Starting phenix.real_space_refine on Thu Mar 5 09:53:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q0s_13751/03_2026/7q0s_13751.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q0s_13751/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7q0s_13751/03_2026/7q0s_13751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q0s_13751/03_2026/7q0s_13751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q0s_13751/03_2026/7q0s_13751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q0s_13751/03_2026/7q0s_13751.map" } 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-5986/lib/python3.9/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: 4.77, per 1000 atoms: 0.23 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: 1.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.71 Time building geometry restraints manager: 2.17 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 - 28.68: 12231 28.68 - 57.37: 502 57.37 - 86.05: 59 86.05 - 114.73: 40 114.73 - 143.41: 20 Dihedral angle restraints: 12852 sinusoidal: 5252 harmonic: 7600 Sorted by residual: dihedral pdb=" C3 G6P C 801 " pdb=" C1 G6P C 801 " pdb=" C2 G6P C 801 " pdb=" O1 G6P C 801 " ideal model delta sinusoidal sigma weight residual 74.65 -68.76 143.41 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3 G6P B 801 " pdb=" C1 G6P B 801 " pdb=" C2 G6P B 801 " pdb=" O1 G6P B 801 " ideal model delta sinusoidal sigma weight residual 74.65 -68.76 143.41 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3 G6P D 801 " pdb=" C1 G6P D 801 " pdb=" C2 G6P D 801 " pdb=" O1 G6P D 801 " ideal model delta sinusoidal sigma weight residual 74.65 -68.74 143.39 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 12849 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: 0.02 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.290 Find NCS groups from input model: 0.130 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 18.143 143.415 7956 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 covalent geometry : bond 0.00346 (21740) covalent geometry : angle 0.63408 (29458) hydrogen bonds : bond 0.14488 ( 1068) hydrogen bonds : angle 6.00035 ( 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 : 0.766 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: 0.1366 time to fit residues: 77.2088 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 : 0.729 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 240 HIS A 610 HIS B 76 GLN B 240 HIS B 610 HIS C 76 GLN C 240 HIS C 610 HIS D 240 HIS D 610 HIS E 340 ASN F 340 ASN G 340 ASN H 340 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102976 restraints weight = 40859.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105553 restraints weight = 27962.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.107405 restraints weight = 21794.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108663 restraints weight = 18373.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109533 restraints weight = 16370.548| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1667 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= 0.116 Angle : 0.562 8.151 29458 Z= 0.284 Chirality : 0.042 0.165 3140 Planarity : 0.003 0.041 3792 Dihedral : 5.337 67.783 2982 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.25 % Allowed : 8.10 % Favored : 90.65 % 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: 1.10 (0.17), residues: 2576 helix: 1.98 (0.15), residues: 1312 sheet: -0.21 (0.30), residues: 290 loop : -0.70 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 303 TYR 0.017 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 B 610 Details of bonding type rmsd covalent geometry : bond 0.00257 (21740) covalent geometry : angle 0.56220 (29458) hydrogen bonds : bond 0.03233 ( 1068) hydrogen bonds : angle 4.26576 ( 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 348 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 320 time to evaluate : 0.842 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: 0.8176 (t80) cc_final: 0.7912 (t80) REVERT: A 94 MET cc_start: 0.7895 (mmp) cc_final: 0.6882 (mmm) REVERT: A 522 MET cc_start: 0.8498 (tpp) cc_final: 0.7912 (mtp) REVERT: A 538 MET cc_start: 0.9061 (mmm) cc_final: 0.8300 (mpp) REVERT: B 88 LYS cc_start: 0.8922 (mmpt) cc_final: 0.8411 (mmmt) REVERT: B 94 MET cc_start: 0.7934 (mmp) cc_final: 0.7617 (mmt) REVERT: B 303 ARG cc_start: 0.6828 (ttt180) cc_final: 0.6493 (ttt180) REVERT: B 505 PHE cc_start: 0.8173 (m-80) cc_final: 0.7778 (m-80) REVERT: B 522 MET cc_start: 0.8469 (tpp) cc_final: 0.7965 (mtp) REVERT: C 22 PHE cc_start: 0.6065 (t80) cc_final: 0.5742 (t80) REVERT: C 88 LYS cc_start: 0.8928 (mmpt) cc_final: 0.8347 (mmmt) REVERT: C 94 MET cc_start: 0.7911 (mmp) cc_final: 0.7612 (mmt) REVERT: C 333 GLU cc_start: 0.8716 (mp0) cc_final: 0.8397 (mp0) REVERT: C 505 PHE cc_start: 0.8140 (m-80) cc_final: 0.7765 (m-80) REVERT: C 522 MET cc_start: 0.8561 (tpp) cc_final: 0.8025 (mtp) REVERT: C 611 MET cc_start: 0.8836 (mmt) cc_final: 0.8493 (mmp) REVERT: D 35 GLU cc_start: 0.7195 (pt0) cc_final: 0.6972 (pt0) REVERT: D 68 TYR cc_start: 0.8167 (t80) cc_final: 0.7963 (t80) REVERT: D 88 LYS cc_start: 0.8940 (mmpt) cc_final: 0.8339 (mmmt) REVERT: D 94 MET cc_start: 0.7906 (mmp) cc_final: 0.6913 (mmm) REVERT: D 333 GLU cc_start: 0.8726 (mp0) cc_final: 0.8465 (mp0) REVERT: D 522 MET cc_start: 0.8515 (tpp) cc_final: 0.7940 (mtp) REVERT: E 333 MET cc_start: 0.9036 (mmm) cc_final: 0.8287 (pmm) REVERT: F 347 THR cc_start: 0.9083 (p) cc_final: 0.8805 (t) REVERT: G 333 MET cc_start: 0.9027 (mmm) cc_final: 0.8245 (pmm) REVERT: H 343 ARG cc_start: 0.8249 (ptp-170) cc_final: 0.8023 (ptt-90) outliers start: 28 outliers final: 17 residues processed: 333 average time/residue: 0.1462 time to fit residues: 76.0374 Evaluate side-chains 277 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 260 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP 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 166 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 350 ASN 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: 1.9990 chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 138 ASN ** 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 138 ASN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN D 138 ASN ** D 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN G 340 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.127932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.098887 restraints weight = 41301.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101291 restraints weight = 28149.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102932 restraints weight = 21913.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103941 restraints weight = 18566.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104799 restraints weight = 16654.500| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21740 Z= 0.166 Angle : 0.566 8.656 29458 Z= 0.290 Chirality : 0.043 0.153 3140 Planarity : 0.004 0.042 3792 Dihedral : 5.334 59.300 2970 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.54 % Allowed : 11.71 % Favored : 85.75 % 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: 0.78 (0.17), residues: 2576 helix: 1.83 (0.15), residues: 1316 sheet: -0.34 (0.27), residues: 312 loop : -1.07 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 303 TYR 0.018 0.001 TYR A 493 PHE 0.013 0.001 PHE D 433 TRP 0.013 0.001 TRP C 182 HIS 0.006 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00376 (21740) covalent geometry : angle 0.56646 (29458) hydrogen bonds : bond 0.03468 ( 1068) hydrogen bonds : angle 4.32073 ( 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 368 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 311 time to evaluate : 0.814 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: 0.8654 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: A 68 TYR cc_start: 0.8176 (t80) cc_final: 0.7948 (t80) REVERT: A 94 MET cc_start: 0.7990 (mmt) cc_final: 0.7621 (mmt) REVERT: A 240 HIS cc_start: 0.8606 (p-80) cc_final: 0.8372 (p90) REVERT: A 306 GLU cc_start: 0.8395 (tp30) cc_final: 0.8167 (tp30) REVERT: A 346 LEU cc_start: 0.8761 (mt) cc_final: 0.8460 (tp) REVERT: A 522 MET cc_start: 0.8584 (tpp) cc_final: 0.8157 (mtp) REVERT: B 31 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: B 88 LYS cc_start: 0.8974 (mmpt) cc_final: 0.8531 (mmmt) REVERT: B 94 MET cc_start: 0.8009 (mmt) cc_final: 0.7559 (mmt) REVERT: B 240 HIS cc_start: 0.8662 (p-80) cc_final: 0.8430 (p90) REVERT: B 522 MET cc_start: 0.8546 (tpp) cc_final: 0.8139 (mtp) REVERT: C 31 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: C 35 GLU cc_start: 0.7205 (pt0) cc_final: 0.6987 (pt0) REVERT: C 94 MET cc_start: 0.8006 (mmt) cc_final: 0.7606 (mmt) REVERT: C 240 HIS cc_start: 0.8611 (p-80) cc_final: 0.8393 (p90) REVERT: C 522 MET cc_start: 0.8682 (tpp) cc_final: 0.8150 (mtp) REVERT: C 538 MET cc_start: 0.8446 (mmm) cc_final: 0.8130 (mpp) REVERT: D 22 PHE cc_start: 0.6112 (t80) cc_final: 0.5893 (t80) REVERT: D 31 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: D 88 LYS cc_start: 0.8985 (mmpt) cc_final: 0.8705 (mmmt) REVERT: D 94 MET cc_start: 0.7979 (mmt) cc_final: 0.7578 (mmt) REVERT: D 240 HIS cc_start: 0.8618 (p-80) cc_final: 0.8383 (p90) REVERT: D 306 GLU cc_start: 0.8380 (tp30) cc_final: 0.8138 (tp30) REVERT: D 346 LEU cc_start: 0.8788 (mt) cc_final: 0.8564 (tp) REVERT: D 522 MET cc_start: 0.8585 (tpp) cc_final: 0.8149 (mtp) REVERT: F 333 MET cc_start: 0.8873 (mmt) cc_final: 0.8072 (pmm) REVERT: H 333 MET cc_start: 0.8845 (mmt) cc_final: 0.8093 (pmm) outliers start: 57 outliers final: 41 residues processed: 338 average time/residue: 0.1344 time to fit residues: 72.9099 Evaluate side-chains 313 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 186 VAL 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 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 262 THR 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 613 LEU Chi-restraints excluded: chain C residue 31 GLU 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 507 SER Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 186 VAL 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 409 LEU 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 326 GLU Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain F residue 326 GLU Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 332 TYR 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 347 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 161 optimal weight: 0.9990 chunk 190 optimal weight: 0.5980 chunk 51 optimal weight: 0.0670 chunk 125 optimal weight: 0.3980 chunk 168 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN C 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.131087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.100767 restraints weight = 41128.