Starting phenix.real_space_refine on Sat Jul 4 14:00:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q0s_13751/07_2026/7q0s_13751.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q0s_13751/07_2026/7q0s_13751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q0s_13751/07_2026/7q0s_13751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q0s_13751/07_2026/7q0s_13751.map" model { file = "/net/cci-nas-00/data/ceres_data/7q0s_13751/07_2026/7q0s_13751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q0s_13751/07_2026/7q0s_13751.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7q0s_13751/07_2026/7q0s_13751.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q0s_13751/07_2026/7q0s_13751.cif" } resolution = 4.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 104 5.16 5 C 13540 2.51 5 N 3628 2.21 5 O 3914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21192 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5002 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5006 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5006 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 5002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5002 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain breaks: 2 Chain: "E" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "F" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "G" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "H" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.15, per 1000 atoms: 0.20 Number of scatterers: 21192 At special positions: 0 Unit cell: (124.89, 114.03, 140.094, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 6 15.00 O 3914 8.00 N 3628 7.00 C 13540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.41 Conformation dependent library (CDL) restraints added in 799.2 milliseconds 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 12 sheets defined 57.7% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.979A pdb=" N VAL A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.658A pdb=" N SER A 122 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA A 123 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TRP A 124 " --> pdb=" O ALA A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 124' Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.514A pdb=" N GLY A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 169 Processing helix chain 'A' and resid 184 through 194 removed outlier: 3.701A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.063A pdb=" N ARG A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 removed outlier: 3.669A pdb=" N ASN A 223 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU A 224 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLU A 225 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 removed outlier: 4.034A pdb=" N GLU A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 283 through 289 removed outlier: 4.341A pdb=" N PHE A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 312 Processing helix chain 'A' and resid 338 through 357 Processing helix chain 'A' and resid 376 through 410 removed outlier: 3.703A pdb=" N LEU A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.926A pdb=" N MET A 419 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.532A pdb=" N GLY A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 578 through 591 Processing helix chain 'A' and resid 592 through 596 removed outlier: 3.575A pdb=" N LEU A 595 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 617 removed outlier: 5.489A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.979A pdb=" N VAL B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 84 through 97 Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.658A pdb=" N SER B 122 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 123 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TRP B 124 " --> pdb=" O ALA B 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 119 through 124' Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.514A pdb=" N GLY B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 169 Processing helix chain 'B' and resid 184 through 194 removed outlier: 3.701A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.063A pdb=" N ARG B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.670A pdb=" N ASN B 223 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU B 224 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU B 225 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 removed outlier: 4.035A pdb=" N GLU B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 283 through 289 removed outlier: 4.341A pdb=" N PHE B 287 " --> pdb=" O ASN B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 338 through 357 Processing helix chain 'B' and resid 376 through 410 removed outlier: 3.703A pdb=" N LEU B 380 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.927A pdb=" N MET B 419 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.533A pdb=" N GLY B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 544 through 548 Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 578 through 591 Processing helix chain 'B' and resid 592 through 596 removed outlier: 3.575A pdb=" N LEU B 595 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 617 removed outlier: 5.489A pdb=" N ARG B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.980A pdb=" N VAL C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 84 through 97 Processing helix chain 'C' and resid 119 through 124 removed outlier: 3.658A pdb=" N SER C 122 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA C 123 " --> pdb=" O GLY C 120 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TRP C 124 " --> pdb=" O ALA C 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 119 through 124' Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.513A pdb=" N GLY C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 169 Processing helix chain 'C' and resid 184 through 194 removed outlier: 3.701A pdb=" N LEU C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.063A pdb=" N ARG C 211 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 227 removed outlier: 3.669A pdb=" N ASN C 223 " --> pdb=" O PHE C 220 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU C 224 " --> pdb=" O TYR C 221 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU C 225 " --> pdb=" O ASN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 removed outlier: 4.035A pdb=" N GLU C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 259 through 270 Processing helix chain 'C' and resid 283 through 289 removed outlier: 4.341A pdb=" N PHE C 287 " --> pdb=" O ASN C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 338 through 357 Processing helix chain 'C' and resid 376 through 410 removed outlier: 3.704A pdb=" N LEU C 380 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.926A pdb=" N MET C 419 " --> pdb=" O MET C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 492 through 500 removed outlier: 3.533A pdb=" N GLY C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 500 " --> pdb=" O PHE C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 Processing helix chain 'C' and resid 532 through 542 Processing helix chain 'C' and resid 544 through 548 Processing helix chain 'C' and resid 559 through 576 Processing helix chain 'C' and resid 578 through 591 Processing helix chain 'C' and resid 592 through 596 removed outlier: 3.574A pdb=" N LEU C 595 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 617 removed outlier: 5.488A pdb=" N ARG C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 removed outlier: 3.980A pdb=" N VAL D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 84 through 97 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.658A pdb=" N SER D 122 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA D 123 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TRP D 124 " --> pdb=" O ALA D 