 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE O 287 " --> pdb=" O ASP O 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 283 through 287' Processing helix chain 'O' and resid 289 through 293 removed outlier: 3.536A pdb=" N GLU O 292 " --> pdb=" O ARG O 289 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 8 through 11 Processing helix chain 'Q' and resid 222 through 224 No H-bonds generated for 'chain 'Q' and resid 222 through 224' Processing helix chain 'X' and resid 73 through 75 No H-bonds generated for 'chain 'X' and resid 73 through 75' Processing helix chain 'X' and resid 83 through 87 removed outlier: 3.614A pdb=" N SER X 87 " --> pdb=" O PRO X 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 75 No H-bonds generated for 'chain 'Y' and resid 73 through 75' Processing helix chain 'Y' and resid 83 through 87 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 83 through 87 removed outlier: 3.655A pdb=" N SER Z 87 " --> pdb=" O PRO Z 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'B' and resid 16 through 21 removed outlier: 5.036A pdb=" N ARG B 21 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ALA B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER B 30 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL B 137 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR B 32 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE B 135 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR B 34 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU B 133 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 36 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA B 131 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 38 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 129 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 127 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 42 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS B 125 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU B 44 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS B 123 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 46 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 140 through 147 removed outlier: 3.713A pdb=" N TYR B 46 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS B 123 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU B 44 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS B 125 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL B 42 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 127 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 129 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 38 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA B 131 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 36 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU B 133 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR B 34 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE B 135 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR B 32 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL B 137 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER B 30 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 268 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 55 Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 55 Processing sheet with id=AA6, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA7, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'B' and resid 300 through 305 removed outlier: 6.667A pdb=" N ILE B 315 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR B 338 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 331 Processing sheet with id=AB2, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AB3, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AB4, first strand: chain 'G' and resid 15 through 19 removed outlier: 7.181A pdb=" N PHE G 132 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE G 36 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN G 130 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU G 38 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER G 128 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR G 126 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL G 42 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA G 124 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU G 44 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR G 122 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR G 46 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU G 120 " --> pdb=" O TYR G 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 141 through 147 removed outlier: 5.200A pdb=" N GLU G 120 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR G 46 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR G 122 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU G 44 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA G 124 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL G 42 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR G 126 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER G 128 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU G 38 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN G 130 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE G 36 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE G 132 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA G 268 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 51 through 52 Processing sheet with id=AB7, first strand: chain 'G' and resid 59 through 61 Processing sheet with id=AB8, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AB9, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AC1, first strand: chain 'G' and resid 220 through 221 removed outlier: 3.561A pdb=" N VAL G 220 " --> pdb=" O THR G 234 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR G 234 " --> pdb=" O VAL G 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 300 through 305 removed outlier: 6.742A pdb=" N ILE G 315 " --> pdb=" O ASN G 304 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR G 338 " --> pdb=" O SER G 357 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 326 through 329 Processing sheet with id=AC4, first strand: chain 'G' and resid 365 through 368 Processing sheet with id=AC5, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AC6, first strand: chain 'J' and resid 33 through 37 removed outlier: 8.561A pdb=" N ILE J 33 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER J 50 " --> pdb=" O ILE J 33 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA J 35 " --> pdb=" O GLN J 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS J 37 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N SER J 50 " --> pdb=" O ASP J 69 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP J 69 " --> pdb=" O SER J 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 33 through 37 removed outlier: 8.561A pdb=" N ILE J 33 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER J 50 " --> pdb=" O ILE J 33 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA J 35 " --> pdb=" O GLN J 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS J 37 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR J 49 " --> pdb=" O TYR J 98 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR J 98 " --> pdb=" O THR