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104013 restraints weight = 29236.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.105785 restraints weight = 20502.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105872 restraints weight = 18101.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.105993 restraints weight = 17185.086| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21740 Z= 0.102 Angle : 0.508 9.387 29458 Z= 0.261 Chirality : 0.040 0.146 3140 Planarity : 0.003 0.037 3792 Dihedral : 4.870 53.458 2970 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.05 % Allowed : 13.98 % Favored : 83.97 % 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: 1.04 (0.17), residues: 2576 helix: 2.06 (0.15), residues: 1312 sheet: -0.39 (0.28), residues: 292 loop : -0.88 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 303 TYR 0.012 0.001 TYR A 144 PHE 0.017 0.001 PHE C 505 TRP 0.011 0.001 TRP C 182 HIS 0.002 0.001 HIS B 610 Details of bonding type rmsd covalent geometry : bond 0.00227 (21740) covalent geometry : angle 0.50829 (29458) hydrogen bonds : bond 0.02949 ( 1068) hydrogen bonds : angle 4.00106 ( 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 353 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 307 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: A 68 TYR cc_start: 0.8177 (t80) cc_final: 0.7963 (t80) REVERT: A 88 LYS cc_start: 0.9111 (mmpt) cc_final: 0.8789 (mmmt) REVERT: A 94 MET cc_start: 0.8126 (mmt) cc_final: 0.7750 (mmt) REVERT: A 240 HIS cc_start: 0.8819 (p-80) cc_final: 0.8517 (p90) REVERT: A 303 ARG cc_start: 0.7061 (ttt180) cc_final: 0.6734 (ttt180) REVERT: A 306 GLU cc_start: 0.8299 (tp30) cc_final: 0.8082 (tp30) REVERT: A 346 LEU cc_start: 0.8785 (mt) cc_final: 0.8559 (tp) REVERT: A 522 MET cc_start: 0.8657 (tpp) cc_final: 0.8218 (mtp) REVERT: B 31 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: B 94 MET cc_start: 0.8055 (mmt) cc_final: 0.7614 (mmt) REVERT: B 240 HIS cc_start: 0.8873 (p-80) cc_final: 0.8566 (p90) REVERT: B 306 GLU cc_start: 0.8374 (tp30) cc_final: 0.8081 (tp30) REVERT: B 522 MET cc_start: 0.8640 (tpp) cc_final: 0.8252 (mtp) REVERT: B 538 MET cc_start: 0.8773 (mmm) cc_final: 0.8032 (mpp) REVERT: C 22 PHE cc_start: 0.6107 (t80) cc_final: 0.5623 (t80) REVERT: C 31 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: C 94 MET cc_start: 0.8125 (mmt) cc_final: 0.7731 (mmt) REVERT: C 240 HIS cc_start: 0.8840 (p-80) cc_final: 0.8547 (p90) REVERT: C 303 ARG cc_start: 0.7051 (ttt180) cc_final: 0.6466 (ttt180) REVERT: C 306 GLU cc_start: 0.8341 (tp30) cc_final: 0.8120 (tp30) REVERT: C 522 MET cc_start: 0.8680 (tpp) cc_final: 0.8229 (mtp) REVERT: C 538 MET cc_start: 0.8642 (mmm) cc_final: 0.8197 (mpp) REVERT: D 22 PHE cc_start: 0.6201 (t80) cc_final: 0.5762 (t80) REVERT: D 31 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: D 88 LYS cc_start: 0.9104 (mmpt) cc_final: 0.8759 (mmmt) REVERT: D 94 MET cc_start: 0.8118 (mmt) cc_final: 0.7743 (mmt) REVERT: D 240 HIS cc_start: 0.8842 (p-80) cc_final: 0.8527 (p90) REVERT: D 303 ARG cc_start: 0.7065 (ttt180) cc_final: 0.6702 (ttt180) REVERT: D 306 GLU cc_start: 0.8303 (tp30) cc_final: 0.8069 (tp30) REVERT: D 522 MET cc_start: 0.8633 (tpp) cc_final: 0.8166 (mtp) REVERT: F 333 MET cc_start: 0.9208 (mmt) cc_final: 0.8459 (pmm) REVERT: G 333 MET cc_start: 0.9262 (mmm) cc_final: 0.8491 (pmm) REVERT: H 326 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6763 (mm-30) REVERT: H 333 MET cc_start: 0.9161 (mmt) cc_final: 0.8467 (pmm) outliers start: 46 outliers final: 30 residues processed: 327 average time/residue: 0.1402 time to fit residues: 71.7286 Evaluate side-chains 304 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 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 188 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 C residue 31 GLU 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 642 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 350 ASN Chi-restraints excluded: chain D residue 409 LEU 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 326 GLU 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 326 GLU Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain G residue 345 LEU 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: 4.9990 chunk 107 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 207 optimal weight: 0.0670 chunk 8 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 101 optimal weight: 0.0870 chunk 23 optimal weight: 6.9990 overall best weight: 3.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.121839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.094614 restraints weight = 42076.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.095969 restraints weight = 30485.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.096831 restraints weight = 24248.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097254 restraints weight = 21234.