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 119 through 124' Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.515A pdb=" N GLY D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 169 Processing helix chain 'D' and resid 184 through 194 removed outlier: 3.701A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 4.063A pdb=" N ARG D 211 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 227 removed outlier: 3.670A pdb=" N ASN D 223 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU D 224 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU D 225 " --> pdb=" O ASN D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 removed outlier: 4.033A pdb=" N GLU D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 259 through 270 Processing helix chain 'D' and resid 283 through 289 removed outlier: 4.341A pdb=" N PHE D 287 " --> pdb=" O ASN D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 312 Processing helix chain 'D' and resid 338 through 357 Processing helix chain 'D' and resid 376 through 410 removed outlier: 3.703A pdb=" N LEU D 380 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 removed outlier: 3.926A pdb=" N MET D 419 " --> pdb=" O MET D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 492 through 500 removed outlier: 3.532A pdb=" N GLY D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS D 500 " --> pdb=" O PHE D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 Processing helix chain 'D' and resid 532 through 542 Processing helix chain 'D' and resid 544 through 548 Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 578 through 591 Processing helix chain 'D' and resid 592 through 596 removed outlier: 3.574A pdb=" N LEU D 595 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 617 removed outlier: 5.488A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 328 Processing helix chain 'E' and resid 337 through 346 removed outlier: 4.119A pdb=" N ILE E 341 " --> pdb=" O SER E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'F' and resid 318 through 328 Processing helix chain 'F' and resid 337 through 346 removed outlier: 4.118A pdb=" N ILE F 341 " --> pdb=" O SER F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 337 through 346 removed outlier: 4.118A pdb=" N ILE G 341 " --> pdb=" O SER G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 347 through 349 No H-bonds generated for 'chain 'G' and resid 347 through 349' Processing helix chain 'H' and resid 318 through 328 Processing helix chain 'H' and resid 337 through 346 removed outlier: 4.118A pdb=" N ILE H 341 " --> pdb=" O SER H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 349 No H-bonds generated for 'chain 'H' and resid 347 through 349' Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.597A pdb=" N TYR A 62 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL A 115 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU A 64 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 117 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY A 66 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL A 254 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR A 200 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR A 256 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE A 202 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 276 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 477 removed outlier: 9.235A pdb=" N LEU A 502 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR A 529 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER A 526 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU A 553 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER A 528 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 375 removed outlier: 5.078A pdb=" N ASN A 374 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.597A pdb=" N TYR B 62 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL B 115 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU B 64 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU B 117 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY B 66 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL B 254 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B 200 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR B 256 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE B 202 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 276 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 477 removed outlier: 9.234A pdb=" N LEU B 502 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N THR B 529 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER B 526 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU B 553 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER B 528 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 372 through 375 removed outlier: 5.079A pdb=" N ASN B 374 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 79 removed outlier: 6.598A pdb=" N TYR C 62 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL C 115 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU C 64 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU C 117 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C 66 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL C 254 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR C 200 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR C 256 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE C 202 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 276 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 477 removed outlier: 9.234A pdb=" N LEU C 502 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N THR C 529 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER C 526 " --> pdb=" O TYR C 551 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU C 553 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER C 528 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 372 through 375 removed outlier: 5.079A pdb=" N ASN C 374 " --> pdb=" O ASN C 447 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.597A pdb=" N TYR D 62 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL D 115 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU D 64 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU D 117 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY D 66 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL D 254 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR D 200 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR D 256 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE D 202 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE D 276 " --> pdb=" O PHE D 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 473 through 477 removed outlier: 9.235A pdb=" N LEU D 502 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR D 529 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER D 526 " --> pdb=" O TYR D 551 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU D 553 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER D 528 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 372 through 375 removed outlier: 5.078A pdb=" N ASN D 374 " --> pdb=" O ASN D 447 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3120 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: 2.80 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6881 1.34 - 1.46: 4033 1.46 - 1.58: 10658 1.58 - 1.69: 12 1.69 - 1.81: 156 Bond restraints: 21740 Sorted by residual: bond pdb=" O6 G6P A 801 " pdb=" P G6P A 801 " ideal model delta sigma weight residual 1.722 1.646 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" O6 G6P C 801 " pdb=" P G6P C 801 " ideal model delta sigma weight residual 1.722 1.647 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O6 G6P B 801 " pdb=" P G6P B 801 " ideal model delta sigma weight residual 1.722 1.647 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O6 G6P D 801 " pdb=" P G6P D 801 " ideal model delta sigma weight residual 1.722 