J 49 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N SER J 51 " --> pdb=" O HIS J 96 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N HIS J 96 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N TYR J 53 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 10.735A pdb=" N ASP J 94 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS J 90 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU J 84 " --> pdb=" O CYS J 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 147 through 154 Processing sheet with id=AC9, first strand: chain 'J' and resid 237 through 238 Processing sheet with id=AD1, first strand: chain 'J' and resid 173 through 174 removed outlier: 3.725A pdb=" N GLU J 173 " --> pdb=" O ARG J 230 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU J 197 " --> pdb=" O TYR J 229 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 179 through 181 removed outlier: 3.954A pdb=" N VAL J 186 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE J 217 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL J 188 " --> pdb=" O LYS J 215 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS J 215 " --> pdb=" O VAL J 188 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 275 through 279 removed outlier: 3.579A pdb=" N LEU J 287 " --> pdb=" O ALA J 315 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA J 315 " --> pdb=" O LEU J 287 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 307 through 311 Processing sheet with id=AD5, first strand: chain 'N' and resid 17 through 19 Processing sheet with id=AD6, first strand: chain 'N' and resid 33 through 37 removed outlier: 7.411A pdb=" N GLN N 48 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL N 36 " --> pdb=" O ARG N 46 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG N 46 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N SER N 50 " --> pdb=" O ASP N 69 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP N 69 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG N 67 " --> pdb=" O GLN N 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 33 through 37 removed outlier: 7.411A pdb=" N GLN N 48 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL N 36 " --> pdb=" O ARG N 46 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG N 46 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR N 98 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N SER N 51 " --> pdb=" O HIS N 96 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N HIS N 96 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N TYR N 53 " --> pdb=" O ASP N 94 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N ASP N 94 " --> pdb=" O TYR N 53 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 83 through 85 Processing sheet with id=AD9, first strand: chain 'N' and resid 147 through 154 Processing sheet with id=AE1, first strand: chain 'N' and resid 237 through 238 Processing sheet with id=AE2, first strand: chain 'N' and resid 173 through 174 removed outlier: 3.860A pdb=" N GLU N 173 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU N 197 " --> pdb=" O TYR N 229 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 179 through 181 Processing sheet with id=AE4, first strand: chain 'N' and resid 275 through 279 removed outlier: 3.689A pdb=" N VAL N 283 " --> pdb=" O PHE N 319 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU N 285 " --> pdb=" O ARG N 317 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG N 317 " --> pdb=" O LEU N 285 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 307 through 311 Processing sheet with id=AE6, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AE7, first strand: chain 'O' and resid 15 through 19 removed outlier: 5.340A pdb=" N ILE O 31 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR O 136 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN O 134 " --> pdb=" O PRO O 33 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS O 35 " --> pdb=" O PHE O 132 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE O 39 " --> pdb=" O SER O 128 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR O 41 " --> pdb=" O THR O 126 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N THR O 126 " --> pdb=" O THR O 41 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASN O 43 " --> pdb=" O ALA O 124 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA O 124 " --> pdb=" O ASN O 43 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLU O 45 " --> pdb=" O TYR O 122 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR O 122 " --> pdb=" O GLU O 45 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL O 47 " --> pdb=" O GLU O 120 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU O 120 " --> pdb=" O VAL O 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 141 through 147 removed outlier: 6.806A pdb=" N GLU O 120 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL O 47 " --> pdb=" O GLU O 120 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR O 122 " --> pdb=" O GLU O 45 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLU O 45 " --> pdb=" O TYR O 122 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA O 124 " --> pdb=" O ASN O 43 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASN O 43 " --> pdb=" O ALA O 124 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N THR O 126 " --> pdb=" O THR O 41 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR O 41 " --> pdb=" O THR O 126 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE O 39 " --> pdb=" O SER O 128 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS O 35 " --> pdb=" O PHE O 132 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN O 134 " --> pdb=" O PRO O 33 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR O 136 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE O 31 " --> pdb=" O THR O 136 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 51 through 55 Processing sheet with id=AF1, first strand: chain 'O' and resid 51 through 55 Processing sheet with id=AF2, first strand: chain 'O' and resid 87 through 88 Processing sheet with id=AF3, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AF4, first strand: chain 'O' and resid 220 through 221 Processing sheet with id=AF5, first strand: chain 'O' and resid 296 through 305 removed outlier: 5.119A pdb=" N ALA O 298 " --> pdb=" O SER O 321 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER O 321 " --> pdb=" O ALA O 298 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE O 315 " --> pdb=" O ASN O 304 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR O 338 " --> pdb=" O SER O 357 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=AF7, first strand: chain 'O' and resid 330 through 331 Processing sheet with id=AF8, first strand: chain 'Q' and resid 17 through 19 Processing sheet with id=AF9, first strand: chain 'Q' and resid 33 through 37 removed outlier: 7.825A pdb=" N ILE Q 33 " --> pdb=" O SER Q 50 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER Q 50 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA Q 35 " --> pdb=" O GLN Q 48 " (cutoff:3.500A) removed outlier: 10.277A pdb=" N SER Q 50 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASP Q 69 " --> pdb=" O SER Q 50 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 33 through 37 removed outlier: 7.825A