Starting phenix.real_space_refine on Mon Apr 6 19:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iar_52784/04_2026/9iar_52784_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iar_52784/04_2026/9iar_52784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iar_52784/04_2026/9iar_52784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iar_52784/04_2026/9iar_52784.map" model { file = "/net/cci-nas-00/data/ceres_data/9iar_52784/04_2026/9iar_52784_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iar_52784/04_2026/9iar_52784_trim.cif" } resolution = 3.2 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= 0.012 sd= 0.233 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 56 5.16 5 Cl 2 4.86 5 C 6728 2.51 5 N 1694 2.21 5 O 1836 1.98 5 H 10560 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20876 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 8668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 8668 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 34, 'TRANS': 523} Chain: "C" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1755 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "A" Number of atoms: 8668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 8668 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 34, 'TRANS': 523} Chain: "D" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1755 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 1, 'NAG': 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: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 1, 'NAG': 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 Time building chain proxies: 3.68, per 1000 atoms: 0.18 Number of scatterers: 20876 At special positions: 0 Unit cell: (87.207, 141.446, 121.239, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 56 16.00 O 1836 8.00 N 1694 7.00 C 6728 6.00 H 10560 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 99 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 294 " " NAG B 601 " - " ASN B 294 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 591.6 milliseconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 64.4% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 35 through 40 removed outlier: 3.703A pdb=" N TRP B 39 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 44 through 74 removed outlier: 3.787A pdb=" N MET B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Proline residue: B 64 - end of helix removed outlier: 3.503A pdb=" N GLU B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 95 removed outlier: 3.925A pdb=" N LEU B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 83 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N CYS B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 116 removed outlier: 3.600A pdb=" N PHE B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 140 removed outlier: 3.513A pdb=" N ALA B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 149 removed outlier: 3.683A pdb=" N PHE B 148 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 149 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 169 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.720A pdb=" N TYR B 188 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 198 through 222 Processing helix chain 'B' and resid 230 through 246 removed outlier: 3.813A pdb=" N SER B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 266 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 308 through 333 Proline residue: B 314 - end of helix removed outlier: 3.547A pdb=" N SER B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 355 removed outlier: 3.710A pdb=" N VAL B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 374 removed outlier: 3.610A pdb=" N GLY B 374 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 395 removed outlier: 4.040A pdb=" N VAL B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 removed outlier: 3.815A pdb=" N PHE B 399 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR B 400 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 416 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 421 through 431 removed outlier: 4.231A pdb=" N ARG B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 446 removed outlier: 3.968A pdb=" N PHE B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 470 removed outlier: 3.538A pdb=" N LEU B 454 " --> pdb=" O GLN B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 493 through 506 Processing helix chain 'B' and resid 525 through 542 removed outlier: 3.589A pdb=" N GLN B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 562 removed outlier: 3.686A pdb=" N VAL