Starting phenix.real_space_refine on Thu Jun 19 15:38:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s88_24890/06_2025/7s88_24890.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s88_24890/06_2025/7s88_24890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s88_24890/06_2025/7s88_24890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s88_24890/06_2025/7s88_24890.map" model { file = "/net/cci-nas-00/data/ceres_data/7s88_24890/06_2025/7s88_24890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s88_24890/06_2025/7s88_24890.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.025 sd= 0.215 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 32 5.49 5 S 160 5.16 5 C 14692 2.51 5 N 3392 2.21 5 O 3924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22201 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "B" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "C" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "D" Number of atoms: 4935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4935 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "A" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 580 Unusual residues: {' CA': 1, 'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 579 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 579 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 579 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 62 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 12.82, per 1000 atoms: 0.58 Number of scatterers: 22201 At special positions: 0 Unit cell: (133.147, 133.147, 122.396, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 160 16.00 P 32 15.00 O 3924 8.00 N 3392 7.00 C 14692 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: 5.83 Conformation dependent library (CDL) restraints added in 2.6 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 66.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 24 through 47 removed outlier: 3.532A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.678A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.541A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.103A pdb=" N GLU A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.540A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.868A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.591A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.569A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.786A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.556A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.072A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 414 through 423 removed outlier: 3.573A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.625A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 488 through 512 removed outlier: 5.169A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.140A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 47 removed outlier: 3.531A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.678A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.542A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.104A pdb=" N GLU B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.540A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.868A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.592A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.569A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 310 removed outlier: 3.787A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.557A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.074A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 414 through 423 removed outlier: 3.572A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.625A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 488 through 512 removed outlier: 5.170A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.140A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 47 removed outlier: 3.531A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.678A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.542A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.104A pdb=" N GLU C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.539A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.867A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.592A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.569A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.786A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.556A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.073A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 414 through 423 removed outlier: 3.572A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.625A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 488 through 512 removed outlier: 5.170A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.141A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 47 removed outlier: 3.531A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.677A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.542A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.104A pdb=" N GLU D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.539A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.867A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.592A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.568A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 310 removed outlier: 3.786A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.556A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.073A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 414 through 423 removed outlier: 3.573A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.624A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.520A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 488 through 512 removed outlier: 5.170A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.140A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.548A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 removed outlier: 3.518A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.731A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.732A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.731A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.732A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1077 hydrogen bonds defined for protein. 3111 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: 6.73 Time building geometry restraints manager: 6.