pdb=" N ILE Q 33 " --> pdb=" O SER Q 50 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER Q 50 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA Q 35 " --> pdb=" O GLN Q 48 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR Q 49 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR Q 98 " --> pdb=" O THR Q 49 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N SER Q 51 " --> pdb=" O HIS Q 96 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N HIS Q 96 " --> pdb=" O SER Q 51 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N TYR Q 53 " --> pdb=" O ASP Q 94 " (cutoff:3.500A) removed outlier: 11.123A pdb=" N ASP Q 94 " --> pdb=" O TYR Q 53 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AG3, first strand: chain 'Q' and resid 147 through 154 removed outlier: 3.830A pdb=" N VAL Q 147 " --> pdb=" O VAL Q 268 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL Q 268 " --> pdb=" O VAL Q 147 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA Q 262 " --> pdb=" O VAL Q 153 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 237 through 238 removed outlier: 3.741A pdb=" N VAL Q 237 " --> pdb=" O HIS Q 168 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS Q 168 " --> pdb=" O VAL Q 237 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY Q 253 " --> pdb=" O MET Q 167 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 173 through 175 removed outlier: 3.978A pdb=" N GLU Q 173 " --> pdb=" O ARG Q 230 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA Q 228 " --> pdb=" O ASP Q 175 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 179 through 181 removed outlier: 3.945A pdb=" N VAL Q 186 " --> pdb=" O PHE Q 217 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 275 through 279 Processing sheet with id=AG8, first strand: chain 'X' and resid 67 through 72 Processing sheet with id=AG9, first strand: chain 'X' and resid 11 through 13 removed outlier: 6.957A pdb=" N VAL X 34 " --> pdb=" O SER X 50 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER X 50 " --> pdb=" O VAL X 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 67 through 72 Processing sheet with id=AH2, first strand: chain 'Y' and resid 11 through 13 removed outlier: 6.935A pdb=" N VAL Y 34 " --> pdb=" O SER Y 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER Y 50 " --> pdb=" O VAL Y 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 3 through 7 Processing sheet with id=AH4, first strand: chain 'Z' and resid 11 through 13 removed outlier: 6.858A pdb=" N VAL Z 34 " --> pdb=" O SER Z 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER Z 50 " --> pdb=" O VAL Z 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP Z 36 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1599 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: 4.16 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6500 1.35 - 1.48: 5333 1.48 - 1.61: 8498 1.61 - 1.74: 0 1.74 - 1.87: 162 Bond restraints: 20493 Sorted by residual: bond pdb=" C ARG N 88 " pdb=" N PRO N 89 " ideal model delta sigma weight residual 1.332 1.360 -0.028 1.30e-02 5.92e+03 4.68e+00 bond pdb=" C GLU N 199 " pdb=" N CYS N 200 " ideal model delta sigma weight residual 1.332 1.362 -0.029 1.40e-02 5.10e+03 4.40e+00 bond pdb=" CA CYS N 226 " pdb=" CB CYS N 226 " ideal model delta sigma weight residual 1.530 1.500 0.031 1.53e-02 4.27e+03 4.02e+00 bond pdb=" N SER Q 1 " pdb=" CA SER Q 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" C GLU N 313 " pdb=" N PRO N 314 " ideal model delta sigma weight residual 1.333 1.351 -0.018 1.01e-02 9.80e+03 3.09e+00 ... (remaining 20488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 27331 2.32 - 4.63: 513 4.63 - 6.95: 36 6.95 - 9.27: 5 9.27 - 11.59: 3 Bond angle restraints: 27888 Sorted by residual: angle pdb=" CA CYS G 259 " pdb=" CB CYS G 259 " pdb=" SG CYS G 259 " ideal model delta sigma weight residual 114.40 125.99 -11.59 2.30e+00 1.89e-01 2.54e+01 angle pdb=" N CYS N 200 " pdb=" CA CYS N 200 " pdb=" C CYS N 200 " ideal model delta sigma weight residual 110.80 121.37 -10.57 2.13e+00 2.20e-01 2.46e+01 angle pdb=" CA CYS Q 226 " pdb=" CB CYS Q 226 " pdb=" SG CYS Q 226 " ideal model delta sigma weight residual 114.40 125.65 -11.25 2.30e+00 1.89e-01 2.39e+01 angle pdb=" N CYS N 226 " pdb=" CA CYS N 226 " pdb=" C CYS N 226 " ideal model delta sigma weight residual 107.88 114.24 -6.36 1.41e+00 5.03e-01 2.04e+01 angle pdb=" CA CYS G 271 " pdb=" CB CYS G 271 " pdb=" SG CYS G 271 " ideal model delta sigma weight residual 114.40 122.49 -8.09 2.30e+00 1.89e-01 1.24e+01 ... (remaining 27883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 11263 17.71 - 35.42: 835 35.42 - 53.13: 149 53.13 - 70.84: 28 70.84 - 88.55: 25 Dihedral angle restraints: 12300 sinusoidal: 4797 harmonic: 7503 Sorted by residual: dihedral pdb=" CB CYS O 62 " pdb=" SG CYS O 62 " pdb=" SG CYS O 94 " pdb=" CB CYS O 94 " ideal model delta sinusoidal sigma weight residual -86.00 -174.55 88.55 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CA ASN O 264 " pdb=" C ASN O 264 " pdb=" N PRO O 265 " pdb=" CA PRO O 265 " ideal model delta harmonic sigma weight residual 180.00 131.81 48.19 0 5.00e+00 4.00e-02 9.29e+01 dihedral pdb=" CB CYS Q 22 " pdb=" SG CYS Q 22 " pdb=" SG CYS Q 27 " pdb=" CB CYS Q 27 " ideal model delta sinusoidal sigma weight residual 93.00 7.11 85.89 1 1.00e+01 1.00e-02 8.91e+01 ... (remaining 12297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2609 0.063 - 0.126: 406 0.126 - 0.190: 47 0.190 - 0.253: 0 0.253 - 0.316: 3 Chirality restraints: 3065 Sorted by residual: chirality pdb=" CA ASN O 264 " pdb=" N ASN O 264 " pdb=" C ASN O 264 " pdb=" CB ASN O 264 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA CYS N 200 " pdb=" N CYS N 200 " pdb=" C CYS N 200 " pdb=" CB CYS N 200 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA CYS G 259 " pdb=" N CYS G 259 " pdb=" C CYS G 259 " pdb=" CB CYS G 259 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 3062 not shown) Planarity restraints: 3622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 264 " -0.089 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO O 265 " 0.233 5.00e-02 4.00e+02 pdb=" CA PRO O 265 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO O 265 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 312 " -0.015 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE O 312 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE O 312 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE O 312 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE O 312 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE O 312 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE O 312 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL J 257 " -0.052 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO J 258 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO J 258 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO J 258 " -0.043 5.00e-02 4.00e+02 ... (remaining 3619 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 266 2.62 - 3.19: 17210 3.19 - 3.76: 28107 3.76 - 4.33: 36865 4.33 - 4.90: 62571 Nonbonded interactions: 145019 Sorted by model distance: nonbonded pdb=" OG1 THR B 98 " pdb=" OE1 GLU B 99 " model vdw 2.052 3.040 nonbonded pdb=" O LYS O 61 " pdb=" OG1 THR O 101 " model vdw 2.063 3.040 