1.647 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C1 G6P C 801 " pdb=" O5 G6P C 801 " ideal model delta sigma weight residual 1.401 1.462 -0.061 2.00e-02 2.50e+03 9.41e+00 ... (remaining 21735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 28758 1.82 - 3.64: 568 3.64 - 5.46: 107 5.46 - 7.28: 21 7.28 - 9.09: 4 Bond angle restraints: 29458 Sorted by residual: angle pdb=" N ILE D 238 " pdb=" CA ILE D 238 " pdb=" C ILE D 238 " ideal model delta sigma weight residual 111.77 107.00 4.77 1.04e+00 9.25e-01 2.10e+01 angle pdb=" N ILE C 238 " pdb=" CA ILE C 238 " pdb=" C ILE C 238 " ideal model delta sigma weight residual 111.77 107.01 4.76 1.04e+00 9.25e-01 2.09e+01 angle pdb=" N ILE B 238 " pdb=" CA ILE B 238 " pdb=" C ILE B 238 " ideal model delta sigma weight residual 111.77 107.02 4.75 1.04e+00 9.25e-01 2.09e+01 angle pdb=" N ILE A 238 " pdb=" CA ILE A 238 " pdb=" C ILE A 238 " ideal model delta sigma weight residual 111.77 107.05 4.72 1.04e+00 9.25e-01 2.06e+01 angle pdb=" N GLU E 326 " pdb=" CA GLU E 326 " pdb=" CB GLU E 326 " ideal model delta sigma weight residual 110.16 115.64 -5.48 1.48e+00 4.57e-01 1.37e+01 ... (remaining 29453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 11311 17.66 - 35.33: 1131 35.33 - 52.99: 226 52.99 - 70.66: 60 70.66 - 88.32: 36 Dihedral angle restraints: 12764 sinusoidal: 5164 harmonic: 7600 Sorted by residual: dihedral pdb=" CA ASN B 228 " pdb=" C ASN B 228 " pdb=" N VAL B 229 " pdb=" CA VAL B 229 " ideal model delta harmonic sigma weight residual 180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ASN D 228 " pdb=" C ASN D 228 " pdb=" N VAL D 229 " pdb=" CA VAL D 229 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ASN C 228 " pdb=" C ASN C 228 " pdb=" N VAL C 229 " pdb=" CA VAL C 229 " ideal model delta harmonic sigma weight residual 180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 12761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 3124 1.020 - 2.039: 0 2.039 - 3.059: 0 3.059 - 4.079: 0 4.079 - 5.099: 16 Chirality restraints: 3140 Sorted by residual: chirality pdb=" C5 G6P C 801 " pdb=" C4 G6P C 801 " pdb=" C6 G6P C 801 " pdb=" O5 G6P C 801 " both_signs ideal model delta sigma weight residual False -2.51 2.59 -5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" C5 G6P D 801 " pdb=" C4 G6P D 801 " pdb=" C6 G6P D 801 " pdb=" O5 G6P D 801 " both_signs ideal model delta sigma weight residual False -2.51 2.58 -5.10 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C5 G6P A 801 " pdb=" C4 G6P A 801 " pdb=" C6 G6P A 801 " pdb=" O5 G6P A 801 " both_signs ideal model delta sigma weight residual False -2.51 2.58 -5.10 2.00e-01 2.50e+01 6.49e+02 ... (remaining 3137 not shown) Planarity restraints: 3792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 433 " 0.009 2.00e-02 2.50e+03 1.72e-02 5.17e+00 pdb=" CG PHE B 433 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE B 433 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 433 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE B 433 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 433 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 433 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 433 " -0.009 2.00e-02 2.50e+03 1.71e-02 5.11e+00 pdb=" CG PHE C 433 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE C 433 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 433 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE C 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 433 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 433 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 433 " 0.009 2.00e-02 2.50e+03 1.71e-02 5.10e+00 pdb=" CG PHE D 433 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE D 433 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE D 433 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE D 433 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 433 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 433 " -0.001 2.00e-02 2.50e+03 ... (remaining 3789 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1952 2.74 - 3.28: 21222 3.28 - 3.82: 35406 3.82 - 4.36: 40314 4.36 - 4.90: 70795 Nonbonded interactions: 169689 Sorted by model distance: nonbonded pdb=" O TYR E 332 " pdb=" OG SER E 337 " model vdw 2.203 3.040 nonbonded pdb=" O TYR G 332 " pdb=" OG SER G 337 " model vdw 2.204 3.040 nonbonded pdb=" O TYR H 332 " pdb=" OG SER H 337 " model vdw 2.204 3.040 nonbonded pdb=" O TYR F 332 " pdb=" OG SER F 337 " model vdw 2.204 3.040 nonbonded pdb=" OG SER E 318 " pdb=" OE1 GLU E 319 " model vdw 2.244 3.040 ... (remaining 169684 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.760 Find NCS groups from input model: 0.180 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21740 Z= 0.175 Angle : 0.634 9.094 29458 Z= 0.344 Chirality : 0.344 5.099 3140 Planarity : 0.004 0.050 3792 Dihedral : 15.331 88.320 7868 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.25 % Allowed : 1.56 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2576 helix: 1.53 (0.15), residues: 1320 sheet: -0.37 (0.27), residues: 360 loop : -0.97 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 556 TYR 0.023 0.002 TYR D 68 PHE 0.038 0.001 PHE B 433 TRP 0.030 0.002 TRP D 58 HIS 0.007 0.001 HIS B 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (21740) covalent geometry : angle 0.63408 / 0.34 (29458) hydrogen bonds : bond 0.14488 / 9.26 ( 1068) hydrogen bonds : angle 6.00035 / 4.31 ( 3120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 351 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8101 (t80) cc_final: 0.7754 (t80) REVERT: A 611 MET cc_start: 0.8864 (mmt) cc_final: 0.8612 (mmt) REVERT: B 88 LYS cc_start: 0.9004 (mmpt) cc_final: 0.8566 (mmmt) REVERT: B 303 ARG cc_start: 0.6505 (ttt180) cc_final: 0.6271 (ttt180) REVERT: C 68 TYR cc_start: 0.8075 (t80) cc_final: 0.7789 (t80) REVERT: C 88 LYS cc_start: 0.8980 (mmpt) cc_final: 0.8487 (mmmt) REVERT: D 35 GLU cc_start: 0.7356 (pt0) cc_final: 0.7147 (pt0) REVERT: D 68 TYR cc_start: 0.8094 (t80) cc_final: 0.7723 (t80) REVERT: D 76 GLN cc_start: 0.7437 (pt0) cc_final: 0.7212 (pt0) REVERT: D 88 LYS cc_start: 0.9017 (mmpt) cc_final: 0.8466 (mmmt) REVERT: D 611 MET cc_start: 0.8902 (mmt) cc_final: 0.8656 (mmt) outliers start: 28 outliers final: 8 residues processed: 357 average time/residue: 0.1302 time to fit residues: 73.8771 Evaluate side-chains 266 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 258 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 531 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 0.1980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 240 HIS A 610 HIS B 76 GLN B 610 HIS C 76 GLN C 240 HIS C 610 HIS ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 HIS E 340 ASN F 340 ASN G 340 ASN H 340 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103452 restraints weight = 40408.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106081 restraints weight = 26890.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107949 restraints weight = 20608.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.109216 restraints weight = 17189.