B 558 " --> pdb=" O PRO B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.631A pdb=" N GLN B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 68 removed outlier: 3.599A pdb=" N LYS C 68 " --> pdb=" O ASP C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 35 through 43 removed outlier: 4.249A pdb=" N LEU A 40 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 44 through 74 removed outlier: 3.527A pdb=" N VAL A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 77 through 95 removed outlier: 3.850A pdb=" N LEU A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET A 86 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N CYS A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 removed outlier: 3.609A pdb=" N PHE A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 140 removed outlier: 3.549A pdb=" N ALA A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 182 through 193 removed outlier: 3.804A pdb=" N TYR A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 198 through 222 Processing helix chain 'A' and resid 230 through 246 Processing helix chain 'A' and resid 246 through 266 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 308 through 333 Proline residue: A 314 - end of helix removed outlier: 3.516A pdb=" N LEU A 318 " --> pdb=" O PRO A 314 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 324 " --> pdb=" O GLU A 320 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 354 removed outlier: 3.588A pdb=" N LEU A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 378 through 395 removed outlier: 4.134A pdb=" N LEU A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 removed outlier: 3.615A pdb=" N TYR A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 416 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 421 through 431 removed outlier: 4.464A pdb=" N ARG A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'A' and resid 448 through 470 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 525 through 542 Processing helix chain 'A' and resid 552 through 562 removed outlier: 3.643A pdb=" N VAL A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'D' and resid 65 through 68 removed outlier: 3.749A pdb=" N LYS D 68 " --> pdb=" O ASP D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AA2, first strand: chain 'B' and resid 473 through 477 removed outlier: 8.598A pdb=" N PHE B 570 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE B 548 " --> pdb=" O PHE B 570 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 11 removed outlier: 3.568A pdb=" N SER C 74 " --> pdb=" O TYR C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 61 through 63 removed outlier: 5.400A pdb=" N LEU C 51 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 42 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR C 37 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 63 removed outlier: 5.400A pdb=" N LEU C 51 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 42 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR C 37 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.378A pdb=" N LEU A 481 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU A 517 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 483 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N PHE A 570 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE A 548 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 6 through 11 Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 63 removed outlier: 5.146A pdb=" N LEU D 51 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG D 42 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR D 37 " --> pdb=" O ARG D 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 61 through 63 removed outlier: 5.146A pdb=" N LEU D 51 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG D 42 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR D 37 " --> pdb=" O ARG D 102 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10542 1.03 - 1.23: 27 1.23 - 1.42: 4321 1.42 - 1.62: 6132 1.62 - 1.82: 90 Bond restraints: 21112 Sorted by residual: bond pdb=" N SER B 26 " pdb=" CA SER B 26 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N SER D 4 " pdb=" CA SER D 4 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N SER A 26 " pdb=" CA SER A 26 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N SER C 4 " pdb=" CA SER C 4 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.65e+00 bond pdb=" N SER C 4 " pdb=" H SER C 4 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.43e+00 ... (remaining 21107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 37479 1.61 - 3.22: 705 3.22 - 4.84: 68 4.84 - 6.45: 7 6.45 - 8.06: 1 Bond angle restraints: 38260 Sorted by residual: angle pdb=" N VAL C 52 " pdb=" CA VAL C 52 " pdb=" C VAL C 52 " ideal model delta sigma weight residual 111.48 108.76 2.72 9.40e-01 1.13e+00 8.39e+00 angle pdb=" N TYR B 358 " pdb=" CA TYR B 358 " pdb=" C TYR B 358 " ideal model delta sigma weight residual 110.31 106.91 3.40 1.20e+00 6.94e-01 8.02e+00 angle pdb=" CB MET B 50 " pdb=" CG MET B 50 " pdb=" SD MET B 50 " ideal model delta sigma weight residual 112.70 120.76 -8.06 3.00e+00 1.11e-01 7.22e+00 angle pdb=" C ARG A 284 " pdb=" N ILE A 285 " pdb=" CA ILE A 285 " ideal model delta sigma weight residual 119.72 124.87 -5.15 2.01e+00 2.48e-01 6.56e+00 angle pdb=" CG ARG A 181 " pdb=" CD ARG A 181 " pdb=" NE ARG A 181 " ideal model delta sigma weight residual 112.00 117.01 -5.01 2.20e+00 2.07e-01 5.19e+00 ... (remaining 38255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 9023 17.81 - 35.63: 558 35.63 - 53.44: 305 53.44 - 71.25: 97 71.25 - 89.06: 11 Dihedral angle restraints: 9994 sinusoidal: 5442 harmonic: 4552 Sorted by residual: dihedral pdb=" CA LYS C 68 " pdb=" C LYS C 68 " pdb=" N GLY C 69 " pdb=" CA GLY C 69 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASN B 332 " pdb=" C ASN B 332 " pdb=" N ASN B 333 " pdb=" CA ASN B 333 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA SER A 509 " pdb=" C SER A 509 " pdb=" N PRO A 510 " pdb=" CA PRO A 510 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 9991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1201 0.040 - 0.079: 376 0.079 - 0.119: 100 0.119 - 0.158: 16 0.158 - 0.198: 3 Chirality restraints: 1696 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 294 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 294 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CB THR A 291 " pdb=" CA THR A 291 " pdb=" OG1 THR A 291 " pdb=" CG2 THR A 291 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1693 not shown) Planarity restraints: 3070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 33 " 0.231 9.50e-02 1.11e+02 7.72e-02 6.49e+00 pdb=" NE ARG A 33 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 33 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 33 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 33 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 33 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 33 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 33 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 33 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 103 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO A 104 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 181 " 0.154 9.50e-02 1.11e+02 5.14e-02 2.89e+00 pdb=" NE ARG A 181 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 181 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 181 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 181 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 181 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 181 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 181 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 181 " 0.002 2.00e-02 2.50e+03 ... (remaining 3067 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 664 2.16 - 2.77: 40167 2.77 - 3.38: 59356 3.38 - 3.99: 75125 3.99 - 4.60: 119597 Nonbonded interactions: 294909 Sorted by model distance: nonbonded pdb=" O ALA A 344 " pdb=" HG1 THR A 348 " model vdw 1.548 2.450 nonbonded pdb=" O SER B 363 " pdb=" HG1 THR B 367 " model vdw 1.582 2.450 nonbonded pdb=" O MET A 229 " pdb=" HE ARG A 234 " model vdw 1.621 2.450 nonbonded pdb=" O PRO B 437 " pdb=" HG1 THR B 441 " model vdw 1.637 2.450 nonbonded pdb=" O PRO A 437 " pdb=" HG1 THR A 441 " model vdw 1.644 2.450 ... (remaining 294904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.650 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10556 Z= 0.137 Angle : 0.600 8.062 14382 Z= 0.315 Chirality : 0.042 0.198 1696 Planarity : 0.006 0.101 1802 Dihedral : 12.889 89.064 3804 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.09 % Allowed : 7.44 % Favored : 92.47 % 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: 1336 helix: 0.25 (0.19), residues: 738 sheet: 0.74 (0.60), residues: 86 loop : -0.88 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 98 TYR 0.022 0.002 TYR B 82 PHE 0.021 0.002 PHE B 85 TRP 0.012 0.002 TRP B 47 HIS 0.006 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00316 (10552) covalent geometry : angle 0.60007 (14372) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.50901 ( 4) hydrogen