nonbonded pdb=" O TYR Q 15 " pdb=" OG SER Q 50 " model vdw 2.077 3.040 nonbonded pdb=" OG1 THR O 207 " pdb=" OG SER O 210 " model vdw 2.087 3.040 nonbonded pdb=" OE1 GLU B 183 " pdb=" OH TYR B 185 " model vdw 2.089 3.040 ... (remaining 145014 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 'B' selection = chain 'G' selection = chain 'O' } ncs_group { reference = (chain 'J' and (resid 2 through 55 or resid 62 through 343)) selection = chain 'N' selection = (chain 'Q' and (resid 2 through 55 or resid 62 through 343)) } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 4.220 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.170 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.004 0.058 20533 Z= 0.182 Angle : 0.749 11.587 27968 Z= 0.399 Chirality : 0.048 0.316 3065 Planarity : 0.005 0.135 3622 Dihedral : 12.930 88.274 7380 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2559 helix: -2.97 (0.54), residues: 59 sheet: 0.01 (0.17), residues: 858 loop : -1.54 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 175 TYR 0.029 0.001 TYR B 262 PHE 0.053 0.001 PHE O 312 TRP 0.009 0.001 TRP Q 339 HIS 0.014 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00390 (20493) covalent geometry : angle 0.74273 (27888) SS BOND : bond 0.00818 ( 40) SS BOND : angle 2.00296 ( 80) hydrogen bonds : bond 0.15488 ( 645) hydrogen bonds : angle 7.43957 ( 1599) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 0.996 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: B 27 LEU cc_start: 0.8883 (mm) cc_final: 0.8469 (mp) REVERT: B 238 SER cc_start: 0.8720 (t) cc_final: 0.8261 (p) REVERT: G 13 ILE cc_start: 0.9479 (mm) cc_final: 0.9148 (mp) REVERT: G 93 TYR cc_start: 0.8617 (t80) cc_final: 0.8340 (t80) REVERT: G 103 VAL cc_start: 0.9526 (m) cc_final: 0.9297 (p) REVERT: G 191 GLU cc_start: 0.7138 (pt0) cc_final: 0.6618 (mp0) REVERT: J 48 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8671 (tm-30) REVERT: J 160 ASN cc_start: 0.8832 (m110) cc_final: 0.8389 (m-40) REVERT: J 167 MET cc_start: 0.8441 (ptp) cc_final: 0.7766 (mtm) REVERT: J 173 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7853 (mt-10) REVERT: J 216 GLN cc_start: 0.8928 (pm20) cc_final: 0.8663 (pm20) REVERT: J 225 GLN cc_start: 0.8187 (mm110) cc_final: 0.7863 (mt0) REVERT: J 339 TRP cc_start: 0.8465 (m100) cc_final: 0.7823 (m100) REVERT: N 9 TYR cc_start: 0.7721 (m-80) cc_final: 0.7492 (m-80) REVERT: N 251 LEU cc_start: 0.8969 (pp) cc_final: 0.8431 (pp) REVERT: N 327 GLU cc_start: 0.7838 (tt0) cc_final: 0.7616 (tt0) REVERT: O 162 THR cc_start: 0.8413 (t) cc_final: 0.8145 (p) REVERT: O 187 TYR cc_start: 0.8773 (t80) cc_final: 0.8554 (t80) REVERT: Q 11 LEU cc_start: 0.8717 (mt) cc_final: 0.8075 (tp) REVERT: Q 110 ILE cc_start: 0.9267 (tp) cc_final: 0.8924 (tt) REVERT: Q 239 ASN cc_start: 0.8608 (p0) cc_final: 0.8249 (p0) REVERT: X 19 ARG cc_start: 0.7673 (ttm-80) cc_final: 0.7421 (ttp80) REVERT: X 29 PHE cc_start: 0.7773 (m-80) cc_final: 0.7445 (m-80) REVERT: X 40 THR cc_start: 0.3021 (m) cc_final: 0.1905 (m) REVERT: X 82 MET cc_start: 0.5444 (ppp) cc_final: 0.4889 (ppp) REVERT: Y 100 TRP cc_start: 0.8022 (p90) cc_final: 0.7738 (p90) REVERT: Z 46 GLU cc_start: 0.7779 (tp30) cc_final: 0.7576 (tp30) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.1489 time to fit residues: 117.9771 Evaluate side-chains 384 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 247 optimal weight: 0.0070 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 331 HIS N 168 HIS N 219 GLN Y 33 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110225 restraints weight = 42019.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109330 restraints weight = 53159.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111169 restraints weight = 45540.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.111569 restraints weight = 28989.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112637 restraints weight = 26198.344| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20533 Z= 0.274 Angle : 0.736 8.692 27968 Z= 0.391 Chirality : 0.047 0.202 3065 Planarity : 0.006 0.100 3622 Dihedral : 5.480 41.349 2802 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.16), residues: 2559 helix: -2.86 (0.53), residues: 57 sheet: -0.01 (0.16), residues: 894 loop : -1.62 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 52A TYR 0.019 0.002 TYR O 46 PHE 0.020 0.002 PHE Z 29 TRP 0.016 0.002 TRP B 89 HIS 0.009 0.002 HIS N 145 Details of bonding type rmsd covalent geometry : bond 0.00627 (20493) covalent geometry : angle 0.72541 (27888) SS BOND : bond 0.00425 ( 40) SS BOND : angle 2.42276 ( 80) hydrogen bonds : bond 0.05034 ( 645) hydrogen bonds : angle 6.25423 ( 1599) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 470 time to evaluate : 0.781 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: B 27 LEU cc_start: 0.9059 (mm) cc_final: 0.8832 (mp) REVERT: B 51 TYR cc_start: 0.9058 (p90) cc_final: 0.8754 (p90) REVERT: G 7 MET cc_start: 0.8119 (tmm) cc_final: 0.7772 (tmm) REVERT: G 103 VAL cc_start: 0.9543 (m) cc_final: 0.9277 (p) REVERT: G 191 GLU cc_start: 0.6018 (pt0) cc_final: 0.5410 (pt0) REVERT: J 125 VAL cc_start: 0.9031 (t) cc_final: 0.8759 (p) REVERT: J 160 ASN cc_start: 0.8815 (m110) cc_final: 0.8519 (m-40) REVERT: J 324 LYS cc_start: 0.9142 (mmmt) cc_final: 0.8475 (mmmt) REVERT: J 339 TRP cc_start: 0.8493 (m100) cc_final: 0.7619 (m100) REVERT: N 31 ILE cc_start: 0.9474 (mm) cc_final: 0.9165 (mm) REVERT: N 117 ASP cc_start: 0.6930 (p0) cc_final: 0.6681 (p0) REVERT: N 241 ASP cc_start: 0.8517 (p0) cc_final: 0.7922 (p0) REVERT: N 327 GLU cc_start: 0.7718 (tt0) cc_final: 0.7485 (tt0) REVERT: N 332 ASN cc_start: 0.9160 (m110) cc_final: 0.8912 (m110) REVERT: O 112 ASP cc_start: 0.8281 (p0) cc_final: 0.8064 (p0) REVERT: O 162 THR cc_start: 0.8648 (t) cc_final: 0.8406 (p) REVERT: O 211 SER cc_start: 0.9087 (m) cc_final: 0.8587 (t) REVERT: Q 11 LEU cc_start: 0.8998 (mt) cc_final: 0.8655 (tp) REVERT: Q 66 MET cc_start: 0.7968 (ttt) cc_final: 0.7699 (ttt) REVERT: Q 110 ILE cc_start: 0.9504 (tp) cc_final: 0.9164 (tt) REVERT: Q 157 ASP cc_start: 0.8376 (p0) cc_final: 0.8075 (p0) REVERT: Q 167 MET cc_start: 0.8644 (pmm) cc_final: 0.7739 (pmm) REVERT: Q 327 GLU cc_start: 0.7343 (tt0) cc_final: 0.7055 (tt0) REVERT: X 4 LEU cc_start: 0.7650 (mt) cc_final: 0.7375 (mt) REVERT: X 40 THR cc_start: 0.2188 (m) cc_final: 0.0791 (m) REVERT: X 82 MET cc_start: 0.6142 (ppp) cc_final: 0.5919 (ppp) REVERT: X 96 VAL cc_start: 0.8364 (m) cc_final: 0.7192 (m) REVERT: Y 33 HIS cc_start: 0.6316 (m90) cc_final: 0.6094 (m90) REVERT: Y 100 TRP cc_start: 0.7528 (p90) cc_final: 0.7315 (p90) REVERT: Z 82 MET cc_start: 0.5587 (ppp) cc_final: 0.4875 (ppp) outliers start: 4 outliers final: 3 residues processed: 474 average time/residue: 0.1541 time to fit residues: 111.9597 Evaluate side-chains 353 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 350 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 29 optimal weight: 0.0060 chunk 96 optimal weight: 0.9980 chunk 230 optimal weight: 40.0000 chunk 148 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 81 GLN O 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.107973 restraints weight = 41506.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106941 restraints weight = 41860.