Starting phenix.real_space_refine on Wed Mar 4 09:35:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nez_12295/03_2026/7nez_12295_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nez_12295/03_2026/7nez_12295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nez_12295/03_2026/7nez_12295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nez_12295/03_2026/7nez_12295.map" model { file = "/net/cci-nas-00/data/ceres_data/7nez_12295/03_2026/7nez_12295_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nez_12295/03_2026/7nez_12295_neut_trim.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 7965 2.51 5 N 2033 2.21 5 O 2279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12345 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4379 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 18, 'TRANS': 544} Chain breaks: 3 Chain: "B" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4379 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 18, 'TRANS': 544} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'TTC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.70, per 1000 atoms: 0.22 Number of scatterers: 12345 At special positions: 0 Unit cell: (101.64, 97.02, 144.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2279 8.00 N 2033 7.00 C 7965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 507.7 milliseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 18 sheets defined 43.4% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.911A pdb=" N ASP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 153 through 163 removed outlier: 4.035A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.895A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.519A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 271 through 277 removed outlier: 4.147A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.565A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.625A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 390 removed outlier: 3.582A pdb=" N SER A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.850A pdb=" N VAL A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 442 Processing helix chain 'A' and resid 444 through 451 removed outlier: 3.633A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.761A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 484 through 498 removed outlier: 4.021A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 528 removed outlier: 3.680A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.620A pdb=" N ILE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.656A pdb=" N ILE A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.640A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.748A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 623 through 650 removed outlier: 3.831A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.911A pdb=" N ASP B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 153 through 163 removed outlier: 4.036A pdb=" N ILE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.894A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.519A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 271 through 277 removed outlier: 4.146A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.566A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.625A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 removed outlier: 3.582A pdb=" N SER B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 413 removed outlier: 3.591A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 441 Processing helix chain 'B' and resid 443 through 451 removed outlier: 3.808A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 465 through 477 removed outlier: 3.761A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 484 Processing helix chain 'B' and resid 484 through 498 removed outlier: 4.021A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 527 removed outlier: 3.680A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 551 removed outlier: 3.647A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.657A pdb=" N ILE B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.640A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.748A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 578 " --> pdb=" O PRO B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 650 removed outlier: 3.832A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.590A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.591A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71 removed outlier: 3.571A pdb=" N GLY A 69 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS A 40 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.191A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 241 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 75 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 268 