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.110134 restraints weight = 15190.449| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21740 Z= 0.117 Angle : 0.559 8.314 29458 Z= 0.282 Chirality : 0.042 0.165 3140 Planarity : 0.003 0.042 3792 Dihedral : 5.020 67.435 2894 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.93 % Allowed : 8.46 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2576 helix: 1.98 (0.15), residues: 1312 sheet: -0.21 (0.30), residues: 290 loop : -0.69 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.018 0.001 TYR B 68 PHE 0.027 0.001 PHE B 433 TRP 0.013 0.001 TRP A 182 HIS 0.006 0.001 HIS D 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (21740) covalent geometry : angle 0.55879 / 0.28 (29458) hydrogen bonds : bond 0.03283 / 2.18 ( 1068) hydrogen bonds : angle 4.29457 / 3.05 ( 3120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 321 time to evaluate : 0.700 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: A 68 TYR cc_start: 0.8178 (t80) cc_final: 0.7934 (t80) REVERT: A 94 MET cc_start: 0.7852 (mmp) cc_final: 0.6846 (mmm) REVERT: A 303 ARG cc_start: 0.6902 (ttt180) cc_final: 0.6661 (ttt180) REVERT: A 333 GLU cc_start: 0.8653 (mp0) cc_final: 0.8442 (mp0) REVERT: A 522 MET cc_start: 0.8506 (tpp) cc_final: 0.7937 (mtp) REVERT: A 538 MET cc_start: 0.9058 (mmm) cc_final: 0.8295 (mpp) REVERT: B 88 LYS cc_start: 0.8906 (mmpt) cc_final: 0.8402 (mmmt) REVERT: B 94 MET cc_start: 0.7904 (mmp) cc_final: 0.7590 (mmt) REVERT: B 303 ARG cc_start: 0.6818 (ttt180) cc_final: 0.6486 (ttt180) REVERT: B 505 PHE cc_start: 0.8166 (m-80) cc_final: 0.7765 (m-80) REVERT: B 522 MET cc_start: 0.8481 (tpp) cc_final: 0.7978 (mtp) REVERT: C 22 PHE cc_start: 0.5984 (t80) cc_final: 0.5671 (t80) REVERT: C 88 LYS cc_start: 0.8904 (mmpt) cc_final: 0.8329 (mmmt) REVERT: C 94 MET cc_start: 0.7878 (mmp) cc_final: 0.7584 (mmt) REVERT: C 303 ARG cc_start: 0.6917 (ttt180) cc_final: 0.6678 (ttt180) REVERT: C 333 GLU cc_start: 0.8717 (mp0) cc_final: 0.8393 (mp0) REVERT: C 505 PHE cc_start: 0.8148 (m-80) cc_final: 0.7776 (m-80) REVERT: C 522 MET cc_start: 0.8568 (tpp) cc_final: 0.8060 (mtp) REVERT: C 611 MET cc_start: 0.8845 (mmt) cc_final: 0.8517 (mmp) REVERT: D 35 GLU cc_start: 0.7192 (pt0) cc_final: 0.6978 (pt0) REVERT: D 88 LYS cc_start: 0.8925 (mmpt) cc_final: 0.8329 (mmmt) REVERT: D 94 MET cc_start: 0.7865 (mmp) cc_final: 0.6882 (mmm) REVERT: D 333 GLU cc_start: 0.8725 (mp0) cc_final: 0.8472 (mp0) REVERT: D 522 MET cc_start: 0.8519 (tpp) cc_final: 0.7949 (mtp) REVERT: F 347 THR cc_start: 0.9059 (p) cc_final: 0.8781 (t) REVERT: G 333 MET cc_start: 0.8982 (mmm) cc_final: 0.8178 (pmm) outliers start: 21 outliers final: 13 residues processed: 332 average time/residue: 0.1331 time to fit residues: 69.5558 Evaluate side-chains 274 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 261 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 199 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 138 ASN B 76 GLN B 240 HIS C 76 GLN C 138 ASN D 76 GLN D 138 ASN D 240 HIS E 340 ASN G 340 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.130617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.099742 restraints weight = 41459.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.102258 restraints weight = 28977.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104009 restraints weight = 22765.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105215 restraints weight = 19350.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105983 restraints weight = 17339.366| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21740 Z= 0.129 Angle : 0.534 8.902 29458 Z= 0.271 Chirality : 0.042 0.153 3140 Planarity : 0.003 0.043 3792 Dihedral : 4.740 59.430 2882 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.96 % Allowed : 11.62 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2576 helix: 2.01 (0.15), residues: 1314 sheet: -0.32 (0.29), residues: 288 loop : -0.80 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 303 TYR 0.018 0.001 TYR D 493 PHE 0.014 0.001 PHE B 433 TRP 0.012 0.001 TRP C 182 HIS 0.003 0.001 HIS D 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21740) covalent geometry : angle 0.53416 / 0.27 (29458) hydrogen bonds : bond 0.03167 / 2.10 ( 1068) hydrogen bonds : angle 4.16885 / 2.95 ( 3120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 310 time to evaluate : 0.605 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: A 31 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: A 68 TYR cc_start: 0.8159 (t80) cc_final: 0.7920 (t80) REVERT: A 94 MET cc_start: 0.8080 (mmt) cc_final: 0.7677 (mmt) REVERT: A 240 HIS cc_start: 0.8676 (p-80) cc_final: 0.8448 (p90) REVERT: A 306 GLU cc_start: 0.8331 (tp30) cc_final: 0.8083 (tp30) REVERT: A 333 GLU cc_start: 0.8689 (mp0) cc_final: 0.8459 (mp0) REVERT: A 346 LEU cc_start: 0.8770 (mt) cc_final: 0.8475 (tp) REVERT: A 505 PHE cc_start: 0.8173 (m-80) cc_final: 0.7884 (m-80) REVERT: A 522 MET cc_start: 0.8605 (tpp) cc_final: 0.8145 (mtp) REVERT: B 31 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: B 35 GLU cc_start: 0.7128 (pt0) cc_final: 0.6902 (pt0) REVERT: B 88 LYS cc_start: 0.9021 (mmpt) cc_final: 0.8549 (mmmt) REVERT: B 94 MET cc_start: 0.8007 (mmt) cc_final: 0.7543 (mmt) REVERT: B 522 MET cc_start: 0.8603 (tpp) cc_final: 0.8214 (mtp) REVERT: C 31 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: C 35 GLU cc_start: 0.7229 (pt0) cc_final: 0.7020 (pt0) REVERT: C 94 MET cc_start: 0.8099 (mmt) cc_final: 0.7660 (mmt) REVERT: C 333 GLU cc_start: 0.8732 (mp0) cc_final: 0.8467 (mp0) REVERT: C 522 MET cc_start: 0.8705 (tpp) cc_final: 0.8245 (mtp) REVERT: C 538 MET cc_start: 0.8522 (mmm) cc_final: 0.8167 (mpp) REVERT: C 611 MET cc_start: 0.8994 (mmt) cc_final: 0.8585 (mmp) REVERT: D 22 PHE cc_start: 0.5978 (t80) cc_final: 0.5735 (t80) REVERT: D 31 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: D 88 LYS cc_start: 0.9042 (mmpt) cc_final: 0.8777 (mmmt) REVERT: D 94 MET cc_start: 0.8087 (mmt) cc_final: 0.7678 (mmt) REVERT: D 306 GLU cc_start: 0.8329 (tp30) cc_final: 0.8116 (tp30) REVERT: D 346 LEU cc_start: 0.8816 (mt) cc_final: 0.8591 (tp) REVERT: D 522 MET cc_start: 0.8596 (tpp) cc_final: 0.8135 (mtp) REVERT: F 333 MET cc_start: 0.9019 (mmt) cc_final: 0.8158 (pmm) REVERT: H 333 MET cc_start: 0.8995 (mmt) cc_final: 0.8200 (pmm) outliers start: 44 outliers final: 33 residues processed: 332 average time/residue: 0.1229 time to fit residues: 65.5120 Evaluate side-chains 300 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 263 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 161 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 238 optimal weight: 0.0060 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 138 ASN ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.093987 restraints weight = 42121.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.096165 restraints weight = 29177.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097640 restraints weight = 23043.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098717 restraints weight = 19747.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.099277 restraints weight = 17739.739| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21740 Z= 0.265 Angle : 0.664 9.049 29458 Z= 0.343 Chirality : 0.046 0.170 3140 Planarity : 0.004 0.044 3792 Dihedral : 5.071 46.959 2882 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.76 % Allowed : 13.18 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.16), residues: 2576 helix: 1.45 (0.14), residues: 1308 sheet: -0.77 (0.26), residues: 316 loop : -1.46 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 303 TYR 0.018 0.002 TYR C 623 PHE 0.021 0.002 PHE D 375 TRP 0.016 0.001 TRP C 182 HIS 0.009 0.002 HIS C 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.27 (21740) covalent geometry : angle 0.66440 / 0.34 (29458) hydrogen bonds : bond 0.04224 / 2.77 ( 1068) hydrogen bonds : angle 4.59081 / 3.25 ( 3120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 296 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6462 (t80) cc_final: 0.5828 (t80) REVERT: A 31 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: A 35 GLU cc_start: 0.7208 (pt0) cc_final: 0.7004 (pt0) REVERT: A 68 TYR cc_start: 0.8215 (t80) cc_final: 0.7964 (t80) REVERT: A 94 MET cc_start: 0.8040 (mmt) cc_final: 0.7680 (mmt) REVERT: A 306 GLU cc_start: 0.8470 (tp30) cc_final: 0.8120 (tp30) REVERT: A 331 ARG cc_start: 0.8708 (mtm110) cc_final: 0.8280 (mtm110) REVERT: A 333 GLU cc_start: 0.8694 (mp0) cc_final: 0.8451 (mp0) REVERT: A 346 LEU cc_start: 0.8836 (mt) cc_final: 0.8556 (tp) REVERT: A 416 MET cc_start: 0.7858 (tpp) cc_final: 0.7531 (tpp) REVERT: A 522 MET cc_start: 0.8647 (tpp) cc_final: 0.8312 (mtp) REVERT: A 538 MET cc_start: 0.8705 (mmm) cc_final: 0.7958 (mpp) REVERT: B 31 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: B 88 LYS cc_start: 0.8908 (mmpt) cc_final: 0.8388 (mmmt) REVERT: B 94 MET cc_start: 0.8052 (mmt) cc_final: 0.7627 (mmt) REVERT: B 333 GLU cc_start: 0.8696 (mp0) cc_final: 0.8447 (mp0) REVERT: B 346 LEU cc_start: 0.8808 (mt) cc_final: 0.8518 (tp) REVERT: B 416 MET cc_start: 0.7695 (tpp) cc_final: 0.7306 (tpp) REVERT: B 522 MET cc_start: 0.8687 (tpp) cc_final: 0.8484 (mtp) REVERT: B 538 MET cc_start: 0.8689 (mmm) cc_final: 0.7834 (mpp) REVERT: B 590 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7471 (tp30) REVERT: B 611 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8250 (mmp) REVERT: C 22 PHE cc_start: 0.6280 (t80) cc_final: 0.5804 (t80) REVERT: C 31 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: C 94 MET cc_start: 0.8148 (mmt) cc_final: 0.7762 (mmt) REVERT: C 303 ARG cc_start: 0.7021 (ttt180) cc_final: 0.6559 (ttm-80) REVERT: C 331 ARG cc_start: 0.8707 (mtm110) cc_final: 0.8266 (mtm110) REVERT: C 333 GLU cc_start: 0.8710 (mp0) cc_final: 0.8477 (mp0) REVERT: C 522 MET cc_start: 0.8758 (tpp) cc_final: 0.8507 (mtp) REVERT: C 611 MET cc_start: 0.8969 (mmt) cc_final: 0.8554 (mmp) REVERT: D 22 PHE cc_start: 0.6393 (t80) cc_final: 0.6021 (t80) REVERT: D 31 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: D 88 LYS cc_start: 0.8916 (mmpt) cc_final: 0.8539 (mmmt) REVERT: D 94 MET cc_start: 0.8139 (mmt) cc_final: 0.7775 (mmt) REVERT: D 303 ARG cc_start: 0.7019 (ttt180) cc_final: 0.6700 (ttt180) REVERT: D 331 ARG cc_start: 0.8733 (mtm110) cc_final: 0.8233 (mtm110) REVERT: D 333 GLU cc_start: 0.8759 (mp0) cc_final: 0.8459 (mp0) REVERT: D 346 LEU cc_start: 0.8852 (mt) cc_final: 0.8569 (tp) REVERT: D 522 MET cc_start: 0.8636 (tpp) cc_final: 0.8311 (mtp) REVERT: D 538 MET cc_start: 0.8631 (mmm) cc_final: 0.7940 (mpp) REVERT: F 326 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6829 (mm-30) REVERT: F 333 MET cc_start: 0.9107 (mmt) cc_final: 0.8573 (pmm) outliers start: 62 outliers final: 40 residues processed: 324 average time/residue: 0.1394 time to fit residues: 69.7536 Evaluate side-chains 308 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain E residue 325 TRP Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain F residue 325 TRP Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain G residue 325 TRP Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain H residue 325 TRP Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.123887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.092995 restraints weight = 42174.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095301 restraints weight = 29446.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.096900 restraints weight = 23404.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097965 restraints weight = 20103.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098508 restraints weight = 18204.175| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21740 Z= 0.189 Angle : 0.586 8.880 29458 Z= 0.301 Chirality : 0.043 0.150 3140 Planarity : 0.004 0.043 3792 Dihedral : 4.791 43.195 2882 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.98 % Allowed : 15.09 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2576 helix: 1.61 (0.14), residues: 1302 sheet: -0.96 (0.26), residues: 320 loop : -1.52 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 303 TYR 0.017 0.001 TYR C 493 PHE 0.016 0.001 PHE C 505 TRP 0.013 0.001 TRP A 182 HIS 0.009 0.001 HIS D 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (21740) covalent geometry : angle 0.58576 / 0.30 (29458) hydrogen bonds : bond 0.03695 / 2.43 ( 1068) hydrogen bonds : angle 4.33626 / 3.06 ( 3120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 304 time to evaluate : 0.830 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: A 22 PHE cc_start: 0.6498 (t80) cc_final: 0.6262 (t80) REVERT: A 31 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: A 68 TYR cc_start: 0.8279 (t80) cc_final: 0.8064 (t80) REVERT: A 94 MET cc_start: 0.8199 (mmt) cc_final: 0.7763 (mmt) REVERT: A 331 ARG cc_start: 0.8708 (mtm110) cc_final: 0.8192 (mtm110) REVERT: A 333 GLU cc_start: 0.8706 (mp0) cc_final: 0.8347 (mp0) REVERT: A 346 LEU cc_start: 0.8860 (mt) cc_final: 0.8635 (tp) REVERT: A 416 MET cc_start: 0.7837 (tpp) cc_final: 0.7450 (tpp) REVERT: A 437 ARG cc_start: 0.7653 (ttp-170) cc_final: 0.7389 (ttp-170) REVERT: A 504 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8413 (m) REVERT: A 522 MET cc_start: 0.8662 (tpp) cc_final: 0.8312 (mtp) REVERT: A 538 MET cc_start: 0.8762 (mmm) cc_final: 0.8010 (mpp) REVERT: B 31 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: B 94 MET cc_start: 0.8205 (mmt) cc_final: 0.7714 (mmt) REVERT: B 240 HIS cc_start: 0.8853 (p-80) cc_final: 0.8601 (p90) REVERT: B 331 ARG cc_start: 0.8740 (mtm110) cc_final: 0.8332 (mtm110) REVERT: B 333 GLU cc_start: 0.8712 (mp0) cc_final: 0.8375 (mp0) REVERT: B 346 LEU cc_start: 0.8826 (mt) cc_final: 0.8581 (tp) REVERT: B 504 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8406 (m) REVERT: B 522 MET cc_start: 0.8699 (tpp) cc_final: 0.8433 (mtp) REVERT: B 538 MET cc_start: 0.8791 (mmm) cc_final: 0.8002 (mpp) REVERT: B 611 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8400 (mmp) REVERT: C 22 PHE cc_start: 0.6362 (t80) cc_final: 0.5838 (t80) REVERT: C 31 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: C 94 MET cc_start: 0.8193 (mmt) cc_final: 0.7739 (mmt) REVERT: C 240 HIS cc_start: 0.8793 (p-80) cc_final: 0.8509 (p90) REVERT: C 303 ARG cc_start: 0.7129 (ttt180) cc_final: 0.6619 (ttm-80) REVERT: C 306 GLU cc_start: 0.8535 (tp30) cc_final: 0.8203 (tp30) REVERT: C 331 ARG cc_start: 0.8701 (mtm110) cc_final: 0.8190 (mtm110) REVERT: C 333 GLU cc_start: 0.8775 (mp0) cc_final: 0.8406 (mp0) REVERT: C 416 MET cc_start: 0.7756 (tpp) cc_final: 0.7420 (tpp) REVERT: C 504 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8397 (m) REVERT: C 522 MET cc_start: 0.8855 (tpp) cc_final: 0.8482 (mtp) REVERT: C 611 MET cc_start: 0.8902 (mmt) cc_final: 0.8669 (mmm) REVERT: D 31 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: D 88 LYS cc_start: 0.9102 (mmpt) cc_final: 0.8699 (mmmt) REVERT: D 94 MET cc_start: 0.8199 (mmt) cc_final: 0.7779 (mmt) REVERT: D 303 ARG cc_start: 0.6914 (ttt180) cc_final: 0.6556 (ttt180) REVERT: D 306 GLU cc_start: 0.8400 (tp30) cc_final: 0.8198 (tp30) REVERT: D 331 ARG cc_start: 0.8708 (mtm110) cc_final: 0.8219 (mtm110) REVERT: D 333 GLU cc_start: 0.8781 (mp0) cc_final: 0.8379 (mp0) REVERT: D 346 LEU cc_start: 0.8871 (mt) cc_final: 0.8643 (tp) REVERT: D 504 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8441 (m) REVERT: D 522 MET cc_start: 0.8707 (tpp) cc_final: 0.8344 (mtp) REVERT: D 538 MET cc_start: 0.8794 (mmm) cc_final: 0.8036 (mpp) REVERT: H 333 MET cc_start: 0.9315 (mmm) cc_final: 0.8520 (pmm) REVERT: H 343 ARG cc_start: 0.8531 (ptt-90) cc_final: 0.8309 (ptt-90) outliers start: 67 outliers final: 45 residues processed: 342 average time/residue: 0.1394 time to fit residues: 73.5561 Evaluate side-chains 322 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain E residue 325 TRP Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain F residue 325 TRP Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain G residue 325 TRP Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain H residue 325 TRP Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 238 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.126907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096127 restraints weight = 41844.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.098572 restraints weight = 29063.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.100240 restraints weight = 22869.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101316 restraints weight = 19605.