bonds : bond 0.19630 ( 633) hydrogen bonds : angle 7.50657 ( 1905) link_NAG-ASN : bond 0.00527 ( 2) link_NAG-ASN : angle 0.49116 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ARG cc_start: 0.7688 (mmt-90) cc_final: 0.7046 (mpt180) REVERT: B 142 LEU cc_start: 0.8347 (mp) cc_final: 0.7993 (mp) REVERT: B 534 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6969 (mm-30) REVERT: C 7 GLN cc_start: 0.8157 (pm20) cc_final: 0.7906 (pm20) REVERT: C 38 MET cc_start: 0.8735 (mtp) cc_final: 0.8402 (mtp) REVERT: C 50 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6496 (tt0) REVERT: C 90 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7602 (mmmt) REVERT: A 50 MET cc_start: 0.7605 (tpp) cc_final: 0.7344 (mmm) REVERT: A 241 TRP cc_start: 0.7864 (t-100) cc_final: 0.7149 (t60) REVERT: A 302 MET cc_start: 0.8921 (mtp) cc_final: 0.8581 (mtp) REVERT: A 333 ASN cc_start: 0.8540 (p0) cc_final: 0.7505 (t0) REVERT: A 448 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7556 (mm-30) REVERT: D 42 ARG cc_start: 0.7199 (ttp80) cc_final: 0.6896 (ttp80) REVERT: D 68 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7285 (mmmt) outliers start: 1 outliers final: 1 residues processed: 156 average time/residue: 0.1874 time to fit residues: 43.1164 Evaluate side-chains 148 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN B 268 GLN A 172 ASN A 304 GLN A 579 HIS D 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.155546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.115797 restraints weight = 33932.776| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.30 r_work: 0.3048 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10556 Z= 0.150 Angle : 0.570 5.389 14382 Z= 0.306 Chirality : 0.042 0.204 1696 Planarity : 0.005 0.042 1802 Dihedral : 5.007 38.957 1507 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.09 % Allowed : 7.08 % Favored : 91.83 % 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: 0.44 (0.23), residues: 1336 helix: 0.96 (0.19), residues: 776 sheet: 0.53 (0.48), residues: 118 loop : -0.87 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 234 TYR 0.017 0.002 TYR A 526 PHE 0.018 0.002 PHE B 328 TRP 0.008 0.001 TRP A 241 HIS 0.004 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00341 (10552) covalent geometry : angle 0.57029 (14372) SS BOND : bond 0.00054 ( 2) SS BOND : angle 0.45850 ( 4) hydrogen bonds : bond 0.04841 ( 633) hydrogen bonds : angle 4.85071 ( 1905) link_NAG-ASN : bond 0.00252 ( 2) link_NAG-ASN : angle 0.73975 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 LEU cc_start: 0.8337 (mp) cc_final: 0.7969 (mp) REVERT: B 333 ASN cc_start: 0.8213 (p0) cc_final: 0.7957 (p0) REVERT: B 499 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6869 (tm-30) REVERT: B 534 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7127 (mm-30) REVERT: C 38 MET cc_start: 0.8651 (mtp) cc_final: 0.8294 (mtp) REVERT: C 48 GLN cc_start: 0.6733 (pm20) cc_final: 0.6312 (mt0) REVERT: C 50 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6453 (tt0) REVERT: A 50 MET cc_start: 0.7684 (tpp) cc_final: 0.7399 (mmm) REVERT: A 332 ASN cc_start: 0.8273 (m-40) cc_final: 0.7834 (m-40) REVERT: A 333 ASN cc_start: 0.8591 (p0) cc_final: 0.7544 (t0) REVERT: A 494 MET cc_start: 0.8628 (tpt) cc_final: 0.8352 (tpp) REVERT: D 68 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7430 (mmmt) outliers start: 12 outliers final: 9 residues processed: 168 average time/residue: 0.1950 time to fit residues: 48.7657 Evaluate side-chains 159 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain D residue 37 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.160944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119874 restraints weight = 33291.852| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.42 r_work: 0.3004 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10556 Z= 0.112 Angle : 0.494 5.174 14382 Z= 0.258 Chirality : 0.040 0.199 1696 Planarity : 0.004 0.043 1802 Dihedral : 4.469 21.067 1504 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.64 % Allowed : 8.44 % Favored : 90.93 % 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: 0.73 (0.23), residues: 1336 helix: 1.33 (0.19), residues: 780 sheet: 0.13 (0.45), residues: 130 loop : -0.92 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 581 TYR 0.011 0.001 TYR C 37 PHE 0.014 0.001 PHE A 328 TRP 0.007 0.001 TRP A 241 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00251 (10552) covalent geometry : angle 0.49432 (14372) SS BOND : bond 0.00020 ( 2) SS BOND : angle 0.38230 ( 4) hydrogen bonds : bond 0.04229 ( 633) hydrogen