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 258 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.570A pdb=" N GLY B 69 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS B 40 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.191A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 75 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N THR B 257 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA B 77 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU B 259 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU B 79 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 268 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 258 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.654A pdb=" N TYR C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.394A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.034A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.034A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.653A pdb=" N TYR E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.394A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AB8, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.034A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.034A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1494 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: 1.99 Time building geometry restraints manager: 0.97 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: 1948 1.31 - 1.43: 3535 1.43 - 1.56: 7021 1.56 - 1.69: 11 1.69 - 1.82: 106 Bond restraints: 12621 Sorted by residual: bond pdb=" C16 TTC A1201 " pdb=" C17 TTC A1201 " ideal model delta sigma weight residual 1.411 1.641 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C13 TTC A1201 " pdb=" C17 TTC A1201 " ideal model delta sigma weight residual 1.359 1.571 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C15 TTC A1201 " pdb=" C16 TTC A1201 " ideal model delta sigma weight residual 1.364 1.557 -0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" C14 TTC A1201 " pdb=" C15 TTC A1201 " ideal model delta sigma weight residual 1.441 1.631 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" C13 TTC A1201 " pdb=" C9 TTC A1201 " ideal model delta sigma weight residual 1.456 1.630 -0.174 2.00e-02 2.50e+03 7.58e+01 ... (remaining 12616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 16762 2.53 - 5.06: 298 5.06 - 7.59: 37 7.59 - 10.13: 5 10.13 - 12.66: 5 Bond angle restraints: 17107 Sorted by residual: angle pdb=" N VAL B 442 " pdb=" CA VAL B 442 " pdb=" C VAL B 442 " ideal model delta sigma weight residual 112.17 100.50 11.67 9.50e-01 1.11e+00 1.51e+02 angle pdb=" N THR A 402 " pdb=" CA THR A 402 " pdb=" C THR A 402 " ideal model delta sigma weight residual 111.36 99.81 11.55 1.09e+00 8.42e-01 1.12e+02 angle pdb=" N GLY A 406 " pdb=" CA GLY A 406 " pdb=" C GLY A 406 " ideal model delta sigma weight residual 113.86 101.20 12.66 1.50e+00 4.44e-01 7.12e+01 angle pdb=" C ILE B 543 " pdb=" CA ILE B 543 " pdb=" CB ILE B 543 " ideal model delta sigma weight residual 112.14 101.79 10.35 1.35e+00 5.49e-01 5.88e+01 angle pdb=" N LEU B 430 " pdb=" CA LEU B 430 " pdb=" C LEU B 430 " ideal model delta sigma weight residual 111.07 103.60 7.47 1.07e+00 8.73e-01 4.88e+01 ... (remaining 17102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 7097 15.75 - 31.50: 309 31.50 - 47.26: 61 47.26 - 63.01: 7 63.01 - 78.76: 8 Dihedral angle restraints: 7482 sinusoidal: 2966 harmonic: 4516 Sorted by residual: dihedral pdb=" C PHE A 439 " pdb=" N PHE A 439 " pdb=" CA PHE A 439 " pdb=" CB PHE A 439 " ideal model delta harmonic sigma weight residual -122.60 -140.56 17.96 0 2.50e+00 1.60e-01 5.16e+01 dihedral pdb=" N PHE A 439 " pdb=" C PHE A 439 " pdb=" CA PHE A 439 " pdb=" CB PHE A 439 " ideal model delta harmonic sigma weight residual 122.80 137.58 -14.78 0 2.50e+00 1.60e-01 3.49e+01 dihedral pdb=" C THR A 402 " pdb=" N THR A 402 " pdb=" CA THR A 402 " pdb=" CB THR A 402 " ideal model delta harmonic sigma weight residual -122.00 -108.52 -13.48 0 2.50e+00 1.60e-01 2.91e+01 ... (remaining 7479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1913 0.152 - 0.304: 28 0.304 - 0.456: 9 0.456 - 0.607: 0 0.607 - 0.759: 1 Chirality restraints: 1951 Sorted by residual: chirality pdb=" CA PHE A 439 " pdb=" N PHE A 439 " pdb=" C PHE A 439 " pdb=" CB PHE A 439 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA GLN B 126 " pdb=" N GLN B 126 " pdb=" C GLN B 126 " pdb=" CB GLN B 126 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" C21 TTC A1201 " pdb=" C16 TTC A1201 " pdb=" C20 TTC A1201 " pdb=" O24 TTC A1201 " both_signs ideal model delta sigma weight residual False -2.50 -2.90 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 1948 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 440 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C SER B 440 " -0.067 2.00e-02 2.50e+03 pdb=" O SER