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.102140 restraints weight = 17695.500| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21740 Z= 0.117 Angle : 0.537 9.551 29458 Z= 0.271 Chirality : 0.041 0.168 3140 Planarity : 0.003 0.040 3792 Dihedral : 4.463 45.785 2882 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.49 % Allowed : 16.65 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2576 helix: 1.88 (0.15), residues: 1308 sheet: -0.71 (0.25), residues: 324 loop : -1.36 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 303 TYR 0.012 0.001 TYR D 44 PHE 0.017 0.001 PHE B 505 TRP 0.009 0.001 TRP D 182 HIS 0.009 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (21740) covalent geometry : angle 0.53660 / 0.27 (29458) hydrogen bonds : bond 0.03194 / 2.13 ( 1068) hydrogen bonds : angle 4.06759 / 2.87 ( 3120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6453 (t80) cc_final: 0.6206 (t80) REVERT: A 68 TYR cc_start: 0.8323 (t80) cc_final: 0.8079 (t80) REVERT: A 88 LYS cc_start: 0.9144 (mmpt) cc_final: 0.8717 (mmmt) REVERT: A 94 MET cc_start: 0.8127 (mmt) cc_final: 0.7733 (mmt) REVERT: A 306 GLU cc_start: 0.8353 (tp30) cc_final: 0.8102 (tp30) REVERT: A 331 ARG cc_start: 0.8686 (mtm110) cc_final: 0.8212 (mtm110) REVERT: A 333 GLU cc_start: 0.8718 (mp0) cc_final: 0.8282 (mp0) REVERT: A 346 LEU cc_start: 0.8762 (mt) cc_final: 0.8500 (tp) REVERT: A 416 MET cc_start: 0.7791 (tpp) cc_final: 0.7392 (tpp) REVERT: A 522 MET cc_start: 0.8676 (tpp) cc_final: 0.8312 (mtp) REVERT: A 538 MET cc_start: 0.8780 (mmm) cc_final: 0.8034 (mpp) REVERT: A 590 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6916 (mt-10) REVERT: B 88 LYS cc_start: 0.9373 (mttt) cc_final: 0.9169 (mtpt) REVERT: B 94 MET cc_start: 0.8089 (mmt) cc_final: 0.7705 (mmt) REVERT: B 240 HIS cc_start: 0.8816 (p-80) cc_final: 0.8401 (p90) REVERT: B 331 ARG cc_start: 0.8688 (mtm110) cc_final: 0.8236 (mtm110) REVERT: B 333 GLU cc_start: 0.8724 (mp0) cc_final: 0.8256 (mp0) REVERT: B 346 LEU cc_start: 0.8734 (mt) cc_final: 0.8499 (tp) REVERT: B 522 MET cc_start: 0.8836 (tpp) cc_final: 0.8465 (mtp) REVERT: B 538 MET cc_start: 0.8818 (mmm) cc_final: 0.8014 (mpp) REVERT: B 611 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8363 (mmp) REVERT: C 22 PHE cc_start: 0.6321 (t80) cc_final: 0.5799 (t80) REVERT: C 94 MET cc_start: 0.8064 (mmt) cc_final: 0.7662 (mmt) REVERT: C 240 HIS cc_start: 0.8777 (p-80) cc_final: 0.8391 (p-80) REVERT: C 306 GLU cc_start: 0.8498 (tp30) cc_final: 0.8229 (tp30) REVERT: C 331 ARG cc_start: 0.8615 (mtm110) cc_final: 0.8050 (mtm110) REVERT: C 333 GLU cc_start: 0.8734 (mp0) cc_final: 0.8326 (mp0) REVERT: C 522 MET cc_start: 0.8861 (tpp) cc_final: 0.8446 (mtp) REVERT: C 538 MET cc_start: 0.8853 (mmm) cc_final: 0.8010 (mpp) REVERT: C 611 MET cc_start: 0.8878 (mmt) cc_final: 0.8649 (mmm) REVERT: D 88 LYS cc_start: 0.9123 (mmpt) cc_final: 0.8667 (mmmt) REVERT: D 94 MET cc_start: 0.8105 (mmt) cc_final: 0.7789 (mmt) REVERT: D 265 GLU cc_start: 0.7820 (pt0) cc_final: 0.7529 (pt0) REVERT: D 303 ARG cc_start: 0.7069 (ttt180) cc_final: 0.6670 (ttt180) REVERT: D 306 GLU cc_start: 0.8376 (tp30) cc_final: 0.8140 (tp30) REVERT: D 331 ARG cc_start: 0.8595 (mtm110) cc_final: 0.8075 (mtm110) REVERT: D 333 GLU cc_start: 0.8782 (mp0) cc_final: 0.8378 (mp0) REVERT: D 346 LEU cc_start: 0.8798 (mt) cc_final: 0.8554 (tp) REVERT: D 522 MET cc_start: 0.8690 (tpp) cc_final: 0.8280 (mtp) REVERT: D 538 MET cc_start: 0.8829 (mmm) cc_final: 0.8084 (mpp) REVERT: F 333 MET cc_start: 0.9365 (mmm) cc_final: 0.8348 (pmm) outliers start: 56 outliers final: 34 residues processed: 346 average time/residue: 0.1390 time to fit residues: 74.2480 Evaluate side-chains 312 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 325 TRP Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 180 optimal weight: 0.5980 chunk 195 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.122937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092224 restraints weight = 42374.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094454 restraints weight = 29870.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096060 restraints weight = 23881.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097066 restraints weight = 20538.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097837 restraints weight = 18630.153| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21740 Z= 0.219 Angle : 0.618 8.846 29458 Z= 0.315 Chirality : 0.044 0.162 3140 Planarity : 0.004 0.060 3792 Dihedral : 4.824 50.112 2882 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.94 % Allowed : 16.52 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2576 helix: 1.54 (0.14), residues: 1312 sheet: -1.05 (0.26), residues: 316 loop : -1.53 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 303 TYR 0.013 0.002 TYR C 44 PHE 0.012 0.002 PHE A 334 TRP 0.016 0.001 TRP D 182 HIS 0.008 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (21740) covalent geometry : angle 0.61844 / 0.32 (29458) hydrogen bonds : bond 0.03829 / 2.52 ( 1068) hydrogen bonds : angle 4.38116 / 3.10 ( 3120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 279 time to evaluate : 0.819 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: A 22 PHE cc_start: 0.6580 (t80) cc_final: 0.6125 (t80) REVERT: A 31 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: A 68 TYR cc_start: 0.8312 (t80) cc_final: 0.7993 (t80) REVERT: A 88 LYS cc_start: 0.9118 (mmpt) cc_final: 0.8695 (mmmt) REVERT: A 94 MET cc_start: 0.8324 (mmt) cc_final: 0.7854 (mmt) REVERT: A 306 GLU cc_start: 0.8478 (tp30) cc_final: 0.8135 (tp30) REVERT: A 331 ARG cc_start: 0.8784 (mtm110) cc_final: 0.8298 (mtm110) REVERT: A 333 GLU cc_start: 0.8666 (mp0) cc_final: 0.8360 (mp0) REVERT: A 416 MET cc_start: 0.7860 (tpp) cc_final: 0.7443 (tpp) REVERT: A 522 MET cc_start: 0.8714 (tpp) cc_final: 0.8481 (mtp) REVERT: A 538 MET cc_start: 0.8705 (mmm) cc_final: 0.7971 (mpp) REVERT: B 31 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: B 94 MET cc_start: 0.8215 (mmt) cc_final: 0.7617 (mmt) REVERT: B 240 HIS cc_start: 0.8834 (p-80) cc_final: 0.8497 (p90) REVERT: B 282 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8447 (pp) REVERT: B 331 ARG cc_start: 0.8800 (mtm110) cc_final: 0.8312 (mtm110) REVERT: B 333 GLU cc_start: 0.8696 (mp0) cc_final: 0.8321 (mp0) REVERT: B 522 MET cc_start: 0.8844 (tpp) cc_final: 0.8583 (mtp) REVERT: B 538 MET cc_start: 0.8764 (mmm) cc_final: 0.8008 (mpp) REVERT: B 611 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8370 (mmp) REVERT: C 22 PHE cc_start: 0.6381 (t80) cc_final: 0.5894 (t80) REVERT: C 31 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: C 94 MET cc_start: 0.8280 (mmt) cc_final: 0.7807 (mmt) REVERT: C 240 HIS cc_start: 0.8795 (p-80) cc_final: 0.8461 (p90) REVERT: C 282 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8475 (pp) REVERT: C 331 ARG cc_start: 0.8773 (mtm110) cc_final: 0.8259 (mtm110) REVERT: C 333 GLU cc_start: 0.8761 (mp0) cc_final: 0.8350 (mp0) REVERT: C 522 MET cc_start: 0.8820 (tpp) cc_final: 0.8539 (mtp) REVERT: C 538 MET cc_start: 0.8818 (mmm) cc_final: 0.8031 (mpp) REVERT: C 611 MET cc_start: 0.8897 (mmt) cc_final: 0.8595 (mmm) REVERT: D 31 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: D 88 LYS cc_start: 0.9146 (mmpt) cc_final: 0.8709 (mmmt) REVERT: D 94 MET cc_start: 0.8356 (mmt) cc_final: 0.7780 (mmt) REVERT: D 303 ARG cc_start: 0.7221 (ttt180) cc_final: 0.6458 (ttt180) REVERT: D 331 ARG cc_start: 0.8758 (mtm110) cc_final: 0.8199 (mtm110) REVERT: D 333 GLU cc_start: 0.8789 (mp0) cc_final: 0.8366 (mp0) REVERT: D 522 MET cc_start: 0.8725 (tpp) cc_final: 0.8443 (mtp) REVERT: D 538 MET cc_start: 0.8774 (mmm) cc_final: 0.8039 (mpp) REVERT: E 343 ARG cc_start: 0.8763 (ptp-170) cc_final: 0.8334 (ptt-90) REVERT: G 343 ARG cc_start: 0.8740 (ptp-170) cc_final: 0.8270 (ptt-90) outliers start: 66 outliers final: 52 residues processed: 324 average time/residue: 0.1390 time to fit residues: 69.7027 Evaluate side-chains 311 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 252 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 507 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 481 PHE Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain E residue 325 TRP Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain F residue 325 TRP Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 325 TRP Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 61 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 230 optimal weight: 0.9990 chunk 104 optimal weight: 0.0270 chunk 102 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 154 optimal weight: 0.0870 chunk 215 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.127799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.098895 restraints weight = 41315.