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3256 1.31 - 1.43: 5696 1.43 - 1.56: 13146 1.56 - 1.69: 122 1.69 - 1.81: 272 Bond restraints: 22492 Sorted by residual: bond pdb=" C21 POV C 702 " pdb=" O21 POV C 702 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C21 POV B 702 " pdb=" O21 POV B 702 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C21 POV A 816 " pdb=" O21 POV A 816 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C21 POV D 706 " pdb=" O21 POV D 706 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C21 POV A 808 " pdb=" O21 POV A 808 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 1.99e+01 ... (remaining 22487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 28746 2.89 - 5.77: 1009 5.77 - 8.66: 235 8.66 - 11.54: 113 11.54 - 14.43: 49 Bond angle restraints: 30152 Sorted by residual: angle pdb=" C ASN B 546 " pdb=" N TYR B 547 " pdb=" CA TYR B 547 " ideal model delta sigma weight residual 121.54 130.82 -9.28 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C ASN D 546 " pdb=" N TYR D 547 " pdb=" CA TYR D 547 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C ASN C 546 " pdb=" N TYR C 547 " pdb=" CA TYR C 547 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C ASN A 546 " pdb=" N TYR A 547 " pdb=" CA TYR A 547 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C12 POV D 706 " pdb=" N POV D 706 " pdb=" C14 POV D 706 " ideal model delta sigma weight residual 107.13 121.56 -14.43 3.00e+00 1.11e-01 2.31e+01 ... (remaining 30147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.74: 13464 30.74 - 61.47: 889 61.47 - 92.20: 103 92.20 - 122.94: 16 122.94 - 153.67: 16 Dihedral angle restraints: 14488 sinusoidal: 7304 harmonic: 7184 Sorted by residual: dihedral pdb=" CA GLU A 68 " pdb=" C GLU A 68 " pdb=" N ASP A 69 " pdb=" CA ASP A 69 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLU D 68 " pdb=" C GLU D 68 " pdb=" N ASP D 69 " pdb=" CA ASP D 69 " ideal model delta harmonic sigma weight residual 180.00 152.01 27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLU B 68 " pdb=" C GLU B 68 " pdb=" N ASP B 69 " pdb=" CA ASP B 69 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 14485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2936 0.092 - 0.185: 272 0.185 - 0.277: 11 0.277 - 0.369: 5 0.369 - 0.461: 8 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CG LEU D 458 " pdb=" CB LEU D 458 " pdb=" CD1 LEU D 458 " pdb=" CD2 LEU D 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CG LEU A 458 " pdb=" CB LEU A 458 " pdb=" CD1 LEU A 458 " pdb=" CD2 LEU A 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CG LEU B 458 " pdb=" CB LEU B 458 " pdb=" CD1 LEU B 458 " pdb=" CD2 LEU B 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.25e+00 ... (remaining 3229 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 423 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO A 424 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 423 " 0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO C 424 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 424 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 424 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 423 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO B 424 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 424 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 424 " -0.041 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4472 2.77 - 3.30: 18784 3.30 - 3.83: 36279 3.83 - 4.37: 48614 4.37 - 4.90: 79694 Nonbonded interactions: 187843 Sorted by model distance: nonbonded pdb=" OG1 THR B 242 " pdb=" OE2 GLU B 282 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR D 242 " pdb=" OE2 GLU D 282 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR C 242 " pdb=" OE2 GLU C 282 " model vdw 2.235 3.040 nonbonded pdb=" OG1 THR A 242 " pdb=" OE2 GLU A 282 " model vdw 2.235 3.040 nonbonded pdb=" O HOH A 906 " pdb=" O HOH A 916 " model vdw 2.249 3.040 ... (remaining 187838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 637 or resid 806)) selection = (chain 'B' and (resid 24 through 637 or resid 706)) selection = (chain 'C' and (resid 24 through 637 or resid 706)) selection = (chain 'D' and (resid 24 through 637 or resid 706)) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.710 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.102 22492 Z= 0.571 Angle : 1.479 14.429 30152 Z= 0.649 Chirality : 0.059 0.461 3232 Planarity : 0.009 0.074 3600 Dihedral : 19.387 153.675 9848 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.31 % Allowed : 1.88 % Favored : 96.81 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.12), residues: 2448 helix: -3.72 (0.07), residues: 1492 sheet: -1.56 (0.51), residues: 88 loop : -2.08 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP D 629 HIS 0.014 0.003 HIS C 522 PHE 0.047 0.004 PHE B 472 TYR 0.023 0.004 TYR D 270 ARG 0.012 0.001 ARG B 492 Details of bonding type rmsd hydrogen bonds : bond 0.27233 ( 1077) hydrogen bonds : angle 8.31696 ( 3111) covalent geometry : bond 0.01271 (22492) covalent geometry : angle 1.47921 (30152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 508 time to evaluate : 2.019 Fit side-chains REVERT: A 176 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6245 (mm-30) REVERT: A 234 LEU cc_start: 0.8562 (mp) cc_final: 0.8242 (mm) REVERT: A 239 GLN cc_start: 0.8634 (mt0) cc_final: 0.8332 (mt0) REVERT: A 263 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7669 (mtt90) REVERT: A 442 MET cc_start: 0.8859 (mtt) cc_final: 0.8659 (mtp) REVERT: A 458 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8579 (mt) REVERT: A 635 ASP cc_start: 0.7488 (t70) cc_final: 0.7181 (p0) REVERT: B 176 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6298 (mm-30) REVERT: B 234 LEU cc_start: 0.8593 (mp) cc_final: 0.8288 (mm) REVERT: B 239 GLN cc_start: 0.8649 (mt0) cc_final: 0.8348 (mt0) REVERT: B 263 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7515 (mtt90) REVERT: B 300 LYS cc_start: 0.8143 (mmtp) cc_final: 0.6977 (mppt) REVERT: B 383 ASP cc_start: 0.8071 (m-30) cc_final: 0.7858 (m-30) REVERT: B 635 ASP cc_start: 0.7393 (t70) cc_final: 0.7153 (p0) REVERT: C 176 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6270 (mm-30) REVERT: C 234 LEU cc_start: 0.8593 (mp) cc_final: 0.8290 (mm) REVERT: C 239 GLN cc_start: 0.8649 (mt0) cc_final: 0.8350 (mt0) REVERT: C 263 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7547 (mtt90) REVERT: C 442 MET cc_start: 0.8848 (mtt) cc_final: 0.8644 (mtp) REVERT: C 622 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6854 (pm20) REVERT: C 635 ASP cc_start: 0.7502 (t70) cc_final: 0.7170 (p0) REVERT: D 176 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6267 (mm-30) REVERT: D 234 LEU cc_start: 0.8619 (mp) cc_final: 0.8293 (mm) REVERT: D 239 GLN cc_start: 0.8646 (mt0) cc_final: 0.8349 (mt0) REVERT: D 263 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7647 (mtt90) REVERT: D 300 LYS cc_start: 0.8142 (mmtp) cc_final: 0.6930 (mppt) REVERT: D 442 MET cc_start: 0.8847 (mtt) cc_final: 0.8644 (mtp) REVERT: D 458 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8632 (mt) REVERT: D 635 ASP cc_start: 0.7446 (t70) cc_final: 0.7130 (p0) outliers start: 28 outliers final: 8 residues processed: 532 average time/residue: 1.3525 time to fit residues: 817.6016 Evaluate side-chains 347 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 337 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 122 HIS A 174 ASN A 185 HIS A 214 GLN A 217 ASN A 369 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 118 GLN B 122 HIS B 174 ASN B 185 HIS B 214 GLN B 217 ASN B 306 GLN B 369 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN B 572 ASN C 37 ASN C 118 GLN C 122 HIS C 174 ASN C 185 HIS C 214 GLN C 217 ASN C 369 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 37 ASN D 122 HIS D 174 ASN D 185 HIS D 214 GLN D 217 ASN D 369 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.177147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.128071 