B 440 " 0.025 2.00e-02 2.50e+03 pdb=" N SER B 441 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 437 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C GLN A 437 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN A 437 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS A 438 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 125 " -0.016 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C VAL B 125 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL B 125 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN B 126 " -0.017 2.00e-02 2.50e+03 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 97 2.55 - 3.13: 10101 3.13 - 3.72: 18747 3.72 - 4.31: 27089 4.31 - 4.90: 44567 Nonbonded interactions: 100601 Sorted by model distance: nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 1.958 3.040 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 1.958 3.040 nonbonded pdb=" OH TYR C 36 " pdb=" OE1 GLN C 89 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR E 36 " pdb=" OE1 GLN E 89 " model vdw 2.183 3.040 nonbonded pdb=" O ILE C 2 " pdb=" OG1 THR C 97 " model vdw 2.183 3.040 ... (remaining 100596 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 35 through 654 or resid 1202)) selection = (chain 'B' and (resid 35 through 654 or resid 702)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'D' and resid 2 through 119) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.100 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 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 : 0.009 0.230 12628 Z= 0.544 Angle : 0.798 12.658 17121 Z= 0.499 Chirality : 0.059 0.759 1951 Planarity : 0.004 0.038 2130 Dihedral : 9.749 78.761 4577 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.67 % Allowed : 3.79 % Favored : 95.54 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.20), residues: 1552 helix: -1.06 (0.19), residues: 602 sheet: -1.96 (0.30), residues: 252 loop : -1.92 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 61 TYR 0.013 0.001 TYR F 95 PHE 0.021 0.002 PHE B 545 TRP 0.011 0.001 TRP B 627 HIS 0.004 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00889 (12621) covalent geometry : angle 0.79619 (17107) SS BOND : bond 0.00221 ( 7) SS BOND : angle 2.24724 ( 14) hydrogen bonds : bond 0.18223 ( 498) hydrogen bonds : angle 7.89009 ( 1494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 384 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LEU cc_start: 0.8216 (mt) cc_final: 0.8014 (tp) REVERT: A 186 VAL cc_start: 0.5535 (t) cc_final: 0.4964 (p) REVERT: A 198 MET cc_start: 0.6399 (mtp) cc_final: 0.6190 (mtp) REVERT: A 264 LEU cc_start: 0.5610 (tp) cc_final: 0.5375 (tp) REVERT: A 446 GLU cc_start: 0.8823 (tt0) cc_final: 0.8373 (tm-30) REVERT: A 450 VAL cc_start: 0.8924 (t) cc_final: 0.8504 (m) REVERT: A 475 LEU cc_start: 0.8404 (tp) cc_final: 0.8156 (mp) REVERT: A 491 CYS cc_start: 0.7666 (m) cc_final: 0.7280 (m) REVERT: A 509 MET cc_start: 0.7875 (ttt) cc_final: 0.7558 (ttp) REVERT: A 534 VAL cc_start: 0.8622 (t) cc_final: 0.8353 (m) REVERT: A 544 CYS cc_start: 0.9028 (m) cc_final: 0.8582 (m) REVERT: B 152 MET cc_start: -0.0101 (mtp) cc_final: -0.0373 (mmp) REVERT: B 198 MET cc_start: 0.6646 (mtp) cc_final: 0.6350 (mmt) REVERT: B 227 LEU cc_start: 0.6829 (tp) cc_final: 0.6305 (tp) REVERT: B 255 SER cc_start: 0.7377 (t) cc_final: 0.6606 (t) REVERT: B 288 ASN cc_start: 0.7414 (t0) cc_final: 0.6931 (p0) REVERT: B 523 MET cc_start: 0.8768 (ttt) cc_final: 0.8416 (ttm) REVERT: B 540 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8651 (mp) REVERT: B 544 CYS cc_start: 0.9257 (m) cc_final: 0.8944 (m) REVERT: B 584 ASN cc_start: 0.7632 (t0) cc_final: 0.7421 (t0) REVERT: C 17 ASP cc_start: 0.7552 (t70) cc_final: 0.7149 (t0) REVERT: D 6 GLU cc_start: 0.8112 (mp0) cc_final: 0.7891 (mp0) REVERT: D 44 LYS cc_start: 0.7895 (mptp) cc_final: 0.7609 (mmtm) REVERT: E 17 ASP cc_start: 0.6756 (t70) cc_final: 0.5919 (m-30) REVERT: E 33 LEU cc_start: 0.8864 (tm) cc_final: 0.8631 (tm) REVERT: E 79 GLN cc_start: 0.8234 (mm110) cc_final: 0.8017 (mm-40) REVERT: F 100 TYR cc_start: 0.7193 (t80) cc_final: 0.6868 (t80) outliers start: 9 outliers final: 3 residues processed: 391 average time/residue: 0.1091 time to fit residues: 61.1386 Evaluate side-chains 236 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 540 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0020 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 66 ASN A 116 ASN A 120 ASN A 243 HIS A 375 HIS A 425 ASN B 109 ASN B 243 HIS B 582 GLN B 617 GLN D 5 GLN D 78 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.151366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.121453 restraints weight = 24083.846| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.91 r_work: 0.3603 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12628 Z= 0.167 Angle : 0.679 7.971 