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108853 restraints weight = 40524.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109409 restraints weight = 24851.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111292 restraints weight = 22478.229| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20533 Z= 0.171 Angle : 0.665 8.859 27968 Z= 0.349 Chirality : 0.045 0.261 3065 Planarity : 0.005 0.113 3622 Dihedral : 5.352 44.080 2802 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.16), residues: 2559 helix: -2.63 (0.55), residues: 57 sheet: 0.10 (0.17), residues: 838 loop : -1.56 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 66 TYR 0.017 0.001 TYR O 187 PHE 0.014 0.001 PHE Y 29 TRP 0.022 0.002 TRP Q 339 HIS 0.006 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00398 (20493) covalent geometry : angle 0.65371 (27888) SS BOND : bond 0.00326 ( 40) SS BOND : angle 2.34151 ( 80) hydrogen bonds : bond 0.04112 ( 645) hydrogen bonds : angle 5.92252 ( 1599) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.917 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: B 27 LEU cc_start: 0.9111 (mm) cc_final: 0.8809 (mp) REVERT: B 51 TYR cc_start: 0.8985 (p90) cc_final: 0.8616 (p90) REVERT: G 13 ILE cc_start: 0.9509 (mm) cc_final: 0.9187 (mm) REVERT: G 51 TYR cc_start: 0.9054 (p90) cc_final: 0.8412 (p90) REVERT: G 191 GLU cc_start: 0.5995 (pt0) cc_final: 0.5335 (pt0) REVERT: J 160 ASN cc_start: 0.8884 (m110) cc_final: 0.8573 (m-40) REVERT: J 324 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8405 (mmmt) REVERT: J 339 TRP cc_start: 0.8495 (m100) cc_final: 0.7663 (m100) REVERT: N 9 TYR cc_start: 0.7739 (m-80) cc_final: 0.7455 (m-10) REVERT: N 152 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7660 (mm-40) REVERT: N 327 GLU cc_start: 0.7702 (tt0) cc_final: 0.7340 (tt0) REVERT: N 332 ASN cc_start: 0.9168 (m110) cc_final: 0.8868 (m110) REVERT: O 99 GLU cc_start: 0.7424 (tt0) cc_final: 0.7122 (tt0) REVERT: O 112 ASP cc_start: 0.8195 (p0) cc_final: 0.7989 (p0) REVERT: O 162 THR cc_start: 0.8570 (t) cc_final: 0.8316 (p) REVERT: Q 11 LEU cc_start: 0.9032 (mt) cc_final: 0.8406 (tp) REVERT: Q 66 MET cc_start: 0.7991 (ttt) cc_final: 0.7768 (ttt) REVERT: Q 70 MET cc_start: 0.8094 (tmm) cc_final: 0.7711 (tmm) REVERT: Q 110 ILE cc_start: 0.9493 (tp) cc_final: 0.9182 (tt) REVERT: Q 157 ASP cc_start: 0.8426 (p0) cc_final: 0.8135 (p0) REVERT: Q 167 MET cc_start: 0.8592 (pmm) cc_final: 0.7612 (pmm) REVERT: Q 327 GLU cc_start: 0.7330 (tt0) cc_final: 0.7002 (tt0) REVERT: X 4 LEU cc_start: 0.7793 (mt) cc_final: 0.7488 (mt) REVERT: X 40 THR cc_start: 0.2456 (m) cc_final: 0.1122 (m) REVERT: Y 100 TRP cc_start: 0.7695 (p90) cc_final: 0.7428 (p90) REVERT: Z 82 MET cc_start: 0.5446 (ppp) cc_final: 0.4644 (ppp) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.1439 time to fit residues: 102.7769 Evaluate side-chains 327 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 128 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 246 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 3 GLN Y 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106217 restraints weight = 41379.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105768 restraints weight = 51941.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107188 restraints weight = 45872.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108056 restraints weight = 28485.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110186 restraints weight = 23925.970| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20533 Z= 0.216 Angle : 0.691 7.954 27968 Z= 0.364 Chirality : 0.046 0.197 3065 Planarity : 0.005 0.095 3622 Dihedral : 5.422 41.259 2802 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.16), residues: 2559 helix: -2.46 (0.59), residues: 57 sheet: 0.05 (0.16), residues: 884 loop : -1.65 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 18 TYR 0.013 0.002 TYR Q 85 PHE 0.019 0.002 PHE G 156 TRP 0.018 0.002 TRP N 339 HIS 0.008 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00500 (20493) covalent geometry : angle 0.68088 (27888) SS BOND : bond 0.00356 ( 40) SS BOND : angle 2.28491 ( 80) hydrogen bonds : bond 0.04396 ( 645) hydrogen bonds : angle 5.80665 ( 1599) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 0.763 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: B 27 LEU cc_start: 0.8999 (mm) cc_final: 0.8741 (mm) REVERT: B 51 TYR cc_start: 0.8984 (p90) cc_final: 0.8677 (p90) REVERT: B 187 TYR cc_start: 0.8576 (t80) cc_final: 0.8356 (t80) REVERT: G 51 TYR cc_start: 0.9102 (p90) cc_final: 0.8493 (p90) REVERT: G 191 GLU cc_start: 0.5721 (pt0) cc_final: 0.5022 (pt0) REVERT: G 366 ARG cc_start: 0.8486 (ttm170) cc_final: 0.8000 (tpt-90) REVERT: J 160 ASN cc_start: 0.8885 (m110) cc_final: 0.8627 (m-40) REVERT: J 167 MET cc_start: 0.8162 (ptp) cc_final: 0.7953 (mtp) REVERT: J 200 CYS cc_start: 0.5096 (t) cc_final: 0.4035 (t) REVERT: J 324 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8465 (mmmt) REVERT: J 339 TRP cc_start: 0.8573 (m100) cc_final: 0.7565 (m100) REVERT: N 9 TYR cc_start: 0.8019 (m-80) cc_final: 0.7777 (m-10) REVERT: N 34 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7598 (mm-30) REVERT: N 152 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7807 (mm-40) REVERT: N 241 ASP cc_start: 0.8140 (p0) cc_final: 0.7939 (p0) REVERT: N 327 GLU cc_start: 0.7799 (tt0) cc_final: 0.7318 (tt0) REVERT: N 332 ASN cc_start: 0.9161 (m110) cc_final: 0.8930 (m110) REVERT: O 287 PHE cc_start: 0.4438 (m-10) cc_final: 0.4106 (m-80) REVERT: Q 11 LEU cc_start: 0.9086 (mt) cc_final: 0.8492 (tp) REVERT: Q 66 MET cc_start: 0.8072 (ttt) cc_final: 0.7859 (ttt) REVERT: Q 70 MET cc_start: 0.8125 (tmm) cc_final: 0.7824 (tmm) REVERT: Q 110 ILE cc_start: 0.9442 (tp) cc_final: 0.9109 (tt) REVERT: Q 157 ASP cc_start: 0.8464 (p0) cc_final: 0.8185 (p0) REVERT: Q 167 MET cc_start: 0.8679 (pmm) cc_final: 0.7611 (pmm) REVERT: Q 327 GLU cc_start: 0.7503 (tt0) cc_final: 0.7260 (tt0) REVERT: X 4 LEU cc_start: 0.7736 (mt) cc_final: 0.7393 (mt) REVERT: X 40 THR cc_start: 0.2441 (m) cc_final: 0.1071 (m) REVERT: Y 5 GLN cc_start: 0.7072 (pm20) cc_final: 0.6871 (pm20) REVERT: Y 100 TRP cc_start: 0.7609 (p90) cc_final: 0.7284 (p90) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.1399 time to fit residues: 96.4217 Evaluate side-chains 331 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 101 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 305 HIS O 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.139692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106870 restraints weight = 41102.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107777 restraints weight = 43831.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108209 restraints weight = 40025.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109041 restraints weight = 23726.