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097773 restraints weight = 20074.600| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 21740 Z= 0.304 Angle : 0.700 9.476 29458 Z= 0.363 Chirality : 0.047 0.163 3140 Planarity : 0.005 0.037 3792 Dihedral : 5.634 58.700 2970 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.16 % Allowed : 14.87 % Favored : 81.97 % 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: -0.02 (0.16), residues: 2576 helix: 1.32 (0.14), residues: 1312 sheet: -0.94 (0.26), residues: 316 loop : -1.59 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 303 TYR 0.011 0.002 TYR C 605 PHE 0.022 0.002 PHE C 375 TRP 0.016 0.002 TRP C 182 HIS 0.011 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00685 (21740) covalent geometry : angle 0.70034 (29458) hydrogen bonds : bond 0.04386 ( 1068) hydrogen bonds : angle 4.66318 ( 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 355 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 284 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: A 68 TYR cc_start: 0.8271 (t80) cc_final: 0.8027 (t80) REVERT: A 94 MET cc_start: 0.8321 (mmt) cc_final: 0.7833 (mmt) REVERT: A 303 ARG cc_start: 0.6898 (ttt180) cc_final: 0.6499 (ttt180) REVERT: A 416 MET cc_start: 0.7918 (tpp) cc_final: 0.7608 (tpp) REVERT: A 522 MET cc_start: 0.8678 (tpp) cc_final: 0.8420 (mtp) REVERT: A 538 MET cc_start: 0.8699 (mmm) cc_final: 0.7985 (mpp) REVERT: B 31 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: B 94 MET cc_start: 0.8188 (mmt) cc_final: 0.7640 (mmt) REVERT: B 306 GLU cc_start: 0.8558 (tp30) cc_final: 0.8186 (tp30) REVERT: B 333 GLU cc_start: 0.8726 (mp0) cc_final: 0.8364 (mp0) REVERT: B 416 MET cc_start: 0.7837 (tpp) cc_final: 0.7461 (tpp) REVERT: B 522 MET cc_start: 0.8676 (tpp) cc_final: 0.8388 (mtp) REVERT: B 538 MET cc_start: 0.8703 (mmm) cc_final: 0.7952 (mpp) REVERT: C 22 PHE cc_start: 0.6380 (t80) cc_final: 0.5836 (t80) REVERT: C 31 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: C 94 MET cc_start: 0.8288 (mmt) cc_final: 0.7773 (mmt) REVERT: C 303 ARG cc_start: 0.6940 (ttt180) cc_final: 0.6550 (ttt180) REVERT: C 306 GLU cc_start: 0.8512 (tp30) cc_final: 0.8165 (tp30) REVERT: C 522 MET cc_start: 0.8656 (tpp) cc_final: 0.8396 (mtp) REVERT: D 31 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: D 88 LYS cc_start: 0.9076 (mmpt) cc_final: 0.8695 (mmmt) REVERT: D 94 MET cc_start: 0.8307 (mmt) cc_final: 0.7822 (mmt) REVERT: D 303 ARG cc_start: 0.6950 (ttt180) cc_final: 0.6555 (ttt180) REVERT: D 333 GLU cc_start: 0.8727 (mp0) cc_final: 0.8379 (mp0) REVERT: D 522 MET cc_start: 0.8676 (tpp) cc_final: 0.8407 (mtp) outliers start: 71 outliers final: 50 residues processed: 320 average time/residue: 0.1411 time to fit residues: 70.9980 Evaluate side-chains 310 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 188 LEU 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 507 SER Chi-restraints excluded: chain B residue 515 THR 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 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 507 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 31 GLU 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 409 LEU 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 326 GLU 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 332 TYR 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 326 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 238 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3787 r_free = 0.3787 target = 0.127215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.098775 restraints weight = 41350.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101362 restraints weight = 29223.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102805 restraints weight = 20668.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102971 restraints weight = 17722.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103218 restraints weight = 16911.862| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21740 Z= 0.112 Angle : 0.533 9.408 29458 Z= 0.272 Chirality : 0.041 0.157 3140 Planarity : 0.003 0.035 3792 Dihedral : 5.123 57.668 2970 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.58 % Allowed : 16.34 % Favored : 81.08 % 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: 0.62 (0.17), residues: 2576 helix: 1.92 (0.15), residues: 1308 sheet: -0.73 (0.25), residues: 322 loop : -1.34 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 303 TYR 0.013 0.001 TYR D 44 PHE 0.016 0.001 PHE B 505 TRP 0.009 0.001 TRP C 182 HIS 0.010 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00253 (21740) covalent geometry : angle 0.53282 (29458) hydrogen bonds : bond 0.03217 ( 1068) hydrogen bonds : angle 4.07144 ( 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 357 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 299 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: A 88 LYS cc_start: 0.9127 (mmpt) cc_final: 0.8698 (mmmt) REVERT: A 94 MET cc_start: 0.8053 (mmt) cc_final: 0.7622 (mmt) REVERT: A 240 HIS cc_start: 0.8742 (p-80) cc_final: 0.8425 (p90) REVERT: A 303 ARG cc_start: 0.7030 (ttt180) cc_final: 0.6650 (ttt180) REVERT: A 346 LEU cc_start: 0.8761 (mt) cc_final: 0.8545 (tp) REVERT: A 416 MET cc_start: 0.7719 (tpp) cc_final: 0.7338 (tpp) REVERT: A 437 ARG cc_start: 0.7461 (ttp-170) cc_final: 0.7222 (ttp-170) REVERT: A 522 MET cc_start: 0.8671 (tpp) cc_final: 0.8229 (mtp) REVERT: A 538 MET cc_start: 0.8778 (mmm) cc_final: 0.8053 (mpp) REVERT: B 94 MET cc_start: 0.8024 (mmt) cc_final: 0.7677 (mmt) REVERT: B 306 GLU cc_start: 0.8503 (tp30) cc_final: 0.8179 (tp30) REVERT: B 331 ARG cc_start: 0.8660 (mtm110) cc_final: 0.8259 (mtm110) REVERT: B 333 GLU cc_start: 0.8730 (mp0) cc_final: 0.8261 (mp0) REVERT: B 346 LEU cc_start: 0.8807 (mt) cc_final: 0.8575 (tp) REVERT: B 522 MET cc_start: 0.8672 (tpp) cc_final: 0.8304 (mtp) REVERT: B 538 MET cc_start: 0.8762 (mmm) cc_final: 