17121 Z= 0.347 Chirality : 0.045 0.210 1951 Planarity : 0.004 0.040 2130 Dihedral : 7.205 62.340 1806 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.20 % Allowed : 10.71 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.21), residues: 1552 helix: -0.21 (0.20), residues: 640 sheet: -1.56 (0.31), residues: 256 loop : -1.81 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.024 0.002 TYR E 91 PHE 0.023 0.002 PHE A 250 TRP 0.018 0.002 TRP B 379 HIS 0.008 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00376 (12621) covalent geometry : angle 0.67858 (17107) SS BOND : bond 0.00666 ( 7) SS BOND : angle 0.92583 ( 14) hydrogen bonds : bond 0.04468 ( 498) hydrogen bonds : angle 5.17117 ( 1494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.5218 (t-90) cc_final: 0.4980 (t-170) REVERT: A 193 ARG cc_start: 0.7371 (mtt180) cc_final: 0.7086 (mtp85) REVERT: A 198 MET cc_start: 0.6918 (mtp) cc_final: 0.6683 (mtp) REVERT: A 211 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6684 (pp20) REVERT: A 227 LEU cc_start: 0.6981 (tp) cc_final: 0.6266 (tp) REVERT: A 242 ILE cc_start: 0.4821 (pt) cc_final: 0.4605 (pt) REVERT: A 451 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7333 (tp30) REVERT: A 475 LEU cc_start: 0.8851 (tp) cc_final: 0.8474 (mp) REVERT: A 483 MET cc_start: 0.7105 (ptt) cc_final: 0.6759 (ppp) REVERT: A 491 CYS cc_start: 0.8362 (m) cc_final: 0.8012 (m) REVERT: A 581 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8927 (mp) REVERT: B 45 ARG cc_start: 0.6806 (ptp90) cc_final: 0.6600 (mtt90) REVERT: B 71 MET cc_start: 0.5539 (mmp) cc_final: 0.5104 (mmt) REVERT: B 152 MET cc_start: 0.0528 (mtp) cc_final: 0.0150 (mmp) REVERT: B 162 ASN cc_start: 0.8791 (t0) cc_final: 0.8274 (m-40) REVERT: B 198 MET cc_start: 0.7400 (mtp) cc_final: 0.6710 (mmt) REVERT: B 231 MET cc_start: 0.8843 (mtt) cc_final: 0.8587 (mtm) REVERT: B 288 ASN cc_start: 0.7688 (t0) cc_final: 0.7084 (p0) REVERT: B 442 VAL cc_start: 0.9231 (p) cc_final: 0.9018 (p) REVERT: B 536 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8449 (p) REVERT: B 540 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B 544 CYS cc_start: 0.9186 (m) cc_final: 0.8857 (m) REVERT: B 620 ASP cc_start: 0.8353 (t0) cc_final: 0.8148 (t0) REVERT: C 17 ASP cc_start: 0.7802 (t70) cc_final: 0.7552 (t0) REVERT: E 17 ASP cc_start: 0.7350 (t70) cc_final: 0.6518 (m-30) REVERT: E 79 GLN cc_start: 0.8337 (mm110) cc_final: 0.7642 (mp10) outliers start: 43 outliers final: 17 residues processed: 287 average time/residue: 0.1032 time to fit residues: 42.8664 Evaluate side-chains 222 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 25 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 23 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 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 120 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN B 76 ASN B 387 ASN B 457 HIS ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN D 5 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.140973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110993 restraints weight = 24414.804| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.96 r_work: 0.3456 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12628 Z= 0.210 Angle : 0.714 10.243 17121 Z= 0.366 Chirality : 0.046 0.199 1951 Planarity : 0.005 0.043 2130 Dihedral : 6.977 67.226 1799 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.72 % Allowed : 13.91 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.21), residues: 1552 helix: 0.06 (0.20), residues: 650 sheet: -1.23 (0.31), residues: 268 loop : -1.71 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 236 TYR 0.041 0.002 TYR B 518 PHE 0.025 0.002 PHE D 79 TRP 0.031 0.002 TRP B 379 HIS 0.010 0.002 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00475 (12621) covalent geometry : angle 0.71349 (17107) SS BOND : bond 0.00628 ( 7) SS BOND : angle 1.30910 ( 14) hydrogen bonds : bond 0.04861 ( 498) hydrogen bonds : angle 4.94193 ( 1494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.6111 (mtt) cc_final: 0.5884 (mmt) REVERT: A 90 LEU cc_start: 0.4569 (OUTLIER) cc_final: 0.3295 (mt) REVERT: A 198 MET cc_start: 0.7020 (mtp) cc_final: 0.6819 (mtp) REVERT: A 200 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6145 (mt) REVERT: A 242 ILE cc_start: 0.5426 (OUTLIER) cc_final: 0.5198 (pt) REVERT: A 407 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8911 (mp) REVERT: A 451 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7686 (tp30) REVERT: A 483 MET cc_start: 0.7334 (ptt) cc_final: 0.6866 (ppp) REVERT: A 491 CYS cc_start: 0.8870 (m) cc_final: 0.8513 (m) REVERT: B 45 ARG cc_start: 0.6953 (ptp90) cc_final: 0.6649 (mtt90) REVERT: B 162 ASN cc_start: 0.8855 (t0) cc_final: 0.8498 (m-40) REVERT: B 288 ASN cc_start: 0.7703 (t0) cc_final: 0.6918 (p0) REVERT: B 451 