restraints weight = 21473.074| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.51 r_work: 0.3320 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22492 Z= 0.151 Angle : 0.611 7.802 30152 Z= 0.303 Chirality : 0.040 0.244 3232 Planarity : 0.006 0.055 3600 Dihedral : 20.976 152.058 5100 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.58 % Allowed : 11.30 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 2448 helix: -0.78 (0.12), residues: 1504 sheet: -1.08 (0.52), residues: 88 loop : -1.23 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 613 HIS 0.004 0.001 HIS A 522 PHE 0.014 0.002 PHE A 537 TYR 0.012 0.002 TYR D 555 ARG 0.003 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 1077) hydrogen bonds : angle 4.01667 ( 3111) covalent geometry : bond 0.00353 (22492) covalent geometry : angle 0.61146 (30152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 369 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7683 (pt0) cc_final: 0.7234 (pm20) REVERT: A 157 CYS cc_start: 0.8313 (m) cc_final: 0.7810 (p) REVERT: A 176 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6026 (mm-30) REVERT: A 177 GLU cc_start: 0.6829 (pm20) cc_final: 0.6609 (pm20) REVERT: A 234 LEU cc_start: 0.8292 (mp) cc_final: 0.8022 (mm) REVERT: A 263 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7849 (mtt90) REVERT: A 279 ASP cc_start: 0.8124 (t0) cc_final: 0.7788 (t0) REVERT: A 300 LYS cc_start: 0.7994 (mmtp) cc_final: 0.6634 (mppt) REVERT: A 314 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7172 (ttmt) REVERT: A 345 MET cc_start: 0.8192 (mtm) cc_final: 0.7738 (mmm) REVERT: A 442 MET cc_start: 0.8492 (mtt) cc_final: 0.8258 (mtp) REVERT: A 618 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7975 (mp) REVERT: A 635 ASP cc_start: 0.7780 (t70) cc_final: 0.7211 (p0) REVERT: B 80 GLU cc_start: 0.7743 (pt0) cc_final: 0.7328 (pm20) REVERT: B 157 CYS cc_start: 0.8281 (m) cc_final: 0.7831 (p) REVERT: B 176 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6116 (mm-30) REVERT: B 177 GLU cc_start: 0.6854 (pm20) cc_final: 0.6644 (pm20) REVERT: B 234 LEU cc_start: 0.8187 (mp) cc_final: 0.7918 (mm) REVERT: B 263 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7595 (mtt90) REVERT: B 279 ASP cc_start: 0.8238 (t0) cc_final: 0.7893 (t0) REVERT: B 300 LYS cc_start: 0.8024 (mmtp) cc_final: 0.6717 (mppt) REVERT: B 314 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7200 (ttmt) REVERT: B 635 ASP cc_start: 0.7798 (t70) cc_final: 0.7151 (p0) REVERT: C 80 GLU cc_start: 0.7698 (pt0) cc_final: 0.7270 (pm20) REVERT: C 157 CYS cc_start: 0.8314 (m) cc_final: 0.7824 (p) REVERT: C 176 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6030 (mm-30) REVERT: C 177 GLU cc_start: 0.6837 (pm20) cc_final: 0.6618 (pm20) REVERT: C 234 LEU cc_start: 0.8220 (mp) cc_final: 0.7958 (mm) REVERT: C 263 ARG cc_start: 0.8132 (mtt-85) cc_final: 0.7848 (mtt90) REVERT: C 279 ASP cc_start: 0.8105 (t0) cc_final: 0.7783 (t0) REVERT: C 284 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: C 300 LYS cc_start: 0.7979 (mmtp) cc_final: 0.6612 (mppt) REVERT: C 314 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7234 (ttmt) REVERT: C 345 MET cc_start: 0.8187 (mtm) cc_final: 0.7775 (mmm) REVERT: C 442 MET cc_start: 0.8468 (mtt) cc_final: 0.8233 (mtp) REVERT: C 618 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7943 (mp) REVERT: C 635 ASP cc_start: 0.7771 (t70) cc_final: 0.7194 (p0) REVERT: D 80 GLU cc_start: 0.7680 (pt0) cc_final: 0.7253 (pm20) REVERT: D 157 CYS cc_start: 0.8323 (m) cc_final: 0.7831 (p) REVERT: D 176 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6106 (mm-30) REVERT: D 177 GLU cc_start: 0.6862 (pm20) cc_final: 0.6634 (pm20) REVERT: D 234 LEU cc_start: 0.8258 (mp) cc_final: 0.7975 (mm) REVERT: D 263 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7670 (mtt90) REVERT: D 279 ASP cc_start: 0.8144 (t0) cc_final: 0.7789 (t0) REVERT: D 284 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: D 300 LYS cc_start: 0.8008 (mmtp) cc_final: 0.6682 (mppt) REVERT: D 314 LYS cc_start: 0.7905 (ttpt) cc_final: 0.7170 (ttmt) REVERT: D 345 MET cc_start: 0.8219 (mtm) cc_final: 0.7777 (mmm) REVERT: D 442 MET cc_start: 0.8456 (mtt) cc_final: 0.8209 (mtp) REVERT: D 615 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6737 (ttt180) REVERT: D 635 ASP cc_start: 0.7777 (t70) cc_final: 0.7203 (p0) outliers start: 55 outliers final: 11 residues processed: 404 average time/residue: 1.2826 time to fit residues: 592.3261 Evaluate side-chains 364 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 346 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 615 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 142 optimal weight: 0.0980 chunk 243 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN B 185 HIS C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127780 restraints weight = 21646.382| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.57 r_work: 0.3340 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22492 Z= 0.118 Angle : 0.530 6.287 30152 Z= 0.267 Chirality : 0.038 0.175 3232 Planarity : 0.005 0.048 3600 Dihedral : 19.403 141.883 5096 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.72 % Allowed : 12.57 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2448 helix: 0.73 (0.13), residues: 1504 sheet: -1.20 (0.51), residues: 88 loop : -0.97 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 613 HIS 0.003 0.001 HIS C 582 PHE 0.012 0.001 PHE C 537 TYR 0.012 0.002 TYR B 555 ARG 0.002 0.000 ARG D 323 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 1077) hydrogen bonds : angle 3.63093 ( 3111) covalent geometry : bond 0.00269 (22492) covalent geometry : angle 0.52998 (30152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 354 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7594 (pt0) cc_final: 0.7350 (pm20) REVERT: A 146 ARG cc_start: 0.7690 (mtm110) cc_final: 0.6964 (mtp85) REVERT: A 157 CYS cc_start: 0.8247 (m) cc_final: 0.7859 (p) REVERT: A 176 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6179 (mm-30) REVERT: A 177 GLU cc_start: 0.6954 (pm20) cc_final: 0.6676 (pm20) REVERT: A 234 LEU cc_start: 0.8222 (mp) cc_final: 0.7918 (mm) REVERT: A 263 ARG cc_start: 0.8156 (mtt-85) cc_final: 0.7670 (mtt90) REVERT: A 279 ASP cc_start: 0.8223 (t0) cc_final: 0.7887 (t0) REVERT: A 300 LYS cc_start: 0.8042 (mmtp) cc_final: 0.6712 (mppt) REVERT: A 314 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7340 (ttmt) REVERT: A 345 MET cc_start: 0.8173 (mtm) cc_final: 0.7784 (mmm) REVERT: A 374 GLN cc_start: 0.8128 (mp-120) cc_final: 0.7815 (pm20) REVERT: A 442 MET cc_start: 0.8426 (mtt) cc_final: 0.8163 (mtp) REVERT: A 618 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7924 (mp) REVERT: A 635 ASP cc_start: 0.7684 (t70) cc_final: 0.7117 (p0) REVERT: B 80 GLU cc_start: 0.7557 (pt0) cc_final: 0.7327 (pm20) REVERT: B 146 ARG cc_start: 0.7626 (mtm110) cc_final: 0.6975 (mtp85) REVERT: B 157 CYS cc_start: 0.8284 (m) cc_final: 0.7927 (p) REVERT: B 176 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6078 (mm-30) REVERT: B 177 GLU cc_start: 0.6913 (pm20) cc_final: 0.6630 (pm20) REVERT: B 234 LEU cc_start: 0.8191 (mp) cc_final: 0.7879 (mm) REVERT: B 263 ARG cc_start: 0.8051 (mtt-85) cc_final: 0.7753 (mtt90) REVERT: B 279 ASP cc_start: 0.8286 (t0) cc_final: 0.7974 (t0) REVERT: B 300 LYS cc_start: 0.8046 (mmtp) cc_final: 0.6768 (mppt) REVERT: B 314 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7299 (ttmt) REVERT: B 345 MET cc_start: 0.8152 (mtm) cc_final: 0.7741 (mmm) REVERT: B 618 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8099 (mp) REVERT: B 628 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7763 (mtp180) REVERT: B 635 ASP cc_start: 0.7669 (t70) cc_final: 0.7038 (p0) REVERT: C 80 GLU cc_start: 0.7584 (pt0) cc_final: 0.7349 (pm20) REVERT: C 146 ARG cc_start: 0.7691 (mtm110) cc_final: 0.6958 (mtp85) REVERT: C 157 CYS cc_start: 0.8280 (m) cc_final: 0.7891 (p) REVERT: C 176 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6072 (mm-30) REVERT: C 177 GLU cc_start: 0.6961 (pm20) cc_final: 0.6661 (pm20) REVERT: C 234 LEU cc_start: 0.8226 (mp) cc_final: 0.7931 (mm) REVERT: C 263 ARG cc_start: 0.8178 (mtt-85) cc_final: 0.7857 (mtt90) REVERT: C 279 ASP cc_start: 0.8202 (t0) cc_final: 0.7865 (t0) REVERT: C 300 LYS cc_start: 0.8009 (mmtp) cc_final: 0.6643 (mppt) REVERT: C 314 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7388 (ttmt) REVERT: C 345 MET cc_start: 0.8133 (mtm) cc_final: 0.7779 (mmm) REVERT: C 374 GLN cc_start: 0.8117 (mp-120) cc_final: 0.7800 (pm20) REVERT: C 442 MET cc_start: 0.8418 (mtt) cc_final: 0.8149 (mtp) REVERT: C 618 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7935 (mp) REVERT: C 635 ASP cc_start: 0.7732 (t70) cc_final: 0.7143 (p0) REVERT: D 80 GLU cc_start: 0.7534 (pt0) cc_final: 0.7303 (pm20) REVERT: D 146 ARG cc_start: 0.7676 (mtm110) cc_final: 0.7038 (mtp85) REVERT: D 157 CYS cc_start: 0.8274 (m) cc_final: 0.7883 (p) REVERT: D 176 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6093 (mm-30) REVERT: D 177 GLU cc_start: 0.6922 (pm20) cc_final: 0.6630 (pm20) REVERT: D 214 GLN cc_start: 0.7760 (mt0) cc_final: 0.7517 (mt0) REVERT: D 234 LEU cc_start: 0.8220 (mp) cc_final: 0.7909 (mm) REVERT: D 263 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7622 (mtt90) REVERT: D 279 ASP cc_start: 0.8227 (t0) cc_final: 0.7878 (t0) REVERT: D 300 LYS cc_start: 0.8035 (mmtp) cc_final: 0.6697 (mppt) REVERT: D 314 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7265 (ttmt) REVERT: D 345 MET cc_start: 0.8139 (mtm) cc_final: 0.7785 (mmm) REVERT: D 374 GLN cc_start: 0.8096 (mp-120) cc_final: 0.7796 (pm20) REVERT: D 442 MET cc_start: 0.8407 (mtt) cc_final: 0.8147 (mtp) REVERT: D 615 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6829 (ttt180) REVERT: D 618 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7977 (mp) REVERT: D 635 ASP cc_start: 0.7678 (t70) cc_final: 0.7113 (p0) outliers start: 58 outliers final: 12 residues processed: 386 average time/residue: 1.3887 time to fit residues: 609.1080 Evaluate side-chains 356 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 336 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 615 ARG Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 110 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 290 GLN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.175365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127246 restraints weight = 21938.551| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.55 r_work: 0.3330 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22492 Z= 0.121 Angle : 0.524 6.096 30152 Z= 0.263 Chirality : 0.038 0.171 3232 Planarity : 0.005 0.046 3600 Dihedral : 18.581 134.866 5096 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.67 % Allowed : 12.52 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2448 helix: 1.25 (0.14), residues: 1504 sheet: -1.14 (0.51), residues: 88 loop : -0.81 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 613 HIS 0.003 0.001 HIS D 582 PHE 0.012 0.001 PHE D 537 TYR 0.012 0.002 TYR C 555 ARG 0.002 0.000 ARG B 414 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 1077) hydrogen bonds : angle 3.55510 ( 3111) covalent geometry : bond 0.00284 (22492) covalent geometry : angle 0.52373 (30152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 339 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7639 (mtm110) cc_final: 0.6976 (mtp85) REVERT: A 157 CYS cc_start: 0.8289 (m) cc_final: 0.7939 (p) REVERT: A 176 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6147 (mm-30) REVERT: A 177 GLU cc_start: 0.6879 (pm20) cc_final: 0.6646 (pm20) REVERT: A 234 LEU cc_start: 0.8262 (mp) cc_final: 0.7932 (mm) REVERT: A 263 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7867 (mtt90) REVERT: A 279 ASP cc_start: 0.8291 (t0) cc_final: 0.7979 (t0) REVERT: A 300 LYS cc_start: 0.8076 (mmtp) cc_final: 0.6745 (mppt) REVERT: A 314 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7330 (ttmt) REVERT: A 345 MET cc_start: 0.8133 (mtm) cc_final: 0.7819 (mmm) REVERT: A 442 MET cc_start: 0.8430 (mtt) cc_final: 0.8178 (mtp) REVERT: A 618 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7975 (mp) REVERT: A 635 ASP cc_start: 0.7606 (t70) cc_final: 0.7012 (p0) REVERT: B 146 ARG cc_start: 0.7646 (mtm110) cc_final: 0.6988 (mtp85) REVERT: B 157 CYS cc_start: 0.8278 (m) cc_final: 0.7954 (p) REVERT: B 176 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6196 (mm-30) REVERT: B 177 GLU cc_start: 0.6904 (pm20) cc_final: 0.6649 (pm20) REVERT: B 234 LEU cc_start: 0.8194 (mp) cc_final: 0.7861 (mm) REVERT: B 263 ARG cc_start: 0.8133 (mtt-85) cc_final: 0.7859 (mtt90) REVERT: B 279 ASP cc_start: 0.8303 (t0) cc_final: 0.7958 (t0) REVERT: B 314 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7354 (ttmt) REVERT: B 323 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7925 (mpt-90) REVERT: B 345 MET cc_start: 0.8169 (mtm) cc_final: 0.7803 (mmm) REVERT: B 618 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8113 (mp) REVERT: B 628 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7766 (mtp180) REVERT: B 635 ASP cc_start: 0.7633 (t70) cc_final: 0.7011 (p0) REVERT: C 146 ARG cc_start: 0.7643 (mtm110) cc_final: 0.6979 (mtp85) REVERT: C 157 CYS cc_start: 0.8313 (m) cc_final: 0.7955 (p) REVERT: C 176 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6130 (mm-30) REVERT: C 177 GLU cc_start: 0.6888 (pm20) cc_final: 0.6645 (pm20) REVERT: C 234 LEU cc_start: 0.8213 (mp) cc_final: 0.7901 (mm) REVERT: C 263 ARG cc_start: 0.8137 (mtt-85) cc_final: 0.7843 (mtt90) REVERT: C 279 ASP cc_start: 0.8309 (t0) cc_final: 0.7981 (t0) REVERT: C 300 LYS cc_start: 0.8049 (mmtp) cc_final: 0.6713 (mppt) REVERT: C 314 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7379 (ttmt) REVERT: C 345 MET cc_start: 0.8126 (mtm) cc_final: 0.7845 (mmm) REVERT: C 442 MET cc_start: 0.8418 (mtt) cc_final: 0.8164 (mtp) REVERT: C 618 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7979 (mp) REVERT: C 635 ASP cc_start: 0.7681 (t70) cc_final: 0.7033 (p0) REVERT: D 146 ARG cc_start: 0.7615 (mtm110) cc_final: 0.6957 (mtp85) REVERT: D 157 CYS cc_start: 0.8274 (m) cc_final: 0.7934 (p) REVERT: D 176 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6146 (mm-30) REVERT: D 177 GLU cc_start: 0.6891 (pm20) cc_final: 0.6664 (pm20) REVERT: D 214 GLN cc_start: 0.7747 (mt0) cc_final: 0.7501 (mt0) REVERT: D 234 LEU