0.8019 (mpp) REVERT: C 22 PHE cc_start: 0.6273 (t80) cc_final: 0.5757 (t80) REVERT: C 31 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: C 94 MET cc_start: 0.7997 (mmt) cc_final: 0.7638 (mmt) REVERT: C 240 HIS cc_start: 0.8732 (p-80) cc_final: 0.8384 (p90) REVERT: C 303 ARG cc_start: 0.6989 (ttt180) cc_final: 0.6464 (ttt180) REVERT: C 306 GLU cc_start: 0.8470 (tp30) cc_final: 0.8182 (tp30) REVERT: C 522 MET cc_start: 0.8641 (tpp) cc_final: 0.8232 (mtp) REVERT: C 538 MET cc_start: 0.8861 (mmm) cc_final: 0.8169 (mpp) REVERT: D 31 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: D 88 LYS cc_start: 0.9099 (mmpt) cc_final: 0.8649 (mmmt) REVERT: D 94 MET cc_start: 0.8035 (mmt) cc_final: 0.7607 (mmt) REVERT: D 240 HIS cc_start: 0.8701 (p-80) cc_final: 0.8350 (p90) REVERT: D 522 MET cc_start: 0.8656 (tpp) cc_final: 0.8216 (mtp) REVERT: D 538 MET cc_start: 0.8827 (mmm) cc_final: 0.8046 (mpp) REVERT: F 333 MET cc_start: 0.9250 (mmm) cc_final: 0.8210 (pmm) REVERT: H 333 MET cc_start: 0.9238 (mmm) cc_final: 0.8251 (pmm) outliers start: 58 outliers final: 42 residues processed: 330 average time/residue: 0.1442 time to fit residues: 74.2830 Evaluate side-chains 311 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU 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 611 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 188 LEU 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 507 SER Chi-restraints excluded: chain B residue 515 THR 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 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 507 SER Chi-restraints excluded: chain C residue 515 THR 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 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 326 GLU 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 G residue 325 TRP Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 180 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 75 optimal weight: 0.2980 chunk 235 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3756 r_free = 0.3756 target = 0.125054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097949 restraints weight = 41618.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099264 restraints weight = 28921.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099550 restraints weight = 24468.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.100215 restraints weight = 21212.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100452 restraints weight = 19358.926| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21740 Z= 0.169 Angle : 0.582 9.517 29458 Z= 0.295 Chirality : 0.043 0.168 3140 Planarity : 0.004 0.052 3792 Dihedral : 5.159 59.655 2970 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.72 % Allowed : 17.36 % Favored : 79.92 % 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: 0.47 (0.17), residues: 2576 helix: 1.75 (0.15), residues: 1318 sheet: -0.82 (0.26), residues: 312 loop : -1.38 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 303 TYR 0.013 0.001 TYR A 68 PHE 0.019 0.001 PHE C 505 TRP 0.014 0.001 TRP C 182 HIS 0.009 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00387 (21740) covalent geometry : angle 0.58221 (29458) hydrogen bonds : bond 0.03506 ( 1068) hydrogen bonds : angle 4.20802 ( 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 337 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 0.750 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 31 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: A 88 LYS cc_start: 0.9126 (mmpt) cc_final: 0.8670 (mmmt) REVERT: A 94 MET cc_start: 0.8236 (mmt) cc_final: 0.7778 (mmt) REVERT: A 416 MET cc_start: 0.7714 (tpp) cc_final: 0.7361 (tpp) REVERT: A 522 MET cc_start: 0.8726 (tpp) cc_final: 0.8389 (mtp) REVERT: A 538 MET cc_start: 0.8742 (mmm) cc_final: 0.8031 (mpp) REVERT: B 31 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: B 94 MET cc_start: 0.8036 (mmt) cc_final: 0.7549 (mmt) REVERT: B 331 ARG cc_start: 0.8700 (mtm110) cc_final: 0.8146 (mtm110) REVERT: B 333 GLU cc_start: 0.8737 (mp0) cc_final: 0.8245 (mp0) REVERT: B 522 MET cc_start: 0.8690 (tpp) cc_final: 0.8382 (mtp) REVERT: B 538 MET cc_start: 0.8771 (mmm) cc_final: 0.8029 (mpp) REVERT: C 22 PHE cc_start: 0.6437 (t80) cc_final: 0.5910 (t80) REVERT: C 31 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: C 94 MET cc_start: 0.8205 (mmt) cc_final: 0.7743 (mmt) REVERT: C 240 HIS cc_start: 0.8750 (p-80) cc_final: 0.8408 (p90) REVERT: C 306 GLU cc_start: 0.8509 (tp30) cc_final: 0.8208 (tp30) REVERT: C 522 MET cc_start: 0.8689 (tpp) cc_final: 0.8346 (mtp) REVERT: C 538 MET cc_start: 0.8794 (mmm) cc_final: 0.8065 (mpp) REVERT: D 31 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: D 88 LYS cc_start: 0.9130 (mmpt) cc_final: 0.8673 (mmmt) REVERT: D 94 MET cc_start: 0.8225 (mmt) cc_final: 0.7778 (mmt) REVERT: D 240 HIS cc_start: 0.8717 (p-80) cc_final: 0.8342 (p-80) REVERT: D 522 MET cc_start: 0.8705 (tpp) cc_final: 0.8368 (mtp) REVERT: D 538 MET cc_start: 0.8832 (mmm) cc_final: 0.8058 (mpp) REVERT: E 343 ARG cc_start: 0.8664 (ptp-170) cc_final: 0.8276 (ptt-90) outliers start: 61 outliers final: 47 residues processed: 311 average time/residue: 0.1479 time to fit residues: 71.4954 Evaluate side-chains 307 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU 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 611 MET 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 84 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 188 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 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 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 507 SER Chi-restraints excluded: chain C residue 515 THR 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 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 326 GLU 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 332 TYR Chi-restraints excluded: chain F residue 345 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 61 optimal weight: 0.0870 chunk 207 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 241 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.127829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.099227 restraints weight = 41373.