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8669 (mt-10) REVERT: B 540 LEU cc_start: 0.8972 (mm) cc_final: 0.8425 (mt) REVERT: B 544 CYS cc_start: 0.9245 (m) cc_final: 0.9021 (m) REVERT: B 558 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9011 (mt) REVERT: F 20 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7595 (mt) outliers start: 50 outliers final: 29 residues processed: 261 average time/residue: 0.0923 time to fit residues: 35.7519 Evaluate side-chains 224 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 49 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 132 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS A 583 HIS B 109 ASN ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** 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 = 0.4048 r_free = 0.4048 target = 0.143471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115103 restraints weight = 24468.671| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.81 r_work: 0.3517 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12628 Z= 0.214 Angle : 0.688 9.134 17121 Z= 0.347 Chirality : 0.045 0.303 1951 Planarity : 0.004 0.045 2130 Dihedral : 6.857 65.094 1797 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.65 % Allowed : 16.37 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.21), residues: 1552 helix: 0.24 (0.20), residues: 648 sheet: -0.98 (0.32), residues: 272 loop : -1.71 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 193 TYR 0.023 0.002 TYR A 44 PHE 0.023 0.002 PHE F 79 TRP 0.022 0.002 TRP B 379 HIS 0.007 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00492 (12621) covalent geometry : angle 0.68673 (17107) SS BOND : bond 0.01661 ( 7) SS BOND : angle 1.66169 ( 14) hydrogen bonds : bond 0.04249 ( 498) hydrogen bonds : angle 4.82491 ( 1494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 90 LEU cc_start: 0.4874 (OUTLIER) cc_final: 0.3720 (mt) REVERT: A 231 MET cc_start: 0.8710 (mmm) cc_final: 0.8434 (mtt) REVERT: A 254 ASP cc_start: 0.4945 (m-30) cc_final: 0.4691 (m-30) REVERT: A 407 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8884 (mp) REVERT: A 451 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7771 (tp30) REVERT: A 483 MET cc_start: 0.7247 (ptt) cc_final: 0.7011 (ppp) REVERT: A 491 CYS cc_start: 0.8863 (m) cc_final: 0.8511 (m) REVERT: B 76 ASN cc_start: 0.7537 (m110) cc_final: 0.7104 (m-40) REVERT: B 247 TYR cc_start: 0.5460 (t80) cc_final: 0.5178 (t80) REVERT: B 288 ASN cc_start: 0.7645 (t0) cc_final: 0.6727 (p0) REVERT: B 451 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8549 (mt-10) REVERT: B 540 LEU cc_start: 0.8975 (mm) cc_final: 0.8540 (mp) REVERT: B 558 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9099 (mt) REVERT: F 20 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7514 (mt) outliers start: 49 outliers final: 32 residues processed: 258 average time/residue: 0.0944 time to fit residues: 36.3843 Evaluate side-chains 231 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 49 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 153 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 138 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 HIS B 601 ASN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.137435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107581 restraints weight = 24440.146| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.92 r_work: 0.3414 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12628 Z= 0.238 Angle : 0.709 9.978 17121 Z= 0.360 Chirality : 0.046 0.216 1951 Planarity : 0.004 0.045 2130 Dihedral : 6.987 68.468 1797 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.69 % Allowed : 16.74 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.21), residues: 1552 helix: 0.26 (0.20), residues: 648 sheet: -0.89 (0.32), residues: 272 loop : -1.69 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 383 TYR 0.032 0.002 TYR A 44 PHE 0.030 0.002 PHE B 506 TRP 0.028 0.002 TRP B 379 HIS 0.028 0.002 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00549 (12621) covalent geometry : angle 0.70745 (17107) SS BOND : bond 0.00509 ( 7) SS BOND : angle 1.53429 ( 14) hydrogen bonds : bond 0.04453 ( 498) hydrogen bonds : angle 4.92544 ( 1494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 90 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.4390 (mt) REVERT: A 131 MET cc_start: 0.7027 (mmm) cc_final: 0.6232 (mmm) REVERT: A 193 ARG cc_start: 0.7603 (mtp85) cc_final: 0.6996 (mtt-85) REVERT: A 227 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7676 (mm) REVERT: A 407 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8870 (mp) REVERT: A 441 SER cc_start: 0.9191 (m) cc_final: 0.8941 (t) REVERT: A 451 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7788 (tp30) REVERT: A 483 MET cc_start: 0.7346 (ptt) cc_final: 0.7053 (ppp) REVERT: A 491 CYS cc_start: 0.8972 (m) cc_final: 0.8606 (m) REVERT: B 71 MET cc_start: 0.6444 (mmt) cc_final: 0.6234 (tpp) REVERT: B 76 ASN cc_start: 0.7727 (m110) cc_final: 0.7210 (m-40) REVERT: B 247 TYR cc_start: 0.5665 (t80) cc_final: 0.5360 (t80) REVERT: B 288 ASN cc_start: 0.7607 (t0) cc_final: 0.6543 (p0) REVERT: B 451 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8723 (mt-10) REVERT: C 79 GLN cc_start: 0.8274 (mm-40) cc_final: 0.8054 (mm110) REVERT: D 5 GLN cc_start: 0.8129 (mm110) cc_final: 0.7869 (mm110) REVERT: F 20 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7523 (mt) outliers start: 63 outliers final: 40 residues processed: 250 average time/residue: 0.0891 time to fit residues: 34.0889 Evaluate side-chains 235 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 49 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 60 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 ASN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.138663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109369 restraints weight = 24210.341| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.88 r_work: 0.3431 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.6679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12628 Z= 0.175 Angle : 0.649 14.366 17121 Z= 0.325 Chirality : 0.043 0.235 1951 Planarity : 0.004 0.044 2130 Dihedral : 6.770 66.098 1797 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.57 % Allowed : 18.60 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.22), residues: 1552 helix: 0.52 (0.20), residues: 642 sheet: -0.81 (0.32), residues: 272 loop : -1.64 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 96 TYR 0.035 0.002 TYR A 44 PHE 0.028 0.002 PHE B 506 TRP 0.030 0.002 TRP B 379 HIS 0.011 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00404 (12621) covalent geometry : angle 0.64808 (17107) SS BOND : bond 0.00399 ( 7) SS BOND : angle 1.21869 ( 14) hydrogen bonds : bond 0.03955 ( 498) hydrogen bonds : angle 4.67107 ( 1494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.5037 (OUTLIER) cc_final: 0.4406 (mt) REVERT: A 131 MET cc_start: 0.6987 (mmm) cc_final: 0.6356 (mmm) REVERT: A 193 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7060 (mtt-85) REVERT: A 227 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7762 (mm) REVERT: A 407 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8858 (mp) REVERT: A 451 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7701 (tp30) REVERT: A 483 MET cc_start: 0.7282 (ptt) cc_final: 0.7010 (ppp) REVERT: A 491 CYS cc_start: 0.8940 (m) cc_final: 0.8569 (m) REVERT: A 510 MET cc_start: 0.8845 (ttp) cc_final: 0.8585 (ttm) REVERT: B 76 ASN cc_start: 0.7740 (m110) cc_final: 0.7379 (m-40) REVERT: B 198 MET cc_start: 0.8424 (ttp) cc_final: 0.7901 (tpp) REVERT: B 247 TYR cc_start: 0.5791 (t80) cc_final: 0.5501 (t80) REVERT: B 283 HIS cc_start: 0.3853 (t-90) cc_final: 0.3188 (m-70) REVERT: D 5 GLN cc_start: 0.8119 (mm110) cc_final: 0.7907 (mm110) REVERT: F 20 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7411 (mt) outliers start: 48 outliers final: 34 residues processed: 250 average time/residue: 0.0870 time to fit residues: 33.0922 Evaluate side-chains 237 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 148 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 234 GLN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** F 40 GLN ** 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 = 0.4021 r_free = 0.4021 target = 0.141619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.112553 restraints weight = 24022.755| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.83 r_work: 0.3507 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12628 Z= 0.163 Angle : 0.637 10.568 17121 Z= 0.321 Chirality : 0.043 0.297 1951 Planarity : 0.004 0.044 2130 Dihedral : 6.659 66.477 1797 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.72 % Allowed : 18.75 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.22), residues: 1552 helix: 0.65 (0.21), residues: 640 sheet: -0.73 (0.32), residues: 272 loop : -1.60 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 18 TYR 0.033 0.002 TYR A 44 PHE 0.030 0.002 PHE B 506 TRP 0.030 0.002 TRP B 379 HIS 0.009 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00379 (12621) covalent geometry : angle 0.63678 (17107) SS BOND : bond 0.00448 ( 7) SS BOND : angle 1.22388 ( 14) hydrogen bonds : bond 0.03867 ( 498) hydrogen bonds : angle 4.58839 ( 1494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.5327 (OUTLIER) cc_final: 0.4910 (mt) REVERT: A 131 MET cc_start: 0.6955 (mmm) cc_final: 0.6457 (mmm) REVERT: A 193 ARG cc_start: 0.7653 (mtp85) cc_final: 0.7068 (mtt-85) REVERT: A 227 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7823 (mm) REVERT: A 407 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8871 (mp) REVERT: A 451 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7702 (tp30) REVERT: A 483 MET cc_start: 0.7198 (ptt) cc_final: 0.6951 (ppp) REVERT: A 491 CYS cc_start: 0.8811 (m) cc_final: 0.8475 (m) REVERT: A 510 MET cc_start: 0.8754 (ttp) cc_final: 0.8504 (ttm) REVERT: B 71 MET cc_start: 0.6309 (tpp) cc_final: 0.5840 (tpp) REVERT: B 76 ASN cc_start: 0.7616 (m110) cc_final: 0.7214 (m-40) REVERT: B 131 MET cc_start: 0.7511 (mmm) cc_final: 0.7146 (mtp) REVERT: B 198 MET cc_start: 0.8389 (ttp) cc_final: 0.8040 (ttt) REVERT: B 247 TYR cc_start: 0.5944 (t80) cc_final: 0.5652 (t80) REVERT: B 271 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 283 HIS cc_start: 0.3626 (t-90) cc_final: 0.2969 (m-70) REVERT: C 82 ASP cc_start: 0.8085 (m-30) cc_final: 0.7727 (t0) REVERT: D 5 GLN cc_start: 0.8092 (mm110) cc_final: 0.7779 (mm110) REVERT: F 20 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7432 (mt) outliers start: 50 outliers final: 37 residues processed: 237 average time/residue: 0.0906 time to fit residues: 32.5016 Evaluate side-chains 240 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 36 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 86 optimal weight: 0.0010 chunk 148 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.143059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.114179 restraints weight = 23992.040| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.84 r_work: 0.3544 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12628 Z= 0.115 Angle : 0.611 15.119 17121 Z= 0.304 Chirality : 0.042 0.253 1951 Planarity : 0.004 0.043 2130 Dihedral : 6.476 66.141 1797 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.83 % Allowed : 20.01 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.22), residues: 1552 helix: 0.78 (0.21), residues: 630 sheet: -0.65 (0.32), residues: 272 loop : -1.44 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 39 TYR 0.033 0.001 TYR A 44 PHE 0.030 0.001 PHE B 506 TRP 0.024 0.001 TRP B 379 HIS 0.025 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00260 (12621) covalent geometry : angle 0.61051 (17107) SS BOND : bond 0.00181 ( 7) SS BOND : angle 1.00910 ( 14) hydrogen bonds : bond 0.03536 ( 498) hydrogen bonds : angle 4.41242 ( 1494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.5016 (mt) REVERT: A 131 MET cc_start: 0.6893 (mmm) cc_final: 0.6466 (mmm) REVERT: A 193 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7069 (mtt-85) REVERT: A 227 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7821 (mm) REVERT: A 407 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8865 (mp) REVERT: A 451 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7558 (tp30) REVERT: A 483 MET cc_start: 0.7115 (ptt) cc_final: 0.6897 (ppp) REVERT: A 491 CYS cc_start: 0.8753 (m) cc_final: 0.8411 (m) REVERT: A 510 MET cc_start: 0.8668 (ttp) cc_final: 0.8421 (ttm) REVERT: B 71 MET cc_start: 0.6261 (tpp) cc_final: 0.5838 (tpp) REVERT: B 76 ASN cc_start: 0.7589 (m110) cc_final: 0.7248 (m-40) REVERT: B 131 MET cc_start: 0.7586 (mmm) cc_final: 0.7141 (mtp) REVERT: B 198 MET cc_start: 0.8324 (ttp) cc_final: 0.7849 (tpp) REVERT: B 247 TYR cc_start: 0.5902 (t80) cc_final: 0.5655 (t80) REVERT: B 271 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 283 HIS cc_start: 0.3638 (t-90) cc_final: 0.3029 (m-70) REVERT: B 451 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8517 (mt-10) REVERT: C 82 ASP cc_start: 0.8044 (m-30) cc_final: 0.7663 (t0) REVERT: F 20 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7388 (mt) outliers start: 38 outliers final: 26 residues processed: 231 average time/residue: 0.0877 time to fit residues: 31.2833 Evaluate side-chains 223 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 110 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 69 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.138242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.108892 restraints weight = 24001.979| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.78 r_work: 0.3502 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.7230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12628 Z= 0.169 Angle : 0.665 12.572 17121 Z= 0.331 Chirality : 0.044 0.271 1951 Planarity : 0.004 0.043 2130 Dihedral : 6.471 65.660 1797 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.60 % Allowed : 20.54 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.22), residues: 1552 helix: 0.74 (0.21), residues: 640 sheet: -0.70 (0.32), residues: 280 loop : -1.42 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 39 TYR 0.029 0.002 TYR A 44 PHE 0.029 0.002 PHE B 506 TRP 0.023 0.001 TRP B 379 HIS 0.005 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00395 (12621) covalent geometry : angle 0.66421 (17107) SS BOND : bond 0.00329 ( 7) SS BOND : angle 1.53100 ( 14) hydrogen bonds : bond 0.03863 ( 498) hydrogen bonds : angle 4.52406 ( 1494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.5076 (mt) REVERT: A 131 MET cc_start: 0.6884 (mmm) cc_final: 0.6436 (mmm) REVERT: A 227 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7820 (mm) REVERT: A 407 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8876 (mp) REVERT: A 451 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7688 (tp30) REVERT: A 483 MET cc_start: 0.7201 (ptt) cc_final: 0.6942 (ppp) REVERT: A 491 CYS cc_start: 0.8840 (m) cc_final: 0.8516 (m) REVERT: A 510 MET cc_start: 0.8710 (ttp) cc_final: 0.8470 (ttm) REVERT: B 131 MET cc_start: 0.7598 (mmm) cc_final: 0.7107 (mtp) REVERT: B 134 LEU cc_start: 0.8735 (tp) cc_final: 0.8530 (tp) REVERT: B 198 MET cc_start: 0.8400 (ttp) cc_final: 0.7390 (tpp) REVERT: B 247 TYR cc_start: 0.6021 (t80) cc_final: 0.5726 (t80) REVERT: B 271 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7613 (tm-30) REVERT: B 283 HIS cc_start: 0.3634 (t-90) cc_final: 0.2978 (m-70) REVERT: B 451 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8553 (mt-10) REVERT: C 82 ASP cc_start: 0.8058 (m-30) cc_final: 0.7681 (t0) REVERT: F 20 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7464 (mt) outliers start: 35 outliers final: 27 residues processed: 219 average time/residue: 0.0913 time to fit residues: 30.3244 Evaluate side-chains 218 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 78 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN B 68 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.138260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.109293 restraints weight = 24099.413| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.94 r_work: 0.3442 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12628 Z= 0.119 Angle : 0.634 13.211 17121 Z= 0.315 Chirality : 0.042 0.241 1951 Planarity : 0.003 0.043 2130 Dihedral : 6.328 65.303 1797 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.23 % Allowed : 21.50 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.22), residues: 1552 helix: 0.84 (0.21), residues: 630 sheet: -0.75 (0.31), residues: 300 loop : -1.20 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 107 TYR 0.026 0.001 TYR A 44 PHE 0.030 0.001 PHE A 506 TRP 0.017 0.001 TRP B 379 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00272 (12621) covalent geometry : angle 0.63299 (17107) SS BOND : bond 0.00196 ( 7) SS BOND : angle 1.22608 ( 14) hydrogen bonds : bond 0.03495 ( 498) hydrogen bonds : angle 4.35176 ( 1494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.6687 (mmm) cc_final: 0.6323 (mmm) REVERT: A 407 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8835 (mp) REVERT: A 451 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7595 (tp30) REVERT: A 483 MET cc_start: 0.7236 (ptt) cc_final: 0.6962 (ppp) REVERT: A 510 MET cc_start: 0.8726 (ttp) cc_final: 0.8465 (ttm) REVERT: B 131 MET cc_start: 0.7420 (mmm) cc_final: 0.6977 (mtp) REVERT: B 134 LEU cc_start: 0.8733 (tp) cc_final: 0.8504 (tp) REVERT: B 198 MET cc_start: 0.8431 (ttp) cc_final: 0.7394 (tpp) REVERT: B 229 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7995 (tmmt) REVERT: B 247 TYR cc_start: 0.6019 (t80) cc_final: 0.5740 (t80) REVERT: B 271 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7601 (tm-30) REVERT: B 283 HIS cc_start: 0.3625 (t-90) cc_final: 0.2978 (m-70) REVERT: B 451 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8560 (mt-10) REVERT: C 82 ASP cc_start: 0.8122 (m-30) cc_final: 0.7766 (t0) REVERT: F 20 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7363 (mt) outliers start: 30 outliers final: 24 residues processed: 212 average time/residue: 0.0875 time to fit residues: 28.5801 Evaluate side-chains 215 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 125 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 145 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109680 restraints weight = 24012.211| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.91 r_work: 0.3453 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.7535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12628 Z= 0.116 Angle : 0.629 13.581 17121 Z= 0.311 Chirality : 0.041 0.236 1951 Planarity : 0.003 0.042 2130 Dihedral : 6.126 63.941 1797 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.38 % Allowed : 21.35 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1552 helix: 0.93 (0.21), residues: 634 sheet: -0.63 (0.31), residues: 298 loop : -1.06 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 107 TYR 0.023 0.001 TYR A 44 PHE 0.030 0.001 PHE B 506 TRP 0.018 0.001 TRP B 379 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00268 (12621) covalent geometry : angle 0.62822 (17107) SS BOND : bond 0.00207 ( 7) SS BOND : angle 0.99616 ( 14) hydrogen bonds : bond 0.03388 ( 498) hydrogen bonds : angle 4.23157 ( 1494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2596.78 seconds wall clock time: 45 minutes 27.95 seconds (2727.95 seconds total)