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110776 restraints weight = 20248.842| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20533 Z= 0.148 Angle : 0.656 8.523 27968 Z= 0.342 Chirality : 0.046 0.242 3065 Planarity : 0.005 0.092 3622 Dihedral : 5.329 40.025 2802 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2559 helix: -2.61 (0.58), residues: 59 sheet: 0.09 (0.17), residues: 861 loop : -1.55 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 64 TYR 0.021 0.001 TYR G 308 PHE 0.015 0.001 PHE G 287 TRP 0.030 0.002 TRP Q 339 HIS 0.005 0.001 HIS Y 33 Details of bonding type rmsd covalent geometry : bond 0.00345 (20493) covalent geometry : angle 0.64537 (27888) SS BOND : bond 0.00335 ( 40) SS BOND : angle 2.32691 ( 80) hydrogen bonds : bond 0.03731 ( 645) hydrogen bonds : angle 5.64256 ( 1599) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.740 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: B 51 TYR cc_start: 0.8852 (p90) cc_final: 0.8490 (p90) REVERT: B 360 ASN cc_start: 0.9244 (p0) cc_final: 0.8744 (p0) REVERT: G 13 ILE cc_start: 0.9488 (mm) cc_final: 0.9144 (mm) REVERT: G 51 TYR cc_start: 0.9089 (p90) cc_final: 0.8404 (p90) REVERT: G 191 GLU cc_start: 0.5749 (pt0) cc_final: 0.5056 (pt0) REVERT: G 233 TYR cc_start: 0.8961 (p90) cc_final: 0.8720 (p90) REVERT: G 366 ARG cc_start: 0.8450 (ttm170) cc_final: 0.8108 (tpt-90) REVERT: J 128 GLU cc_start: 0.7276 (tm-30) cc_final: 0.5861 (tm-30) REVERT: J 130 LYS cc_start: 0.8969 (ttmm) cc_final: 0.8731 (tppt) REVERT: J 160 ASN cc_start: 0.8844 (m110) cc_final: 0.8565 (m-40) REVERT: J 324 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8495 (mmmt) REVERT: J 339 TRP cc_start: 0.8569 (m100) cc_final: 0.7667 (m100) REVERT: N 9 TYR cc_start: 0.8035 (m-80) cc_final: 0.7791 (m-10) REVERT: N 53 TYR cc_start: 0.8320 (m-80) cc_final: 0.7927 (m-10) REVERT: N 70 MET cc_start: 0.7964 (tpp) cc_final: 0.7737 (tpt) REVERT: N 152 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7647 (mm-40) REVERT: N 164 TYR cc_start: 0.8741 (m-10) cc_final: 0.8538 (m-10) REVERT: N 327 GLU cc_start: 0.7635 (tt0) cc_final: 0.7154 (tt0) REVERT: O 27 LEU cc_start: 0.8978 (mp) cc_final: 0.8752 (mm) REVERT: O 56 ASP cc_start: 0.8663 (t70) cc_final: 0.8441 (t0) REVERT: O 162 THR cc_start: 0.8539 (t) cc_final: 0.8294 (p) REVERT: Q 11 LEU cc_start: 0.9110 (mt) cc_final: 0.8557 (tp) REVERT: Q 39 ASP cc_start: 0.6927 (t70) cc_final: 0.6724 (t70) REVERT: Q 70 MET cc_start: 0.8081 (tmm) cc_final: 0.7863 (tmm) REVERT: Q 110 ILE cc_start: 0.9563 (tp) cc_final: 0.9250 (tt) REVERT: Q 157 ASP cc_start: 0.8454 (p0) cc_final: 0.8222 (p0) REVERT: Q 199 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8143 (tm-30) REVERT: Q 221 THR cc_start: 0.7594 (m) cc_final: 0.7076 (t) REVERT: Q 327 GLU cc_start: 0.7476 (tt0) cc_final: 0.7175 (tt0) REVERT: Q 339 TRP cc_start: 0.8475 (m100) cc_final: 0.8194 (m100) REVERT: X 4 LEU cc_start: 0.7491 (mt) cc_final: 0.7281 (mt) REVERT: X 40 THR cc_start: 0.2360 (m) cc_final: 0.1102 (m) REVERT: Y 100 TRP cc_start: 0.7644 (p90) cc_final: 0.7376 (p90) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.1426 time to fit residues: 101.4200 Evaluate side-chains 334 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 103 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 chunk 244 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 240 optimal weight: 20.0000 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 270 ASN O 331 HIS Z 33 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107865 restraints weight = 40851.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105488 restraints weight = 36387.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106699 restraints weight = 37437.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109126 restraints weight = 24907.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109380 restraints weight = 20041.609| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20533 Z= 0.116 Angle : 0.642 8.960 27968 Z= 0.334 Chirality : 0.045 0.251 3065 Planarity : 0.005 0.086 3622 Dihedral : 5.209 39.716 2802 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.16), residues: 2559 helix: -2.70 (0.56), residues: 59 sheet: 0.20 (0.17), residues: 873 loop : -1.45 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 18 TYR 0.018 0.001 TYR G 308 PHE 0.029 0.001 PHE G 156 TRP 0.020 0.001 TRP Q 339 HIS 0.008 0.001 HIS Z 33 Details of bonding type rmsd covalent geometry : bond 0.00265 (20493) covalent geometry : angle 0.63280 (27888) SS BOND : bond 0.00407 ( 40) SS BOND : angle 2.13789 ( 80) hydrogen bonds : bond 0.03378 ( 645) hydrogen bonds : angle 5.50671 ( 1599) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.800 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: B 21 ARG cc_start: 0.8313 (tpp80) cc_final: 0.7618 (tpp80) REVERT: B 27 LEU cc_start: 0.9059 (mm) cc_final: 0.8795 (mp) REVERT: B 187 TYR cc_start: 0.8512 (t80) cc_final: 0.8287 (t80) REVERT: G 13 ILE cc_start: 0.9508 (mm) cc_final: 0.9208 (mm) REVERT: G 51 TYR cc_start: 0.9059 (p90) cc_final: 0.8380 (p90) REVERT: G 156 PHE cc_start: 0.8782 (p90) cc_final: 0.8570 (p90) REVERT: G 191 GLU cc_start: 0.5849 (pt0) cc_final: 0.5484 (mp0) REVERT: G 204 GLN cc_start: 0.9007 (mm110) cc_final: 0.8770 (mm-40) REVERT: G 320 TYR cc_start: 0.8220 (p90) cc_final: 0.8014 (p90) REVERT: J 125 VAL cc_start: 0.8770 (t) cc_final: 0.8511 (p) REVERT: J 128 GLU cc_start: 0.7287 (tm-30) cc_final: 0.5786 (tm-30) REVERT: J 130 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8732 (tppt) REVERT: J 160 ASN cc_start: 0.8866 (m110) cc_final: 0.8600 (m-40) REVERT: J 324 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8522 (mmmt) REVERT: J 339 TRP cc_start: 0.8530 (m100) cc_final: 0.7651 (m100) REVERT: N 9 TYR cc_start: 0.8039 (m-80) cc_final: 0.7815 (m-10) REVERT: N 31 ILE cc_start: 0.9478 (mm) cc_final: 0.9141 (mm) REVERT: N 53 TYR cc_start: 0.8378 (m-80) cc_final: 0.7890 (m-10) REVERT: N 70 MET cc_start: 0.7979 (tpp) cc_final: 0.7735 (tpt) REVERT: N 152 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7579 (mm-40) REVERT: N 327 GLU cc_start: 0.7548 (tt0) cc_final: 0.7123 (tt0) REVERT: O 162 THR cc_start: 0.8507 (t) cc_final: 0.8238 (p) REVERT: O 187 TYR cc_start: 0.8832 (t80) cc_final: 0.8630 (t80) REVERT: Q 11 LEU cc_start: 0.9084 (mt) cc_final: 0.8610 (tp) REVERT: Q 34 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7458 (tm-30) REVERT: Q 110 ILE cc_start: 0.9486 (tp) cc_final: 0.9206 (tt) REVERT: Q 157 ASP cc_start: 0.8479 (p0) cc_final: 0.8276 (p0) REVERT: Q 167 MET cc_start: 0.8803 (pmm) cc_final: 0.7470 (pmm) REVERT: Q 199 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7951 (tm-30) REVERT: Q 327 GLU cc_start: 0.7317 (tt0) cc_final: 0.7074 (tt0) REVERT: X 40 THR cc_start: 0.2396 (m) cc_final: 0.1129 (m) REVERT: Y 100 TRP cc_start: 0.7819 (p90) cc_final: 0.7566 (p90) REVERT: Z 102 LEU cc_start: 0.7284 (mt) cc_final: 0.7006 (mt) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.1434 time to fit residues: 99.0355 Evaluate side-chains 335 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 115 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 234 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 241 optimal weight: 40.0000 chunk 29 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 183 optimal weight: 0.7980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 HIS Y 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106300 restraints weight = 41231.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105833 restraints weight = 42971.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107117 restraints weight = 39566.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107579 restraints weight = 23743.