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.101238 restraints weight = 30392.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103234 restraints weight = 21975.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103783 restraints weight = 18013.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103939 restraints weight = 16636.959| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3795 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= 0.110 Angle : 0.544 9.607 29458 Z= 0.274 Chirality : 0.041 0.165 3140 Planarity : 0.003 0.034 3792 Dihedral : 4.955 58.051 2970 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.27 % Allowed : 17.90 % Favored : 79.83 % 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: 0.78 (0.17), residues: 2576 helix: 1.96 (0.15), residues: 1314 sheet: -0.70 (0.26), residues: 318 loop : -1.14 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 303 TYR 0.017 0.001 TYR D 44 PHE 0.021 0.001 PHE B 505 TRP 0.011 0.001 TRP A 58 HIS 0.006 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00252 (21740) covalent geometry : angle 0.54351 (29458) hydrogen bonds : bond 0.03084 ( 1068) hydrogen bonds : angle 4.03800 ( 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 344 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 293 time to evaluate : 0.789 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: 0.6316 (t80) cc_final: 0.5867 (t80) REVERT: A 31 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: A 88 LYS cc_start: 0.9164 (mmpt) cc_final: 0.8692 (mmmt) REVERT: A 94 MET cc_start: 0.8232 (mmt) cc_final: 0.7884 (mmt) REVERT: A 240 HIS cc_start: 0.8782 (p-80) cc_final: 0.8490 (p-80) REVERT: A 306 GLU cc_start: 0.8325 (tp30) cc_final: 0.8054 (tp30) REVERT: A 416 MET cc_start: 0.7654 (tpp) cc_final: 0.7280 (tpp) REVERT: A 522 MET cc_start: 0.8708 (tpp) cc_final: 0.8390 (mtp) REVERT: A 538 MET cc_start: 0.8786 (mmm) cc_final: 0.8034 (mpp) REVERT: A 590 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6898 (mt-10) REVERT: B 31 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: B 94 MET cc_start: 0.8065 (mmt) cc_final: 0.7698 (mmt) REVERT: B 331 ARG cc_start: 0.8657 (mtm110) cc_final: 0.8198 (mtm110) REVERT: B 333 GLU cc_start: 0.8711 (mp0) cc_final: 0.8191 (mp0) REVERT: B 522 MET cc_start: 0.8731 (tpp) cc_final: 0.8402 (mtp) REVERT: B 538 MET cc_start: 0.8802 (mmm) cc_final: 0.8030 (mpp) REVERT: B 611 MET cc_start: 0.8545 (mmp) cc_final: 0.8319 (mmp) REVERT: C 22 PHE cc_start: 0.6321 (t80) cc_final: 0.5811 (t80) REVERT: C 31 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: C 94 MET cc_start: 0.8196 (mmt) cc_final: 0.7952 (mmt) REVERT: C 240 HIS cc_start: 0.8735 (p-80) cc_final: 0.8392 (p-80) REVERT: C 306 GLU cc_start: 0.8468 (tp30) cc_final: 0.8143 (tp30) REVERT: C 522 MET cc_start: 0.8676 (tpp) cc_final: 0.8371 (mtp) REVERT: C 538 MET cc_start: 0.8804 (mmm) cc_final: 0.7991 (mpp) REVERT: C 590 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6920 (mt-10) REVERT: C 611 MET cc_start: 0.8956 (mmm) cc_final: 0.8512 (mmt) REVERT: D 31 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: D 88 LYS cc_start: 0.9160 (mmpt) cc_final: 0.8671 (mmmt) REVERT: D 94 MET cc_start: 0.8226 (mmt) cc_final: 0.7883 (mmt) REVERT: D 240 HIS cc_start: 0.8851 (p-80) cc_final: 0.8393 (p-80) REVERT: D 522 MET cc_start: 0.8686 (tpp) cc_final: 0.8336 (mtp) REVERT: D 538 MET cc_start: 0.8840 (mmm) cc_final: 0.8029 (mpp) REVERT: D 590 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6872 (mt-10) REVERT: E 343 ARG cc_start: 0.8599 (ptp-170) cc_final: 0.8124 (ptt-90) REVERT: G 343 ARG cc_start: 0.8636 (ptp-170) cc_final: 0.8194 (ptt-90) outliers start: 51 outliers final: 36 residues processed: 326 average time/residue: 0.1456 time to fit residues: 73.7899 Evaluate side-chains 306 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 209 LEU 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 611 MET Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 188 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 C residue 31 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 166 LEU 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 507 SER Chi-restraints excluded: chain C residue 515 THR 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 409 LEU 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 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 G residue 347 THR Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 345 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 115 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 184 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.098881 restraints weight = 41254.