cc_start: 0.8257 (mp) cc_final: 0.7923 (mm) REVERT: D 263 ARG cc_start: 0.8119 (mtt-85) cc_final: 0.7661 (mtt90) REVERT: D 279 ASP cc_start: 0.8329 (t0) cc_final: 0.7966 (t0) REVERT: D 290 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: D 300 LYS cc_start: 0.8040 (mmtp) cc_final: 0.6693 (mppt) REVERT: D 314 LYS cc_start: 0.7996 (ttpt) cc_final: 0.7350 (ttmt) REVERT: D 345 MET cc_start: 0.8175 (mtm) cc_final: 0.7844 (mmm) REVERT: D 442 MET cc_start: 0.8415 (mtt) cc_final: 0.8161 (mtp) REVERT: D 618 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8020 (mp) REVERT: D 635 ASP cc_start: 0.7631 (t70) cc_final: 0.7005 (p0) outliers start: 57 outliers final: 17 residues processed: 365 average time/residue: 1.3012 time to fit residues: 543.0878 Evaluate side-chains 340 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 315 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 136 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 242 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 144 optimal weight: 0.5980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 185 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 369 GLN C 185 HIS C 369 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.171728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122922 restraints weight = 21978.906| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.56 r_work: 0.3272 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22492 Z= 0.198 Angle : 0.605 6.884 30152 Z= 0.300 Chirality : 0.042 0.200 3232 Planarity : 0.005 0.048 3600 Dihedral : 18.382 129.586 5096 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.63 % Allowed : 12.76 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.17), residues: 2448 helix: 1.32 (0.14), residues: 1500 sheet: -1.11 (0.49), residues: 88 loop : -0.76 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 613 HIS 0.004 0.001 HIS B 582 PHE 0.013 0.002 PHE D 537 TYR 0.014 0.002 TYR B 555 ARG 0.002 0.000 ARG C 470 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 1077) hydrogen bonds : angle 3.64657 ( 3111) covalent geometry : bond 0.00489 (22492) covalent geometry : angle 0.60452 (30152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 336 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7083 (mtp85) REVERT: A 157 CYS cc_start: 0.8262 (m) cc_final: 0.7772 (p) REVERT: A 176 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6167 (mm-30) REVERT: A 234 LEU cc_start: 0.8328 (mp) cc_final: 0.7951 (mm) REVERT: A 263 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7803 (mtt90) REVERT: A 279 ASP cc_start: 0.8434 (t0) cc_final: 0.8127 (t0) REVERT: A 314 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7275 (ttmt) REVERT: A 442 MET cc_start: 0.8507 (mtt) cc_final: 0.8250 (mtp) REVERT: A 610 ARG cc_start: 0.7751 (tpp-160) cc_final: 0.7506 (tpp-160) REVERT: A 618 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7971 (mp) REVERT: B 157 CYS cc_start: 0.8250 (m) cc_final: 0.7777 (p) REVERT: B 176 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6164 (mm-30) REVERT: B 234 LEU cc_start: 0.8281 (mp) cc_final: 0.7866 (mm) REVERT: B 263 ARG cc_start: 0.8205 (mtt-85) cc_final: 0.7726 (mtt90) REVERT: B 279 ASP cc_start: 0.8413 (t0) cc_final: 0.8112 (t0) REVERT: B 314 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7238 (ttmt) REVERT: B 323 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7909 (mpt-90) REVERT: B 618 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8077 (mp) REVERT: B 628 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7750 (mtp180) REVERT: C 146 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7090 (mtp85) REVERT: C 157 CYS cc_start: 0.8282 (m) cc_final: 0.7783 (p) REVERT: C 176 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6126 (mm-30) REVERT: C 234 LEU cc_start: 0.8301 (mp) cc_final: 0.7928 (mm) REVERT: C 263 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7740 (mtt90) REVERT: C 279 ASP cc_start: 0.8452 (t0) cc_final: 0.8228 (t0) REVERT: C 314 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7389 (ttmt) REVERT: C 442 MET cc_start: 0.8525 (mtt) cc_final: 0.8273 (mtp) REVERT: C 610 ARG cc_start: 0.7729 (tpp-160) cc_final: 0.7499 (tpp-160) REVERT: C 618 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7986 (mp) REVERT: D 157 CYS cc_start: 0.8265 (m) cc_final: 0.7771 (p) REVERT: D 176 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6139 (mm-30) REVERT: D 177 GLU cc_start: 0.7045 (pm20) cc_final: 0.6723 (pm20) REVERT: D 234 LEU cc_start: 0.8318 (mp) cc_final: 0.7925 (mm) REVERT: D 263 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.7810 (mtt90) REVERT: D 314 LYS cc_start: 0.7984 (ttpt) cc_final: 0.7275 (ttmt) REVERT: D 442 MET cc_start: 0.8479 (mtt) cc_final: 0.8249 (mtp) REVERT: D 610 ARG cc_start: 0.7708 (tpp-160) cc_final: 0.7482 (tpp-160) REVERT: D 618 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8073 (mp) outliers start: 56 outliers final: 29 residues processed: 356 average time/residue: 1.3260 time to fit residues: 540.5026 Evaluate side-chains 355 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 319 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 42 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 369 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.172086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123676 restraints weight = 21853.212| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.55 r_work: 0.3282 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22492 Z= 0.174 Angle : 0.577 6.685 30152 Z= 0.288 Chirality : 0.041 0.199 3232 Planarity : 0.005 0.048 3600 Dihedral : 17.801 123.353 5096 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.81 % Allowed : 13.23 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2448 helix: 1.42 (0.13), residues: 1500 sheet: -1.05 (0.49), residues: 88 loop : -0.73 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 613 HIS 0.003 0.001 HIS A 582 PHE 0.011 0.001 PHE B 512 TYR 0.013 0.002 TYR B 555 ARG 0.002 0.000 ARG A 584 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 1077) hydrogen bonds : angle 3.59621 ( 3111) covalent geometry : bond 0.00424 (22492) covalent geometry : angle 0.57692 (30152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 322 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7757 (mtm110) cc_final: 0.7092 (mtp85) REVERT: A 157 CYS cc_start: 0.8235 (m) cc_final: 0.7779 (p) REVERT: A 176 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6208 (mm-30) REVERT: A 177 GLU cc_start: 0.7029 (pm20) cc_final: 0.6817 (pm20) REVERT: A 234 LEU cc_start: 0.8293 (mp) cc_final: 0.7941 (mm) REVERT: A 263 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.7805 (mtt90) REVERT: A 279 ASP cc_start: 0.8439 (t0) cc_final: 0.8103 (t0) REVERT: A 314 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7335 (ttmt) REVERT: A 442 MET cc_start: 0.8490 (mtt) cc_final: 0.8195 (mtp) REVERT: A 610 ARG cc_start: 0.7716 (tpp-160) cc_final: 0.7461 (tpp-160) REVERT: A 618 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8032 (mp) REVERT: B 157 CYS cc_start: 0.8235 (m) cc_final: 0.7810 (p) REVERT: B 176 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6208 (mm-30) REVERT: B 177 GLU cc_start: 