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110243 restraints weight = 21264.792| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20533 Z= 0.163 Angle : 0.673 10.806 27968 Z= 0.351 Chirality : 0.045 0.275 3065 Planarity : 0.005 0.111 3622 Dihedral : 5.244 43.871 2802 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.16), residues: 2559 helix: -2.71 (0.57), residues: 59 sheet: 0.11 (0.16), residues: 892 loop : -1.48 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 66 TYR 0.019 0.001 TYR Y 90 PHE 0.024 0.001 PHE G 156 TRP 0.029 0.002 TRP N 339 HIS 0.005 0.001 HIS O 331 Details of bonding type rmsd covalent geometry : bond 0.00375 (20493) covalent geometry : angle 0.66157 (27888) SS BOND : bond 0.00409 ( 40) SS BOND : angle 2.40983 ( 80) hydrogen bonds : bond 0.03785 ( 645) hydrogen bonds : angle 5.53515 ( 1599) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.798 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: B 51 TYR cc_start: 0.8792 (p90) cc_final: 0.8558 (p90) REVERT: B 187 TYR cc_start: 0.8576 (t80) cc_final: 0.8333 (t80) REVERT: G 13 ILE cc_start: 0.9501 (mm) cc_final: 0.9206 (mm) REVERT: G 51 TYR cc_start: 0.9063 (p90) cc_final: 0.8425 (p90) REVERT: G 191 GLU cc_start: 0.5917 (pt0) cc_final: 0.5196 (pt0) REVERT: G 305 GLU cc_start: 0.5012 (mt-10) cc_final: 0.4568 (mt-10) REVERT: J 160 ASN cc_start: 0.8874 (m110) cc_final: 0.8626 (m-40) REVERT: J 167 MET cc_start: 0.7940 (mtm) cc_final: 0.7731 (mtm) REVERT: J 324 LYS cc_start: 0.9158 (mmmt) cc_final: 0.8773 (mmmt) REVERT: J 339 TRP cc_start: 0.8645 (m100) cc_final: 0.7530 (m100) REVERT: N 31 ILE cc_start: 0.9550 (mm) cc_final: 0.9264 (mm) REVERT: N 70 MET cc_start: 0.7911 (tpp) cc_final: 0.7637 (tpt) REVERT: N 100 LEU cc_start: 0.9143 (tp) cc_final: 0.8849 (tp) REVERT: N 152 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7657 (mm-40) REVERT: N 164 TYR cc_start: 0.8794 (m-10) cc_final: 0.8569 (m-10) REVERT: N 327 GLU cc_start: 0.7589 (tt0) cc_final: 0.7209 (tt0) REVERT: O 162 THR cc_start: 0.8477 (t) cc_final: 0.8226 (p) REVERT: O 187 TYR cc_start: 0.8808 (t80) cc_final: 0.8606 (t80) REVERT: Q 11 LEU cc_start: 0.9033 (mt) cc_final: 0.8479 (tp) REVERT: Q 110 ILE cc_start: 0.9556 (tp) cc_final: 0.9111 (tt) REVERT: Q 157 ASP cc_start: 0.8471 (p0) cc_final: 0.8259 (p0) REVERT: Q 199 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8009 (tm-30) REVERT: Q 276 ILE cc_start: 0.9298 (tt) cc_final: 0.9034 (tt) REVERT: Q 327 GLU cc_start: 0.7448 (tt0) cc_final: 0.7182 (tt0) REVERT: X 4 LEU cc_start: 0.7544 (mt) cc_final: 0.7340 (mt) REVERT: X 40 THR cc_start: 0.2417 (m) cc_final: 0.1200 (m) REVERT: Y 100 TRP cc_start: 0.7749 (p90) cc_final: 0.7514 (p90) REVERT: Z 80 LEU cc_start: 0.7677 (tp) cc_final: 0.7296 (tp) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.1411 time to fit residues: 96.4752 Evaluate side-chains 325 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 94 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 305 HIS N 232 GLN Y 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106114 restraints weight = 41043.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106859 restraints weight = 44207.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107538 restraints weight = 39970.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108207 restraints weight = 24339.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109988 restraints weight = 21378.297| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20533 Z= 0.152 Angle : 0.674 9.616 27968 Z= 0.351 Chirality : 0.046 0.279 3065 Planarity : 0.005 0.112 3622 Dihedral : 5.243 45.173 2802 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.16), residues: 2559 helix: -2.76 (0.56), residues: 59 sheet: 0.09 (0.16), residues: 906 loop : -1.44 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 66 TYR 0.015 0.001 TYR G 308 PHE 0.009 0.001 PHE J 6 TRP 0.026 0.002 TRP N 330 HIS 0.010 0.001 HIS J 305 Details of bonding type rmsd covalent geometry : bond 0.00354 (20493) covalent geometry : angle 0.66236 (27888) SS BOND : bond 0.00408 ( 40) SS BOND : angle 2.41538 ( 80) hydrogen bonds : bond 0.03707 ( 645) hydrogen bonds : angle 5.45100 ( 1599) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ARG cc_start: 0.8373 (tpp80) cc_final: 0.8008 (tpp80) REVERT: B 51 TYR cc_start: 0.8792 (p90) cc_final: 0.8514 (p90) REVERT: B 187 TYR cc_start: 0.8581 (t80) cc_final: 0.8334 (t80) REVERT: G 13 ILE cc_start: 0.9497 (mm) cc_final: 0.9166 (mm) REVERT: G 51 TYR cc_start: 0.9069 (p90) cc_final: 0.8517 (p90) REVERT: G 191 GLU cc_start: 0.5790 (pt0) cc_final: 0.4974 (pt0) REVERT: G 305 GLU cc_start: 0.5072 (mt-10) cc_final: 0.4681 (mt-10) REVERT: J 128 GLU cc_start: 0.7400 (tm-30) cc_final: 0.5880 (tm-30) REVERT: J 130 LYS cc_start: 0.8986 (ttmm) cc_final: 0.8729 (tppt) REVERT: J 160 ASN cc_start: 0.8839 (m110) cc_final: 0.8600 (m-40) REVERT: J 324 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8737 (mmmt) REVERT: J 339 TRP cc_start: 0.8601 (m100) cc_final: 0.7551 (m100) REVERT: N 9 TYR cc_start: 0.7770 (m-10) cc_final: 0.7512 (m-10) REVERT: N 31 ILE cc_start: 0.9510 (mm) cc_final: 0.9178 (mm) REVERT: N 100 LEU cc_start: 0.9172 (tp) cc_final: 0.8847 (tp) REVERT: N 164 TYR cc_start: 0.8795 (m-10) cc_final: 0.8564 (m-10) REVERT: N 306 TYR cc_start: 0.8128 (p90) cc_final: 0.7910 (p90) REVERT: N 327 GLU cc_start: 0.7649 (tt0) cc_final: 0.7394 (tt0) REVERT: O 162 THR cc_start: 0.8551 (t) cc_final: 0.8280 (p) REVERT: Q 11 LEU cc_start: 0.9050 (mt) cc_final: 0.8470 (tp) REVERT: Q 110 ILE cc_start: 0.9592 (tp) cc_final: 0.9206 (tt) REVERT: Q 157 ASP cc_start: 0.8536 (p0) cc_final: 0.8302 (p0) REVERT: Q 199 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8076 (tm-30) REVERT: Q 276 ILE cc_start: 0.9299 (tt) cc_final: 0.9012 (tt) REVERT: Q 327 GLU cc_start: 0.7379 (tt0) cc_final: 0.7168 (tt0) REVERT: X 4 LEU cc_start: 0.7569 (mt) cc_final: 0.7322 (mt) REVERT: X 40 THR cc_start: 0.2379 (m) cc_final: 0.1140 (m) REVERT: Z 73 ASN cc_start: 0.7973 (p0) cc_final: 0.7748 (p0) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.1411 time to fit residues: 95.9520 Evaluate side-chains 340 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 140 optimal weight: 8.9990 chunk 131 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 0.0070 chunk 199 optimal weight: 10.0000 chunk 210 optimal weight: 0.0570 chunk 88 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.8918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 368 GLN Y 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.140939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107955 restraints weight = 40572.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107407 restraints weight = 40879.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108673 restraints weight = 40615.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109440 restraints weight = 24578.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111359 restraints weight = 22048.832| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20533 Z= 0.119 Angle : 0.676 9.508 27968 Z= 0.351 Chirality : 0.046 0.352 3065 Planarity : 0.005 0.127 3622 Dihedral : 5.191 50.806 2802 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.05 % Allowed : 0.60 % Favored : 99.