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.101339 restraints weight = 27803.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103047 restraints weight = 21450.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104220 restraints weight = 18061.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104776 restraints weight = 16065.909| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21740 Z= 0.119 Angle : 0.573 9.537 29458 Z= 0.285 Chirality : 0.041 0.178 3140 Planarity : 0.003 0.046 3792 Dihedral : 4.922 56.289 2970 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.91 % Allowed : 18.74 % Favored : 79.34 % 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: 0.78 (0.17), residues: 2576 helix: 1.92 (0.15), residues: 1318 sheet: -0.56 (0.27), residues: 314 loop : -1.14 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 437 TYR 0.020 0.001 TYR D 44 PHE 0.020 0.001 PHE B 505 TRP 0.011 0.001 TRP D 58 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00274 (21740) covalent geometry : angle 0.57331 (29458) hydrogen bonds : bond 0.03136 ( 1068) hydrogen bonds : angle 4.04251 ( 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 321 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6255 (t80) cc_final: 0.5773 (t80) REVERT: A 31 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: A 88 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8677 (mmmt) REVERT: A 94 MET cc_start: 0.8226 (mmt) cc_final: 0.7599 (mmt) REVERT: A 240 HIS cc_start: 0.8664 (p-80) cc_final: 0.8454 (p-80) REVERT: A 303 ARG cc_start: 0.6777 (ttt180) cc_final: 0.6420 (ttt180) REVERT: A 306 GLU cc_start: 0.8339 (tp30) cc_final: 0.8058 (tp30) REVERT: A 522 MET cc_start: 0.8709 (tpp) cc_final: 0.8429 (mtp) REVERT: A 590 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6874 (mt-10) REVERT: B 31 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: B 94 MET cc_start: 0.8062 (mmt) cc_final: 0.7634 (mmt) REVERT: B 303 ARG cc_start: 0.6706 (ttt180) cc_final: 0.6414 (ttt180) REVERT: B 306 GLU cc_start: 0.8407 (tp30) cc_final: 0.8187 (tp30) REVERT: B 331 ARG cc_start: 0.8652 (mtm110) cc_final: 0.8120 (mtm110) REVERT: B 333 GLU cc_start: 0.8677 (mp0) cc_final: 0.8139 (mp0) REVERT: B 522 MET cc_start: 0.8735 (tpp) cc_final: 0.8429 (mtp) REVERT: B 538 MET cc_start: 0.8805 (mmm) cc_final: 0.8029 (mpp) REVERT: C 22 PHE cc_start: 0.6292 (t80) cc_final: 0.5818 (t80) REVERT: C 31 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: C 94 MET cc_start: 0.8289 (mmt) cc_final: 0.7702 (mmt) REVERT: C 240 HIS cc_start: 0.8724 (p-80) cc_final: 0.8315 (p-80) REVERT: C 303 ARG cc_start: 0.6769 (ttt180) cc_final: 0.6488 (ttt180) REVERT: C 306 GLU cc_start: 0.8450 (tp30) cc_final: 0.8128 (tp30) REVERT: C 522 MET cc_start: 0.8667 (tpp) cc_final: 0.8394 (mtp) REVERT: C 538 MET cc_start: 0.8818 (mmm) cc_final: 0.8014 (mpp) REVERT: C 590 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6936 (mt-10) REVERT: C 611 MET cc_start: 0.8948 (mmm) cc_final: 0.8501 (mmt) REVERT: D 31 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: D 88 LYS cc_start: 0.9147 (mmpt) cc_final: 0.8664 (mmmt) REVERT: D 94 MET cc_start: 0.8221 (mmt) cc_final: 0.7600 (mmt) REVERT: D 240 HIS cc_start: 0.8728 (p-80) cc_final: 0.8338 (p-80) REVERT: D 303 ARG cc_start: 0.6994 (ttt180) cc_final: 0.6630 (ttt180) REVERT: D 522 MET cc_start: 0.8706 (tpp) cc_final: 0.8387 (mtp) REVERT: D 538 MET cc_start: 0.8846 (mmm) cc_final: 0.8034 (mpp) REVERT: D 590 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6839 (mt-10) REVERT: E 343 ARG cc_start: 0.8528 (ptp-170) cc_final: 0.8048 (ptt-90) REVERT: G 343 ARG cc_start: 0.8525 (ptp-170) cc_final: 0.8041 (ptt-90) outliers start: 43 outliers final: 34 residues processed: 306 average time/residue: 0.1481 time to fit residues: 70.9664 Evaluate side-chains 289 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU 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 611 MET Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 188 LEU 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 507 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 166 LEU 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 507 SER Chi-restraints excluded: chain C residue 515 THR 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 507 SER Chi-restraints excluded: chain D residue 515 THR 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 G residue 347 THR Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 97 optimal weight: 2.9990 chunk 212 optimal weight: 0.2980 chunk 116 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 150 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.125805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096531 restraints weight = 42419.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098066 restraints weight = 30039.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099012 restraints weight = 24403.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.099996 restraints weight = 21356.