bonds : angle 4.41183 ( 1905) link_NAG-ASN : bond 0.00367 ( 2) link_NAG-ASN : angle 0.73234 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 142 LEU cc_start: 0.8196 (mp) cc_final: 0.7815 (mp) REVERT: B 333 ASN cc_start: 0.8119 (p0) cc_final: 0.7879 (p0) REVERT: B 534 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6556 (mt-10) REVERT: C 50 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6447 (tt0) REVERT: A 50 MET cc_start: 0.7622 (tpp) cc_final: 0.7376 (mmm) REVERT: A 332 ASN cc_start: 0.8060 (m-40) cc_final: 0.7563 (m-40) REVERT: A 333 ASN cc_start: 0.8610 (p0) cc_final: 0.7438 (t0) REVERT: A 523 SER cc_start: 0.8852 (t) cc_final: 0.8614 (p) REVERT: D 68 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7346 (mmmt) REVERT: D 98 TYR cc_start: 0.7860 (m-10) cc_final: 0.7623 (m-10) outliers start: 7 outliers final: 7 residues processed: 159 average time/residue: 0.1936 time to fit residues: 45.6384 Evaluate side-chains 157 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain D residue 48 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 0.4980 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 0.0370 chunk 109 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.154598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.115088 restraints weight = 33856.789| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.27 r_work: 0.3032 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10556 Z= 0.111 Angle : 0.483 5.032 14382 Z= 0.253 Chirality : 0.039 0.197 1696 Planarity : 0.004 0.043 1802 Dihedral : 4.332 19.711 1504 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.54 % Allowed : 9.26 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1336 helix: 1.50 (0.19), residues: 776 sheet: 0.18 (0.46), residues: 130 loop : -0.86 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 33 TYR 0.011 0.001 TYR D 37 PHE 0.014 0.001 PHE A 328 TRP 0.007 0.001 TRP A 241 HIS 0.002 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00252 (10552) covalent geometry : angle 0.48281 (14372) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.41325 ( 4) hydrogen bonds : bond 0.03659 ( 633) hydrogen bonds : angle 4.20384 ( 1905) link_NAG-ASN : bond 0.00314 ( 2) link_NAG-ASN : angle 0.72090 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 ASN cc_start: 0.8108 (p0) cc_final: 0.7877 (p0) REVERT: B 494 MET cc_start: 0.8341 (tpt) cc_final: 0.8130 (tpp) REVERT: B 534 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6393 (mt-10) REVERT: C 7 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: C 50 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6359 (tt0) REVERT: A 50 MET cc_start: 0.7545 (tpp) cc_final: 0.7283 (mmm) REVERT: A 332 ASN cc_start: 0.7897 (m-40) cc_final: 0.7365 (m-40) REVERT: A 333 ASN cc_start: 0.8573 (p0) cc_final: 0.7409 (t0) REVERT: A 517 GLU cc_start: 0.8172 (tt0) cc_final: 0.7799 (tt0) REVERT: A 523 SER cc_start: 0.8802 (t) cc_final: 0.8542 (p) REVERT: D 42 ARG cc_start: 0.7300 (ttp80) cc_final: 0.6912 (ttp80) REVERT: D 68 LYS cc_start: 0.7762 (mmmt) cc_final: 0.7286 (mmmt) outliers start: 6 outliers final: 3 residues processed: 161 average time/residue: 0.1939 time to fit residues: 46.8869 Evaluate side-chains 157 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 572 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.150339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109887 restraints weight = 34111.491| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.33 r_work: 0.2986 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10556 Z= 0.143 Angle : 0.493 5.112 14382 Z= 0.258 Chirality : 0.040 0.201 1696 Planarity : 0.004 0.043 1802 Dihedral : 4.265 18.658 1504 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.64 % Allowed : 9.44 % Favored : 89.93 % 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 (0.24), residues: 1336 helix: 1.52 (0.19), residues: 776 sheet: 0.21 (0.46), residues: 130 loop : -0.93 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.013 0.001 TYR C 37 PHE 0.016 0.001 PHE A 328 TRP 0.007 0.001 TRP A 241 HIS 0.003 0.001 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00343 (10552) covalent geometry : angle 0.49275 (14372) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.55952 ( 4) hydrogen bonds : bond 0.03681 ( 633) hydrogen bonds : angle 4.12001 ( 1905) link_NAG-ASN : bond 0.00277 ( 2) link_NAG-ASN : angle 0.91250 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 333 ASN cc_start: 0.8218 (p0) cc_final: 0.7974 (p0) REVERT: B 463 MET cc_start: 0.8488 (mtp) cc_final: 0.8241 (mtp) REVERT: B 534 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6608 (mt-10) REVERT: C 48 GLN cc_start: 0.6892 (pm20) cc_final: 0.6407 (mt0) REVERT: C 50 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6417 (tt0) REVERT: A 33 ARG cc_start: 0.7684 (mmm160) cc_final: 0.7321 (mpt180) REVERT: A 50 MET cc_start: 0.7643 (tpp) cc_final: 0.7372 (mmm) REVERT: A 332 ASN cc_start: 0.8070 (m-40) cc_final: 0.7560 (m-40) REVERT: A 333 ASN cc_start: 0.8684 (p0) cc_final: 0.7512 (t0) REVERT: A 517 GLU cc_start: 0.8221 (tt0) cc_final: 0.7878 (tt0) REVERT: A 523 SER cc_start: 0.8901 (t) cc_final: 0.8657 (p) REVERT: D 42 ARG cc_start: 0.7439 (ttp80) cc_final: 0.7091 (ttp80) REVERT: D 68 LYS cc_start: 0.7709 (mmmt) cc_final: 0.7239 (mmmt) outliers start: 7 outliers final: 6 residues processed: 162 average time/residue: 0.1968 time to fit residues: 47.1446 Evaluate side-chains 161 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain D residue 37 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 1 optimal weight: 0.0020 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.154501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114718 restraints weight = 33668.710| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.28 r_work: 0.3024 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10556 Z= 0.106 Angle : 0.468 5.349 14382 Z= 0.242 Chirality : 0.039 0.192 1696 Planarity : 0.004 0.043 1802 Dihedral : 4.134 17.799 1504 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.54 % Allowed : 9.53 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.24), residues: 1336 helix: 1.72 (0.19), residues: 776 sheet: 0.28 (0.47), residues: 130 loop : -0.93 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.011 0.001 TYR D 37 PHE 0.014 0.001 PHE A 328 TRP 0.007 0.001 TRP A 241 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00241 (10552) covalent geometry : angle 0.46782 (14372) SS BOND : bond 0.00010 ( 2) SS BOND : angle 0.40640 ( 4) hydrogen bonds : bond 0.03303 ( 633) hydrogen bonds : angle 3.94874 ( 1905) link_NAG-ASN : bond 0.00317 ( 2) link_NAG-ASN : angle 0.76303 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 320 GLU cc_start: 0.7200 (tt0) cc_final: 0.6742 (mt-10) REVERT: B 534 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6326 (mt-10) REVERT: C 50 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6271 (tt0) REVERT: A 33 ARG cc_start: 0.7470 (mmm160) cc_final: 0.7075 (mpt180) REVERT: A 50 MET cc_start: 0.7526 (tpp) cc_final: 0.7234 (mmm) REVERT: A 332 ASN cc_start: 0.7832 (m-40) cc_final: 0.7298 (m-40) REVERT: A 333 ASN cc_start: 0.8631 (p0) cc_final: 0.7489 (t0) REVERT: A 517 GLU cc_start: 0.8126 (tt0) cc_final: 0.7797 (tt0) REVERT: A 523 SER cc_start: 0.8744 (t) cc_final: 0.8454 (p) REVERT: A 579 HIS cc_start: 0.6764 (m-70) cc_final: 0.6444 (m-70) REVERT: D 42 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6887 (ttp80) REVERT: D 50 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6553 (mt-10) REVERT: D 68 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7220 (mmmt) outliers start: 6 outliers final: 5 residues processed: 168 average time/residue: 0.1789 time to fit residues: 45.0226 Evaluate side-chains 167 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain D residue 37 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 0.0060 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.153860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.113988 restraints weight = 33851.872| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.34 r_work: 0.3011 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10556 Z= 0.115 Angle : 0.471 5.948 14382 Z= 0.243 Chirality : 0.039 0.192 1696 Planarity : 0.004 0.043 1802 Dihedral : 4.054 17.256 1504 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.54 % Allowed : 9.89 % Favored : 89.56 % 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: 1.17 (0.24), residues: 1336 helix: 1.79 (0.19), residues: 778 sheet: 0.27 (0.47), residues: 130 loop : -0.95 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.012 0.001 TYR D 37 PHE 0.015 0.001 PHE A 328 TRP 0.008 0.001 TRP A 241 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00275 (10552) covalent geometry : angle 0.47027 (14372) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.54967 ( 4) hydrogen bonds : bond 0.03264 ( 633) hydrogen bonds : angle 3.88794 ( 1905) link_NAG-ASN : bond 0.00290 ( 2) link_NAG-ASN : angle 0.88270 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 320 GLU cc_start: 0.7498 (tt0) cc_final: 0.7037 (mt-10) REVERT: B 534 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6743 (mt-10) REVERT: B 537 