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.16), residues: 2559 helix: -2.81 (0.55), residues: 59 sheet: 0.15 (0.16), residues: 920 loop : -1.34 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 66 TYR 0.028 0.001 TYR O 187 PHE 0.032 0.001 PHE G 156 TRP 0.052 0.002 TRP Q 339 HIS 0.004 0.001 HIS Y 33 Details of bonding type rmsd covalent geometry : bond 0.00275 (20493) covalent geometry : angle 0.66502 (27888) SS BOND : bond 0.00381 ( 40) SS BOND : angle 2.39820 ( 80) hydrogen bonds : bond 0.03272 ( 645) hydrogen bonds : angle 5.36567 ( 1599) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 455 time to evaluate : 0.846 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: B 27 LEU cc_start: 0.9033 (mm) cc_final: 0.8795 (mp) REVERT: B 51 TYR cc_start: 0.8754 (p90) cc_final: 0.8460 (p90) REVERT: B 187 TYR cc_start: 0.8527 (t80) cc_final: 0.8326 (t80) REVERT: G 13 ILE cc_start: 0.9499 (mm) cc_final: 0.9170 (mm) REVERT: G 51 TYR cc_start: 0.9029 (p90) cc_final: 0.8484 (p90) REVERT: G 305 GLU cc_start: 0.4704 (mt-10) cc_final: 0.4354 (mt-10) REVERT: G 373 TYR cc_start: 0.7850 (m-10) cc_final: 0.7326 (m-10) REVERT: J 128 GLU cc_start: 0.7339 (tm-30) cc_final: 0.5800 (tm-30) REVERT: J 130 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8739 (tppt) REVERT: J 160 ASN cc_start: 0.8806 (m110) cc_final: 0.8575 (m-40) REVERT: J 324 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8622 (mmmt) REVERT: J 339 TRP cc_start: 0.8486 (m100) cc_final: 0.7628 (m100) REVERT: N 9 TYR cc_start: 0.7728 (m-10) cc_final: 0.7502 (m-10) REVERT: N 332 ASN cc_start: 0.9169 (m110) cc_final: 0.8931 (m110) REVERT: O 162 THR cc_start: 0.8527 (t) cc_final: 0.8270 (p) REVERT: Q 11 LEU cc_start: 0.9091 (mt) cc_final: 0.8421 (tp) REVERT: Q 110 ILE cc_start: 0.9452 (tp) cc_final: 0.9140 (tt) REVERT: Q 199 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8059 (tm-30) REVERT: Q 276 ILE cc_start: 0.9264 (tt) cc_final: 0.9004 (tt) REVERT: Q 327 GLU cc_start: 0.7406 (tt0) cc_final: 0.7065 (tt0) REVERT: X 4 LEU cc_start: 0.7569 (mt) cc_final: 0.7324 (mt) REVERT: Y 33 HIS cc_start: 0.5737 (m90) cc_final: 0.5517 (m-70) REVERT: Z 73 ASN cc_start: 0.8052 (p0) cc_final: 0.7826 (p0) REVERT: Z 82 MET cc_start: 0.4553 (pmm) cc_final: 0.4326 (pmm) outliers start: 1 outliers final: 0 residues processed: 456 average time/residue: 0.1376 time to fit residues: 98.8101 Evaluate side-chains 345 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 34 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 58 optimal weight: 0.0270 chunk 75 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 overall best weight: 2.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 396 GLN ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.139472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106564 restraints weight = 41081.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106112 restraints weight = 43862.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107113 restraints weight = 43959.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107861 restraints weight = 27243.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109693 restraints weight = 23359.537| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20533 Z= 0.157 Angle : 0.687 9.727 27968 Z= 0.358 Chirality : 0.046 0.338 3065 Planarity : 0.005 0.117 3622 Dihedral : 5.261 51.846 2802 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.16), residues: 2559 helix: -2.84 (0.55), residues: 59 sheet: 0.06 (0.16), residues: 929 loop : -1.33 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 366 TYR 0.017 0.001 TYR G 308 PHE 0.030 0.001 PHE B 95 TRP 0.036 0.002 TRP Q 339 HIS 0.006 0.001 HIS O 390 Details of bonding type rmsd covalent geometry : bond 0.00370 (20493) covalent geometry : angle 0.67505 (27888) SS BOND : bond 0.00345 ( 40) SS BOND : angle 2.45726 ( 80) hydrogen bonds : bond 0.03668 ( 645) hydrogen bonds : angle 5.46713 ( 1599) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.798 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: B 21 ARG cc_start: 0.8343 (tpp80) cc_final: 0.7988 (tpp80) REVERT: B 27 LEU cc_start: 0.8921 (mm) cc_final: 0.8704 (mp) REVERT: B 51 TYR cc_start: 0.8807 (p90) cc_final: 0.8502 (p90) REVERT: B 187 TYR cc_start: 0.8597 (t80) cc_final: 0.8365 (t80) REVERT: G 7 MET cc_start: 0.8117 (tmm) cc_final: 0.7879 (tmm) REVERT: G 13 ILE cc_start: 0.9505 (mm) cc_final: 0.9171 (mm) REVERT: G 51 TYR cc_start: 0.9067 (p90) cc_final: 0.8503 (p90) REVERT: G 305 GLU cc_start: 0.5042 (mt-10) cc_final: 0.4700 (mt-10) REVERT: J 160 ASN cc_start: 0.8846 (m110) cc_final: 0.8615 (m-40) REVERT: J 324 LYS cc_start: 0.9159 (mmmt) cc_final: 0.8754 (mmmt) REVERT: J 339 TRP cc_start: 0.8538 (m100) cc_final: 0.7526 (m100) REVERT: N 9 TYR cc_start: 0.7916 (m-10) cc_final: 0.7648 (m-10) REVERT: N 100 LEU cc_start: 0.9188 (tp) cc_final: 0.8844 (tp) REVERT: N 327 GLU cc_start: 0.7548 (tt0) cc_final: 0.7229 (tt0) REVERT: O 161 ILE cc_start: 0.8403 (mt) cc_final: 0.8186 (mm) REVERT: O 162 THR cc_start: 0.8554 (t) cc_final: 0.8306 (p) REVERT: Q 11 LEU cc_start: 0.9060 (mt) cc_final: 0.8398 (tp) REVERT: Q 110 ILE cc_start: 0.9600 (tp) cc_final: 0.9216 (tt) REVERT: Q 199 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7931 (tm-30) REVERT: Q 276 ILE cc_start: 0.9315 (tt) cc_final: 0.9015 (tt) REVERT: Q 327 GLU cc_start: 0.7450 (tt0) cc_final: 0.7162 (tt0) REVERT: X 4 LEU cc_start: 0.7623 (mt) cc_final: 0.7301 (mt) REVERT: Y 33 HIS cc_start: 0.5813 (m90) cc_final: 0.5577 (m-70) REVERT: Z 73 ASN cc_start: 0.8069 (p0) cc_final: 0.7848 (p0) REVERT: Z 92 CYS cc_start: 0.0744 (t) cc_final: 0.0443 (t) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.1420 time to fit residues: 96.1157 Evaluate side-chains 327 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 3 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 241 optimal weight: 50.0000 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 228 optimal weight: 40.0000 chunk 108 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 308 HIS Z 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106154 restraints weight = 41104.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106902 restraints weight = 43562.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107451 restraints weight = 41667.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108211 restraints weight = 24868.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110036 restraints weight = 21406.325| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20533 Z= 0.147 Angle : 0.691 9.572 27968 Z= 0.359 Chirality : 0.046 0.312 3065 Planarity : 0.005 0.120 3622 Dihedral : 5.257 51.376 2802 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2559 helix: -2.85 (0.55), residues: 59 sheet: 0.06 (0.16), residues: 928 loop : -1.36 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 66 TYR 0.017 0.001 TYR G 308 PHE 0.033 0.001 PHE G 156 TRP 0.035 0.002 TRP Q 339 HIS 0.007 0.001 HIS J 308 Details of bonding type rmsd covalent geometry : bond 0.00346 (20493) covalent geometry : angle 0.67950 (27888) SS BOND : bond 0.00354 ( 40) SS BOND : angle 2.45203 ( 80) hydrogen bonds : bond 0.03638 ( 645) hydrogen bonds : angle 5.45538 ( 1599) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3246.55 seconds wall clock time: 57 minutes 15.62 seconds (3435.62 seconds total)