0.7087 (pm20) cc_final: 0.6857 (pm20) REVERT: B 234 LEU cc_start: 0.8304 (mp) cc_final: 0.7932 (mm) REVERT: B 263 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7792 (mtt90) REVERT: B 279 ASP cc_start: 0.8452 (t0) cc_final: 0.8134 (t0) REVERT: B 314 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7301 (ttmt) REVERT: B 323 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7912 (mpt-90) REVERT: B 618 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8126 (mp) REVERT: B 628 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7767 (mtp180) REVERT: C 146 ARG cc_start: 0.7757 (mtm110) cc_final: 0.7087 (mtp85) REVERT: C 157 CYS cc_start: 0.8297 (m) cc_final: 0.7832 (p) REVERT: C 176 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6159 (mm-30) REVERT: C 214 GLN cc_start: 0.7626 (mt0) cc_final: 0.7401 (mt0) REVERT: C 234 LEU cc_start: 0.8293 (mp) cc_final: 0.7946 (mm) REVERT: C 263 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7795 (mtt90) REVERT: C 279 ASP cc_start: 0.8477 (t0) cc_final: 0.8157 (t0) REVERT: C 314 LYS cc_start: 0.8008 (ttpt) cc_final: 0.7433 (ttmt) REVERT: C 442 MET cc_start: 0.8501 (mtt) cc_final: 0.8214 (mtp) REVERT: C 610 ARG cc_start: 0.7704 (tpp-160) cc_final: 0.7474 (tpp-160) REVERT: C 618 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8044 (mp) REVERT: D 157 CYS cc_start: 0.8281 (m) cc_final: 0.7811 (p) REVERT: D 176 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6185 (mm-30) REVERT: D 234 LEU cc_start: 0.8292 (mp) cc_final: 0.7928 (mm) REVERT: D 263 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7811 (mtt90) REVERT: D 314 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7293 (ttmt) REVERT: D 442 MET cc_start: 0.8487 (mtt) cc_final: 0.8193 (mtp) REVERT: D 610 ARG cc_start: 0.7688 (tpp-160) cc_final: 0.7463 (tpp-160) REVERT: D 618 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8127 (mp) outliers start: 60 outliers final: 29 residues processed: 350 average time/residue: 1.3221 time to fit residues: 528.5349 Evaluate side-chains 354 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 317 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 32 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 191 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 369 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 369 GLN B 546 ASN C 185 HIS C 369 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.174072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125918 restraints weight = 21826.305| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.54 r_work: 0.3316 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22492 Z= 0.127 Angle : 0.525 6.240 30152 Z= 0.263 Chirality : 0.039 0.184 3232 Planarity : 0.005 0.048 3600 Dihedral : 16.977 109.129 5096 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.44 % Allowed : 13.84 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2448 helix: 1.62 (0.14), residues: 1500 sheet: -1.00 (0.50), residues: 88 loop : -0.62 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 495 HIS 0.002 0.001 HIS A 201 PHE 0.009 0.001 PHE A 537 TYR 0.012 0.001 TYR B 555 ARG 0.002 0.000 ARG C 33 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 1077) hydrogen bonds : angle 3.49412 ( 3111) covalent geometry : bond 0.00300 (22492) covalent geometry : angle 0.52535 (30152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 309 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7616 (mtm110) cc_final: 0.6940 (mtp85) REVERT: A 157 CYS cc_start: 0.8208 (m) cc_final: 0.7819 (p) REVERT: A 176 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6143 (mm-30) REVERT: A 177 GLU cc_start: 0.6911 (pm20) cc_final: 0.6672 (pm20) REVERT: A 234 LEU cc_start: 0.8236 (mp) cc_final: 0.7890 (mm) REVERT: A 263 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7878 (mtt90) REVERT: A 279 ASP cc_start: 0.8398 (t0) cc_final: 0.8088 (t0) REVERT: A 314 LYS cc_start: 0.7883 (ttpt) cc_final: 0.7186 (ttmt) REVERT: A 442 MET cc_start: 0.8378 (mtt) cc_final: 0.8120 (mtp) REVERT: A 610 ARG cc_start: 0.7629 (tpp-160) cc_final: 0.7387 (tpp-160) REVERT: A 618 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8032 (mp) REVERT: B 146 ARG cc_start: 0.7639 (mtm110) cc_final: 0.6988 (mtp85) REVERT: B 157 CYS cc_start: 0.8210 (m) cc_final: 0.7863 (p) REVERT: B 176 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6145 (mm-30) REVERT: B 177 GLU cc_start: 0.6880 (pm20) cc_final: 0.6654 (pm20) REVERT: B 234 LEU cc_start: 0.8217 (mp) cc_final: 0.7851 (mm) REVERT: B 263 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7832 (mtt90) REVERT: B 279 ASP cc_start: 0.8422 (t0) cc_final: 0.8113 (t0) REVERT: B 314 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7160 (ttmt) REVERT: B 323 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7870 (mpt-90) REVERT: B 618 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8075 (mp) REVERT: B 628 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7681 (mtp180) REVERT: C 146 ARG cc_start: 0.7596 (mtm110) cc_final: 0.6921 (mtp85) REVERT: C 157 CYS cc_start: 0.8234 (m) cc_final: 0.7841 (p) REVERT: C 176 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6110 (mm-30) REVERT: C 234 LEU cc_start: 0.8220 (mp) cc_final: 0.7879 (mm) REVERT: C 263 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7686 (mtt90) REVERT: C 279 ASP cc_start: 0.8449 (t0) cc_final: 0.8110 (t0) REVERT: C 314 LYS cc_start: 0.7862 (ttpt) cc_final: 0.7275 (ttmt) REVERT: C 442 MET cc_start: 0.8411 (mtt) cc_final: 0.8161 (mtp) REVERT: C 610 ARG cc_start: 0.7670 (tpp-160) cc_final: 0.7441 (tpp-160) REVERT: C 618 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8029 (mp) REVERT: D 146 ARG cc_start: 0.7573 (mtm110) cc_final: 0.6874 (mtp85) REVERT: D 157 CYS cc_start: 0.8246 (m) cc_final: 0.7859 (p) REVERT: D 176 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6148 (mm-30) REVERT: D 234 LEU cc_start: 0.8221 (mp) cc_final: 0.7860 (mm) REVERT: D 263 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7877 (mtt90) REVERT: D 279 ASP cc_start: 0.8430 (t0) cc_final: 0.8115 (t0) REVERT: D 290 GLN cc_start: 0.8459 (mt0) cc_final: 0.8189 (mt0) REVERT: D 314 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7140 (ttmt) REVERT: D 442 MET cc_start: 0.8391 (mtt) cc_final: 0.8136 (mtp) REVERT: D 610 ARG cc_start: 0.7664 (tpp-160) cc_final: 0.7439 (tpp-160) REVERT: D 618 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8024 (mp) outliers start: 52 outliers final: 29 residues processed: 333 average time/residue: 1.4058 time to fit residues: 537.0103 Evaluate side-chains 341 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 611 CYS Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 553 PHE Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 137 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 369 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.173692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126388 restraints weight = 21991.381| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.59 r_work: 0.3317 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22492 Z= 0.138 Angle : 0.541 6.330 30152 Z= 0.271 Chirality : 0.039 0.188 3232 Planarity : 0.005 0.048 3600 Dihedral : 16.699 98.282 5096 