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102237 restraints weight = 28988.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103655 restraints weight = 19841.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103648 restraints weight = 16820.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103978 restraints weight = 16995.181| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21740 Z= 0.105 Angle : 0.538 9.369 29458 Z= 0.273 Chirality : 0.041 0.163 3140 Planarity : 0.003 0.038 3792 Dihedral : 4.443 49.719 2882 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.96 % Allowed : 18.43 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.17), residues: 2576 helix: 1.95 (0.15), residues: 1304 sheet: -0.86 (0.26), residues: 320 loop : -1.21 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.014 0.001 TYR C 44 PHE 0.015 0.001 PHE B 505 TRP 0.009 0.001 TRP A 58 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (21740) covalent geometry : angle 0.53784 / 0.27 (29458) hydrogen bonds : bond 0.03134 / 2.11 ( 1068) hydrogen bonds : angle 4.03028 / 2.85 ( 3120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 0.810 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: A 22 PHE cc_start: 0.6491 (t80) cc_final: 0.5999 (t80) REVERT: A 31 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: A 68 TYR cc_start: 0.8321 (t80) cc_final: 0.8028 (t80) REVERT: A 88 LYS cc_start: 0.9155 (mmpt) cc_final: 0.8683 (mmmt) REVERT: A 94 MET cc_start: 0.8092 (mmt) cc_final: 0.7726 (mmt) REVERT: A 306 GLU cc_start: 0.8392 (tp30) cc_final: 0.8133 (tp30) REVERT: A 331 ARG cc_start: 0.8688 (mtm110) cc_final: 0.8164 (mtm110) REVERT: A 333 GLU cc_start: 0.8620 (mp0) cc_final: 0.8340 (mp0) REVERT: A 346 LEU cc_start: 0.8755 (mt) cc_final: 0.8554 (tp) REVERT: A 522 MET cc_start: 0.8665 (tpp) cc_final: 0.8379 (mtp) REVERT: A 538 MET cc_start: 0.8798 (mmm) cc_final: 0.8034 (mpp) REVERT: A 590 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6839 (mt-10) REVERT: B 31 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: B 58 TRP cc_start: 0.8365 (m100) cc_final: 0.8126 (m100) REVERT: B 94 MET cc_start: 0.8067 (mmt) cc_final: 0.7756 (mmt) REVERT: B 240 HIS cc_start: 0.8793 (p-80) cc_final: 0.8351 (p-80) REVERT: B 331 ARG cc_start: 0.8637 (mtm110) cc_final: 0.8134 (mtm110) REVERT: B 333 GLU cc_start: 0.8609 (mp0) cc_final: 0.8313 (mp0) REVERT: B 522 MET cc_start: 0.8848 (tpp) cc_final: 0.8503 (mtp) REVERT: B 538 MET cc_start: 0.8821 (mmm) cc_final: 0.8035 (mpp) REVERT: C 22 PHE cc_start: 0.6324 (t80) cc_final: 0.5860 (t80) REVERT: C 31 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: C 240 HIS cc_start: 0.8785 (p-80) cc_final: 0.8247 (p-80) REVERT: C 282 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8414 (pp) REVERT: C 306 GLU cc_start: 0.8380 (tp30) cc_final: 0.7985 (tp30) REVERT: C 331 ARG cc_start: 0.8608 (mtm110) cc_final: 0.8055 (mtm110) REVERT: C 333 GLU cc_start: 0.8671 (mp0) cc_final: 0.8292 (mp0) REVERT: C 522 MET cc_start: 0.8865 (tpp) cc_final: 0.8483 (mtp) REVERT: C 538 MET cc_start: 0.8874 (mmm) cc_final: 0.8053 (mpp) REVERT: C 611 MET cc_start: 0.8925 (mmt) cc_final: 0.8654 (mmm) REVERT: D 31 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: D 88 LYS cc_start: 0.9161 (mmpt) cc_final: 0.8690 (mmmt) REVERT: D 94 MET cc_start: 0.8132 (mmt) cc_final: 0.7740 (mmt) REVERT: D 303 ARG cc_start: 0.7313 (ttt180) cc_final: 0.6627 (ttt180) REVERT: D 306 GLU cc_start: 0.8296 (tp30) cc_final: 0.7940 (tp30) REVERT: D 331 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8025 (mtm110) REVERT: D 333 GLU cc_start: 0.8726 (mp0) cc_final: 0.8293 (mp0) REVERT: D 522 MET cc_start: 0.8678 (tpp) cc_final: 0.8335 (mtp) REVERT: D 538 MET cc_start: 0.8844 (mmm) cc_final: 0.8086 (mpp) REVERT: D 590 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6868 (mt-10) REVERT: E 343 ARG cc_start: 0.8597 (ptp-170) cc_final: 0.8118 (ptt-90) REVERT: F 343 ARG cc_start: 0.8500 (ptt-90) cc_final: 0.8267 (ptp90) REVERT: G 343 ARG cc_start: 0.8715 (ptp-170) cc_final: 0.8197 (ptt-90) outliers start: 44 outliers final: 31 residues processed: 323 average time/residue: 0.1431 time to fit residues: 71.8952 Evaluate side-chains 306 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 115 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.0040 chunk 184 optimal weight: 4.9990 chunk 231 optimal weight: 0.0470 chunk 153 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS B 178 HIS C 178 HIS D 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.128776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099670 restraints weight = 41108.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103237 restraints weight = 28528.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.105226 restraints weight = 19226.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105208 restraints weight = 15369.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105600 restraints weight = 15816.125| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21740 Z= 0.100 Angle : 0.546 9.445 29458 Z= 0.273 Chirality : 0.041 0.158 3140 Planarity : 0.003 0.037 3792 Dihedral : 4.372 53.952 2882 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.74 % Allowed : 19.06 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2576 helix: 2.05 (0.15), residues: 1298 sheet: -0.59 (0.27), residues: 320 loop : -1.14 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 303 TYR 0.015 0.001 TYR C 44 PHE 0.019 0.001 PHE B 505 TRP 0.015 0.001 TRP D 58 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (21740) covalent geometry : angle 0.54571 / 0.27 (29458) hydrogen bonds : bond 0.02994 / 2.01 ( 1068) hydrogen bonds : angle 3.96004 / 2.80 ( 3120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 292 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6390 (t80) cc_final: 0.5797 (t80) REVERT: A 31 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: A 68 TYR cc_start: 0.8318 (t80) cc_final: 0.8048 (t80) REVERT: A 88 LYS cc_start: 0.9174 (mmpt) cc_final: 0.8699 (mmmt) REVERT: A 94 MET cc_start: 0.8214 (mmt) cc_final: 0.7829 (mmt) REVERT: A 303 ARG cc_start: 0.6846 (ttt180) cc_final: 0.6525 (ttt180) REVERT: A 331 ARG cc_start: 0.8647 (mtm110) cc_final: 0.8107 (mtm110) REVERT: A 333 GLU cc_start: 0.8599 (mp0) cc_final: 0.8249 (mp0) REVERT: A 522 MET cc_start: 0.8646 (tpp) cc_final: 0.8381 (mtp) REVERT: A 590 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6860 (mt-10) REVERT: B 31 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: B 94 MET cc_start: 0.8129 (mmt) cc_final: 0.7491 (mmt) REVERT: B 240 HIS cc_start: 0.8772 (p-80) cc_final: 0.8396 (p-80) REVERT: B 282 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8474 (pp) REVERT: B 303 ARG cc_start: 0.6866 (ttt180) cc_final: 0.6495 (ttt180) REVERT: B 331 ARG cc_start: 0.8604 (mtm110) cc_final: 0.8078 (mtm110) REVERT: B 333 GLU cc_start: 0.8621 (mp0) cc_final: 0.8248 (mp0) REVERT: B 522 MET cc_start: 0.8814 (tpp) cc_final: 0.8525 (mtp) REVERT: C 22 PHE cc_start: 0.6341 (t80) cc_final: 0.5811 (t80) REVERT: C 31 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: C 240 HIS cc_start: 0.8778 (p-80) cc_final: 