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100220 restraints weight = 19884.199| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4051 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= 0.148 Angle : 0.604 9.246 29458 Z= 0.302 Chirality : 0.042 0.172 3140 Planarity : 0.004 0.075 3792 Dihedral : 5.005 58.159 2970 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.91 % Allowed : 18.92 % Favored : 79.16 % 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: 0.64 (0.17), residues: 2576 helix: 1.82 (0.15), residues: 1316 sheet: -0.59 (0.27), residues: 308 loop : -1.24 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 303 TYR 0.019 0.001 TYR D 44 PHE 0.021 0.001 PHE B 505 TRP 0.013 0.001 TRP C 143 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00339 (21740) covalent geometry : angle 0.60362 (29458) hydrogen bonds : bond 0.03377 ( 1068) hydrogen bonds : angle 4.17783 ( 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: 43 poor density : 268 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6406 (t80) cc_final: 0.5895 (t80) REVERT: A 31 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: A 88 LYS cc_start: 0.9173 (mmpt) cc_final: 0.8695 (mmmt) REVERT: A 94 MET cc_start: 0.8281 (mmt) cc_final: 0.7767 (mmt) REVERT: A 240 HIS cc_start: 0.8800 (p-80) cc_final: 0.8447 (p90) REVERT: A 303 ARG cc_start: 0.7015 (ttt180) cc_final: 0.6386 (ttt180) REVERT: A 306 GLU cc_start: 0.8431 (tp30) cc_final: 0.7898 (mm-30) REVERT: A 522 MET cc_start: 0.8746 (tpp) cc_final: 0.8470 (mtp) REVERT: A 590 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6943 (mt-10) REVERT: B 31 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: B 88 LYS cc_start: 0.9424 (mttt) cc_final: 0.9121 (mtpt) REVERT: B 94 MET cc_start: 0.8190 (mmt) cc_final: 0.7729 (mmt) REVERT: B 303 ARG cc_start: 0.6849 (ttt180) cc_final: 0.6398 (ttt180) REVERT: B 331 ARG cc_start: 0.8763 (mtm110) cc_final: 0.8203 (mtm110) REVERT: B 333 GLU cc_start: 0.8658 (mp0) cc_final: 0.8183 (mp0) REVERT: B 522 MET cc_start: 0.8769 (tpp) cc_final: 0.8467 (mtp) REVERT: B 538 MET cc_start: 0.8755 (mmm) cc_final: 0.8007 (mpp) REVERT: B 611 MET cc_start: 0.8591 (mmp) cc_final: 0.8388 (mmp) REVERT: C 22 PHE cc_start: 0.6406 (t80) cc_final: 0.5893 (t80) REVERT: C 31 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: C 94 MET cc_start: 0.8396 (mmt) cc_final: 0.7879 (mmt) REVERT: C 240 HIS cc_start: 0.8827 (p-80) cc_final: 0.8473 (p-80) REVERT: C 306 GLU cc_start: 0.8517 (tp30) cc_final: 0.8195 (tp30) REVERT: C 522 MET cc_start: 0.8686 (tpp) cc_final: 0.8392 (mtp) REVERT: C 538 MET cc_start: 0.8763 (mmm) cc_final: 0.7995 (mpp) REVERT: D 31 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: D 88 LYS cc_start: 0.9183 (mmpt) cc_final: 0.8700 (mmmt) REVERT: D 94 MET cc_start: 0.8272 (mmt) cc_final: 0.7770 (mmt) REVERT: D 240 HIS cc_start: 0.8868 (p-80) cc_final: 0.8410 (p-80) REVERT: D 303 ARG cc_start: 0.7030 (ttt180) cc_final: 0.6610 (ttt180) REVERT: D 522 MET cc_start: 0.8721 (tpp) cc_final: 0.8414 (mtp) REVERT: D 538 MET cc_start: 0.8793 (mmm) cc_final: 0.8007 (mpp) REVERT: D 590 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6920 (mt-10) REVERT: E 326 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7265 (mm-30) REVERT: E 343 ARG cc_start: 0.8621 (ptp-170) cc_final: 0.8039 (ptt-90) REVERT: G 343 ARG cc_start: 0.8619 (ptp-170) cc_final: 0.8057 (ptt-90) outliers start: 43 outliers final: 36 residues processed: 297 average time/residue: 0.1540 time to fit residues: 71.2526 Evaluate side-chains 301 residues out of total 2246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU 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 611 MET Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 188 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 C residue 31 GLU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 166 LEU 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 507 SER 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 209 LEU 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 507 SER Chi-restraints excluded: chain D residue 515 THR 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 G residue 347 THR Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain H residue 347 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 134 optimal weight: 0.9990 chunk 250 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 213 optimal weight: 0.6980 chunk 205 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.127580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098750 restraints weight = 41570.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.101294 restraints weight = 28169.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103036 restraints weight = 21556.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104203 restraints weight = 18097.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104779 restraints weight = 16083.316| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4081 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= 0.116 Angle : 0.581 9.471 29458 Z= 0.290 Chirality : 0.042 0.243 3140 Planarity : 0.003 0.047 3792 Dihedral : 4.848 55.491 2970 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.05 % Allowed : 19.01 % Favored : 78.94 % 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: 1306 sheet: -0.51 (0.27), residues: 312 loop : -1.11 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 303 TYR 0.020 0.001 TYR D 44 PHE 0.020 0.001 PHE B 505 TRP 0.009 0.001 TRP C 143 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00266 (21740) covalent geometry : angle 0.58066 (29458) hydrogen bonds : bond 0.03098 ( 1068) hydrogen bonds : angle 4.04121 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2935.05 seconds wall clock time: 51 minutes 55.47 seconds (3115.47 seconds total)