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.49 % Allowed : 14.21 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.17), residues: 2448 helix: 1.65 (0.14), residues: 1500 sheet: -0.95 (0.50), residues: 88 loop : -0.57 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 583 HIS 0.003 0.001 HIS B 201 PHE 0.010 0.001 PHE D 537 TYR 0.012 0.002 TYR C 555 ARG 0.002 0.000 ARG D 589 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 1077) hydrogen bonds : angle 3.49319 ( 3111) covalent geometry : bond 0.00329 (22492) covalent geometry : angle 0.54084 (30152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 308 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7569 (mtm110) cc_final: 0.6886 (mtp85) REVERT: A 157 CYS cc_start: 0.8201 (m) cc_final: 0.7801 (p) REVERT: A 176 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6115 (mm-30) REVERT: A 177 GLU cc_start: 0.6897 (pm20) cc_final: 0.6640 (pm20) REVERT: A 234 LEU cc_start: 0.8262 (mp) cc_final: 0.7918 (mm) REVERT: A 263 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7884 (mtt90) REVERT: A 279 ASP cc_start: 0.8392 (t0) cc_final: 0.8095 (t0) REVERT: A 314 LYS cc_start: 0.7889 (ttpt) cc_final: 0.7189 (ttmt) REVERT: A 442 MET cc_start: 0.8380 (mtt) cc_final: 0.8111 (mtp) REVERT: A 610 ARG cc_start: 0.7683 (tpp-160) cc_final: 0.7451 (tpp-160) REVERT: A 618 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8044 (mp) REVERT: B 157 CYS cc_start: 0.8224 (m) cc_final: 0.7846 (p) REVERT: B 176 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6163 (mm-30) REVERT: B 177 GLU cc_start: 0.6895 (pm20) cc_final: 0.6627 (pm20) REVERT: B 234 LEU cc_start: 0.8211 (mp) cc_final: 0.7843 (mm) REVERT: B 263 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7849 (mtt90) REVERT: B 279 ASP cc_start: 0.8402 (t0) cc_final: 0.8093 (t0) REVERT: B 314 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7155 (ttmt) REVERT: B 323 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7880 (mpt-90) REVERT: B 618 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8071 (mp) REVERT: B 628 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7718 (mtp180) REVERT: C 146 ARG cc_start: 0.7581 (mtm110) cc_final: 0.6901 (mtp85) REVERT: C 157 CYS cc_start: 0.8232 (m) cc_final: 0.7819 (p) REVERT: C 176 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6123 (mm-30) REVERT: C 177 GLU cc_start: 0.6760 (pm20) cc_final: 0.6079 (pt0) REVERT: C 214 GLN cc_start: 0.7506 (mt0) cc_final: 0.7287 (mt0) REVERT: C 234 LEU cc_start: 0.8234 (mp) cc_final: 0.7893 (mm) REVERT: C 263 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7675 (mtt90) REVERT: C 279 ASP cc_start: 0.8430 (t0) cc_final: 0.8114 (t0) REVERT: C 314 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7278 (ttmt) REVERT: C 442 MET cc_start: 0.8415 (mtt) cc_final: 0.8153 (mtp) REVERT: C 610 ARG cc_start: 0.7685 (tpp-160) cc_final: 0.7470 (tpp-160) REVERT: C 618 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8044 (mp) REVERT: D 146 ARG cc_start: 0.7606 (mtm110) cc_final: 0.6963 (mtp85) REVERT: D 157 CYS cc_start: 0.8240 (m) cc_final: 0.7825 (p) REVERT: D 176 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6143 (mm-30) REVERT: D 177 GLU cc_start: 0.6760 (pm20) cc_final: 0.6068 (pt0) REVERT: D 234 LEU cc_start: 0.8214 (mp) cc_final: 0.7860 (mm) REVERT: D 263 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7881 (mtt90) REVERT: D 279 ASP cc_start: 0.8419 (t0) cc_final: 0.8103 (t0) REVERT: D 290 GLN cc_start: 0.8455 (mt0) cc_final: 0.8187 (mt0) REVERT: D 314 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7140 (ttmt) REVERT: D 442 MET cc_start: 0.8354 (mtt) cc_final: 0.8088 (mtp) REVERT: D 610 ARG cc_start: 0.7671 (tpp-160) cc_final: 0.7463 (tpp-160) REVERT: D 618 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8078 (mp) outliers start: 53 outliers final: 31 residues processed: 332 average time/residue: 1.3490 time to fit residues: 511.4104 Evaluate side-chains 347 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 308 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 234 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.173161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125838 restraints weight = 21762.264| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.54 r_work: 0.3314 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22492 Z= 0.150 Angle : 0.555 6.965 30152 Z= 0.277 Chirality : 0.040 0.192 3232 Planarity : 0.005 0.048 3600 Dihedral : 16.544 91.779 5096 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.39 % Allowed : 14.26 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.17), residues: 2448 helix: 1.63 (0.14), residues: 1500 sheet: -0.94 (0.49), residues: 88 loop : -0.55 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 583 HIS 0.003 0.001 HIS B 201 PHE 0.010 0.001 PHE A 512 TYR 0.013 0.002 TYR B 555 ARG 0.002 0.000 ARG B 584 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 1077) hydrogen bonds : angle 3.50702 ( 3111) covalent geometry : bond 0.00362 (22492) covalent geometry : angle 0.55493 (30152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 311 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7032 (mtp85) REVERT: A 157 CYS cc_start: 0.8214 (m) cc_final: 0.7804 (p) REVERT: A 176 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6446 (mp0) REVERT: A 177 GLU cc_start: 0.6923 (pm20) cc_final: 0.6632 (pm20) REVERT: A 234 LEU cc_start: 0.8288 (mp) cc_final: 0.7955 (mm) REVERT: A 263 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7927 (mtt90) REVERT: A 279 ASP cc_start: 0.8400 (t0) cc_final: 0.8119 (t0) REVERT: A 314 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7216 (ttmt) REVERT: A 442 MET cc_start: 0.8446 (mtt) cc_final: 0.8185 (mtp) REVERT: A 589 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7946 (ttp-110) REVERT: A 610 ARG cc_start: 0.7707 (tpp-160) cc_final: 0.7478 (tpp-160) REVERT: A 618 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8086 (mp) REVERT: B 146 ARG cc_start: 0.7650 (mtm110) cc_final: 0.6901 (mtp85) REVERT: B 157 CYS cc_start: 0.8225 (m) cc_final: 0.7840 (p) REVERT: B 176 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6139 (mm-30) REVERT: B 177 GLU cc_start: 0.6953 (pm20) cc_final: 0.6653 (pm20) REVERT: B 234 LEU cc_start: 0.8270 (mp) cc_final: 0.7905 (mm) REVERT: B 263 ARG cc_start: 0.8149 (mtt-85) cc_final: 0.7909 (mtt90) REVERT: B 279 ASP cc_start: 0.8412 (t0) cc_final: 0.8124 (t0) REVERT: B 314 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7230 (ttmt) REVERT: B 323 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7904 (mpt-90) REVERT: B 618 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8118 (mp) REVERT: B 628 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7746 (mtp180) REVERT: C 146 ARG cc_start: 0.7650 (mtm110) cc_final: 0.6970 (mtp85) REVERT: C 157 CYS cc_start: 0.8255 (m) cc_final: 0.7837 (p) REVERT: C 176 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6173 (mm-30) REVERT: C 214 GLN cc_start: 0.7650 (mt0) cc_final: 0.7429 (mt0) REVERT: C 234 LEU cc_start: 0.8273 (mp) cc_final: 0.7944 (mm) REVERT: C 263 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7756 (mtt90) REVERT: C 314 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7332 (ttmt) REVERT: C 442 MET cc_start: 0.8454 (mtt) cc_final: 0.8201 (mtp) REVERT: C 610 ARG cc_start: 0.7742 (tpp-160) cc_final: 0.7529 (tpp-160) REVERT: C 618 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8088 (mp) REVERT: D 157 CYS cc_start: 0.8257 (m) cc_final: 0.7825 (p) REVERT: D 176 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6177 (mm-30) REVERT: D 177 GLU cc_start: 0.6851 (pm20) cc_final: 0.6125 (pt0) REVERT: D 214 GLN cc_start: 0.7669 (mt0) cc_final: 0.7450 (mt0) REVERT: D 234 LEU cc_start: 0.8255 (mp) cc_final: 0.7890 (mm) REVERT: D 263 ARG cc_start: 0.8165 (mtt-85) cc_final: 0.7929 (mtt90) REVERT: D 290 GLN cc_start: 0.8460 (mt0) cc_final: 0.8193 (mt0) REVERT: D 314 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7260 (ttmt) REVERT: D 442 MET cc_start: 0.8451 (mtt) cc_final: 0.8192 (mtp) REVERT: D 610 ARG cc_start: 0.7697 (tpp-160) cc_final: 0.7492 (tpp-160) REVERT: D 618 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8118 (mp) outliers start: 51 outliers final: 32 residues processed: 333 average time/residue: 1.4315 time to fit residues: 541.3793 Evaluate side-chains 349 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 308 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 90 optimal weight: 0.0980 chunk 27 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 190 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 369 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN C 185 HIS C 369 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 369 GLN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.174080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.126921 restraints weight = 21867.906| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.58 r_work: 0.3323 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22492 Z= 0.131 Angle : 0.535 7.730 30152 Z= 0.267 Chirality : 0.039 0.187 3232 Planarity : 0.005 0.048 3600 Dihedral : 16.270 87.156 5096 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.97 % Allowed : 14.73 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2448 helix: 1.72 (0.14), residues: 1500 sheet: -0.88 (0.50), residues: 88 loop : -0.51 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 583 HIS 0.003 0.001 HIS B 185 PHE 0.009 0.001 PHE D 537 TYR 0.012 0.002 TYR C 555 ARG 0.001 0.000 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 1077) hydrogen bonds : angle 3.46346 ( 3111) covalent geometry : bond 0.00311 (22492) covalent geometry : angle 0.53489 (30152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7575 (mtm110) cc_final: 0.6889 (mtp85) REVERT: A 157 CYS cc_start: 0.8178 (m) cc_final: 0.7804 (p) REVERT: A 176 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6422 (mp0) REVERT: A 177 GLU cc_start: 0.6909 (pm20) cc_final: 0.6675 (pm20) REVERT: A 234 LEU cc_start: 0.8257 (mp) cc_final: 0.7927 (mm) REVERT: A 263 ARG cc_start: 0.8137 (mtt-85) cc_final: 0.7903 (mtt90) REVERT: A 279 ASP cc_start: 0.8388 (t0) cc_final: 0.8095 (t0) REVERT: A 314 LYS cc_start: 0.7884 (ttpt) cc_final: 0.7182 (ttmt) REVERT: A 442 MET cc_start: 0.8355 (mtt) cc_final: 0.8088 (mtp) REVERT: A 589 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7912 (ttp-110) REVERT: A 610 ARG cc_start: 0.7684 (tpp-160) cc_final: 0.7462 (tpp-160) REVERT: A 618 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8053 (mp) REVERT: B 146 ARG cc_start: 0.7556 (mtm110) cc_final: 0.6821 (mtp85) REVERT: B 157 CYS cc_start: 0.8181 (m) cc_final: 0.7856 (p) REVERT: B 176 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6373 (mp0) REVERT: B 177 GLU cc_start: 0.6912 (pm20) cc_final: 0.6595 (pm20) REVERT: B 234 LEU cc_start: 0.8196 (mp) cc_final: 0.7838 (mm) REVERT: B 263 ARG cc_start: 0.8091 (mtt-85) cc_final: 0.7865 (mtt90) REVERT: B 279 ASP cc_start: 0.8391 (t0) cc_final: 0.8089 (t0) REVERT: B 314 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7124 (ttmt) REVERT: B 323 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7850 (mpt-90) REVERT: B 618 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8061 (mp) REVERT: C 146 ARG cc_start: 0.7556 (mtm110) cc_final: 0.6870 (mtp85) REVERT: C 157 CYS cc_start: 0.8202 (m) cc_final: 0.7821 (p) REVERT: C 176 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6121 (mm-30) REVERT: C 177 GLU cc_start: 0.6745 (pm20) cc_final: 0.6047 (pt0) REVERT: C 214 GLN cc_start: 0.7487 (mt0) cc_final: 0.7266 (mt0) REVERT: C 234 LEU cc_start: 0.8249 (mp) cc_final: 0.7921 (mm) REVERT: C 263 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7844 (mtt90) REVERT: C 279 ASP cc_start: 0.8337 (t0) cc_final: 0.8067 (t0) REVERT: C 314 LYS cc_start: 0.7848 (ttpt) cc_final: 0.7259 (ttmt) REVERT: C 442 MET cc_start: 0.8360 (mtt) cc_final: 0.8097 (mtp) REVERT: C 610 ARG cc_start: 0.7664 (tpp-160) cc_final: 0.7453 (tpp-160) REVERT: C 618 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8043 (mp) REVERT: D 146 ARG cc_start: 0.7585 (mtm110) cc_final: 0.6945 (mtp85) REVERT: D 157 CYS cc_start: 0.8240 (m) cc_final: 0.7844 (p) REVERT: D 176 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6138 (mm-30) REVERT: D 177 GLU cc_start: 0.6809 (pm20) cc_final: 0.6098 (pt0) REVERT: D 234 LEU cc_start: 0.8225 (mp) cc_final: 0.7867 (mm) REVERT: D 263 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7886 (mtt90) REVERT: D 279 ASP cc_start: 0.8309 (t0) cc_final: 0.8044 (t0) REVERT: D 290 GLN cc_start: 0.8461 (mt0) cc_final: 0.8200 (mt0) REVERT: D 314 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7130 (ttmt) REVERT: D 442 MET cc_start: 0.8344 (mtt) cc_final: 0.8073 (mtp) REVERT: D 589 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7921 (ttp-110) REVERT: D 618 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8087 (mp) outliers start: 42 outliers final: 30 residues processed: 323 average time/residue: 1.4790 time to fit residues: 544.8148 Evaluate side-chains 338 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 299 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 76 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS B 369 GLN C 185 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.172233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124764 restraints weight = 21821.903| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.55 r_work: 0.3295 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 45 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22492 Z= 0.179 Angle : 0.585 8.068 30152 Z= 0.290 Chirality : 0.041 0.196 3232 Planarity : 0.005 0.048 3600 Dihedral : 16.470 91.404 5096 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.30 % Allowed : 14.45 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.17), residues: 2448 helix: 1.61 (0.13), residues: 1500 sheet: -0.91 (0.49), residues: 88 loop : -0.57 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 583 HIS 0.004 0.001 HIS B 185 PHE 0.012 0.001 PHE A 512 TYR 0.014 0.002 TYR C 555 ARG 0.002 0.000 ARG C 584 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 1077) hydrogen bonds : angle 3.54572 ( 3111) covalent geometry : bond 0.00437 (22492) covalent geometry : angle 0.58461 (30152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19227.50 seconds wall clock time: 328 minutes 49.91 seconds (19729.91 seconds total)