0.8321 (p-80) REVERT: C 282 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8396 (pp) REVERT: C 331 ARG cc_start: 0.8560 (mtm110) cc_final: 0.7991 (mtm110) REVERT: C 333 GLU cc_start: 0.8601 (mp0) cc_final: 0.8217 (mp0) REVERT: C 522 MET cc_start: 0.8850 (tpp) cc_final: 0.8521 (mtp) REVERT: C 538 MET cc_start: 0.8855 (mmm) cc_final: 0.8006 (mpp) REVERT: C 611 MET cc_start: 0.8936 (mmt) cc_final: 0.8703 (mmp) REVERT: D 31 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: D 88 LYS cc_start: 0.9133 (mmpt) cc_final: 0.8624 (mmmt) REVERT: D 94 MET cc_start: 0.8175 (mmt) cc_final: 0.7801 (mmt) REVERT: D 303 ARG cc_start: 0.7228 (ttt180) cc_final: 0.6666 (ttt180) REVERT: D 306 GLU cc_start: 0.8272 (tp30) cc_final: 0.8068 (tp30) REVERT: D 331 ARG cc_start: 0.8570 (mtm110) cc_final: 0.7968 (mtm110) REVERT: D 333 GLU cc_start: 0.8685 (mp0) cc_final: 0.8146 (mp0) REVERT: D 522 MET cc_start: 0.8665 (tpp) cc_final: 0.8368 (mtp) REVERT: D 590 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6841 (mt-10) REVERT: E 343 ARG cc_start: 0.8603 (ptp-170) cc_final: 0.8083 (ptt-90) REVERT: F 343 ARG cc_start: 0.8488 (ptt-90) cc_final: 0.8230 (ptp90) REVERT: G 343 ARG cc_start: 0.8629 (ptp-170) cc_final: 0.8077 (ptt-90) REVERT: H 343 ARG cc_start: 0.8442 (ptt-90) cc_final: 0.8044 (ptp90) outliers start: 39 outliers final: 26 residues processed: 321 average time/residue: 0.1436 time to fit residues: 71.0532 Evaluate side-chains 299 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain H residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 97 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 184 optimal weight: 7.9990 chunk 93 optimal weight: 0.0970 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.128358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098572 restraints weight = 42126.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.101094 restraints weight = 30344.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.102456 restraints weight = 22134.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102638 restraints weight = 19325.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.102863 restraints weight = 18537.606| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21740 Z= 0.111 Angle : 0.565 9.627 29458 Z= 0.282 Chirality : 0.041 0.153 3140 Planarity : 0.003 0.060 3792 Dihedral : 4.437 57.900 2882 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.60 % Allowed : 19.63 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2576 helix: 2.01 (0.15), residues: 1302 sheet: -0.49 (0.27), residues: 320 loop : -1.12 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 303 TYR 0.020 0.001 TYR D 62 PHE 0.035 0.001 PHE C 220 TRP 0.011 0.001 TRP B 182 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (21740) covalent geometry : angle 0.56468 / 0.28 (29458) hydrogen bonds : bond 0.03047 / 2.04 ( 1068) hydrogen bonds : angle 3.97958 / 2.81 ( 3120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6391 (t80) cc_final: 0.5923 (t80) REVERT: A 31 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: A 68 TYR cc_start: 0.8297 (t80) cc_final: 0.8074 (t80) REVERT: A 88 LYS cc_start: 0.9178 (mmpt) cc_final: 0.8573 (mmmt) REVERT: A 94 MET cc_start: 0.8238 (mmt) cc_final: 0.7836 (mmt) REVERT: A 143 TRP cc_start: 0.8244 (p90) cc_final: 0.7887 (p90) REVERT: A 303 ARG cc_start: 0.6885 (ttt180) cc_final: 0.6345 (ttt180) REVERT: A 306 GLU cc_start: 0.8436 (tp30) cc_final: 0.7920 (mm-30) REVERT: A 331 ARG cc_start: 0.8692 (mtm110) cc_final: 0.8101 (mtm110) REVERT: A 333 GLU cc_start: 0.8606 (mp0) cc_final: 0.8213 (mp0) REVERT: A 522 MET cc_start: 0.8676 (tpp) cc_final: 0.8435 (mtp) REVERT: A 590 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6936 (mt-10) REVERT: A 627 GLU cc_start: 0.8285 (pt0) cc_final: 0.7859 (mp0) REVERT: B 31 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: B 94 MET cc_start: 0.8184 (mmt) cc_final: 0.7711 (mmt) REVERT: B 240 HIS cc_start: 0.8760 (p-80) cc_final: 0.8327 (p-80) REVERT: B 265 GLU cc_start: 0.7799 (pt0) cc_final: 0.7567 (pt0) REVERT: B 282 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8378 (pp) REVERT: B 303 ARG cc_start: 0.6914 (ttt180) cc_final: 0.6582 (ttt180) REVERT: B 331 ARG cc_start: 0.8651 (mtm110) cc_final: 0.8091 (mtm110) REVERT: B 333 GLU cc_start: 0.8566 (mp0) cc_final: 0.8169 (mp0) REVERT: B 522 MET cc_start: 0.8817 (tpp) cc_final: 0.8556 (mtp) REVERT: C 22 PHE cc_start: 0.6298 (t80) cc_final: 0.5770 (t80) REVERT: C 31 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: C 240 HIS cc_start: 0.8800 (p-80) cc_final: 0.8302 (p-80) REVERT: C 282 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8278 (pp) REVERT: C 331 ARG cc_start: 0.8629 (mtm110) cc_final: 0.8056 (mtm110) REVERT: C 333 GLU cc_start: 0.8579 (mp0) cc_final: 0.8173 (mp0) REVERT: C 522 MET cc_start: 0.8825 (tpp) cc_final: 0.8546 (mtp) REVERT: C 538 MET cc_start: 0.8829 (mmm) cc_final: 0.8037 (mpp) REVERT: C 611 MET cc_start: 0.8943 (mmt) cc_final: 0.8698 (mmp) REVERT: D 31 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: D 88 LYS cc_start: 0.9139 (mmpt) cc_final: 0.8623 (mmmt) REVERT: D 94 MET cc_start: 0.8204 (mmt) cc_final: 0.7775 (mmt) REVERT: D 143 TRP cc_start: 0.8406 (p90) cc_final: 0.8188 (p90) REVERT: D 303 ARG cc_start: 0.7329 (ttt180) cc_final: 0.7108 (ttt180) REVERT: D 306 GLU cc_start: 0.8292 (tp30) cc_final: 0.8066 (tp30) REVERT: D 331 ARG cc_start: 0.8627 (mtm110) cc_final: 0.8000 (mtm110) REVERT: D 333 GLU cc_start: 0.8617 (mp0) cc_final: 0.8150 (mp0) REVERT: D 522 MET cc_start: 0.8706 (tpp) cc_final: 0.8413 (mtp) REVERT: D 590 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6880 (mt-10) REVERT: E 343 ARG cc_start: 0.8621 (ptp-170) cc_final: 0.8063 (ptt-90) REVERT: F 343 ARG cc_start: 0.8532 (ptt-90) cc_final: 0.8262 (ptp90) REVERT: G 343 ARG cc_start: 0.8636 (ptp-170) cc_final: 0.8038 (ptt-90) REVERT: H 343 ARG cc_start: 0.8500 (ptt-90) cc_final: 0.8134 (ptp90) outliers start: 36 outliers final: 26 residues processed: 303 average time/residue: 0.1406 time to fit residues: 65.5559 Evaluate side-chains 295 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 565 SER Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 565 SER Chi-restraints excluded: chain D residue 623 TYR Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain H residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 134 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 31 optimal weight: 0.4980 chunk 254 optimal weight: 10.0000 chunk 132 optimal weight: 0.0570 chunk 19 optimal weight: 0.0980 chunk 124 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.129324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.100725 restraints weight = 42110.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102719 restraints weight = 29678.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.103348 restraints weight = 23466.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103735 restraints weight = 20673.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104039 restraints weight = 20415.936| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21740 Z= 0.103 Angle : 0.562 9.396 29458 Z= 0.280 Chirality : 0.041 0.218 3140 Planarity : 0.003 0.043 3792 Dihedral : 4.440 58.793 2882 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.38 % Allowed : 20.39 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.17), residues: 2576 helix: 2.03 (0.15), residues: 1300 sheet: -0.32 (0.27), residues: 314 loop : -1.09 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 303 TYR 0.017 0.001 TYR D 62 PHE 0.036 0.001 PHE C 220 TRP 0.015 0.001 TRP B 58 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (21740) covalent geometry : angle 0.56153 / 0.28 (29458) hydrogen bonds : bond 0.02998 / 1.99 ( 1068) hydrogen bonds : angle 3.96442 / 2.79 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2881.64 seconds wall clock time: 51 minutes 1.48 seconds (3061.48 seconds total)