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6425 (mt0) REVERT: C 50 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6493 (tt0) REVERT: A 33 ARG cc_start: 0.7659 (mmm160) cc_final: 0.7254 (mpt180) REVERT: A 50 MET cc_start: 0.7739 (tpp) cc_final: 0.7433 (mmm) REVERT: A 332 ASN cc_start: 0.8082 (m-40) cc_final: 0.7655 (m-40) REVERT: A 333 ASN cc_start: 0.8729 (p0) cc_final: 0.7501 (t0) REVERT: A 517 GLU cc_start: 0.8173 (tt0) cc_final: 0.7875 (tt0) REVERT: A 523 SER cc_start: 0.8856 (t) cc_final: 0.8606 (p) REVERT: A 579 HIS cc_start: 0.6956 (m-70) cc_final: 0.6644 (m-70) REVERT: D 42 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7176 (ttp80) REVERT: D 50 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6690 (mt-10) REVERT: D 68 LYS cc_start: 0.7747 (mmmt) cc_final: 0.7293 (mmmt) REVERT: D 76 GLU cc_start: 0.7920 (tt0) cc_final: 0.7577 (tt0) outliers start: 6 outliers final: 6 residues processed: 165 average time/residue: 0.1715 time to fit residues: 43.7551 Evaluate side-chains 165 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain D residue 37 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 84 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.150592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110148 restraints weight = 34092.600| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.35 r_work: 0.2988 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10556 Z= 0.130 Angle : 0.478 4.931 14382 Z= 0.248 Chirality : 0.039 0.194 1696 Planarity : 0.004 0.044 1802 Dihedral : 4.066 17.277 1504 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.82 % Allowed : 9.80 % Favored : 89.38 % 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: 1.15 (0.24), residues: 1336 helix: 1.79 (0.19), residues: 782 sheet: 0.28 (0.46), residues: 130 loop : -1.01 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.012 0.001 TYR D 37 PHE 0.016 0.001 PHE B 328 TRP 0.007 0.001 TRP A 241 HIS 0.003 0.001 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00312 (10552) covalent geometry : angle 0.47792 (14372) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.57309 ( 4) hydrogen bonds : bond 0.03300 ( 633) hydrogen bonds : angle 3.87613 ( 1905) link_NAG-ASN : bond 0.00273 ( 2) link_NAG-ASN : angle 0.93939 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 320 GLU cc_start: 0.7447 (tt0) cc_final: 0.6985 (mt-10) REVERT: B 534 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6681 (mt-10) REVERT: B 537 GLN cc_start: 0.7083 (mm-40) cc_final: 0.6399 (mt0) REVERT: C 50 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6476 (tt0) REVERT: A 33 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7218 (mpt180) REVERT: A 50 MET cc_start: 0.7701 (tpp) cc_final: 0.7430 (mmm) REVERT: A 499 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6851 (tm-30) REVERT: A 517 GLU cc_start: 0.8179 (tt0) cc_final: 0.7873 (tt0) REVERT: A 523 SER cc_start: 0.8844 (t) cc_final: 0.8586 (p) REVERT: A 541 LYS cc_start: 0.8172 (mttt) cc_final: 0.7808 (mtmt) REVERT: A 579 HIS cc_start: 0.6945 (m-70) cc_final: 0.6622 (m-70) REVERT: D 42 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7166 (ttp80) REVERT: D 50 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6698 (mt-10) REVERT: D 68 LYS cc_start: 0.7759 (mmmt) cc_final: 0.7182 (mmmt) REVERT: D 76 GLU cc_start: 0.7900 (tt0) cc_final: 0.7544 (tt0) outliers start: 9 outliers final: 7 residues processed: 167 average time/residue: 0.1808 time to fit residues: 45.9732 Evaluate side-chains 168 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain D residue 37 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.149766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109136 restraints weight = 34170.921| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.34 r_work: 0.3065 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10556 Z= 0.121 Angle : 0.476 4.879 14382 Z= 0.246 Chirality : 0.039 0.192 1696 Planarity : 0.004 0.043 1802 Dihedral : 4.019 16.924 1504 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.64 % Allowed : 10.16 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1336 helix: 1.82 (0.19), residues: 782 sheet: 0.70 (0.49), residues: 118 loop : -1.01 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.012 0.001 TYR B 526 PHE 0.019 0.001 PHE B 270 TRP 0.007 0.001 TRP A 241 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00288 (10552) covalent geometry : angle 0.47521 (14372) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.55854 ( 4) hydrogen bonds : bond 0.03257 ( 633) hydrogen bonds : angle 3.85075 ( 1905) link_NAG-ASN : bond 0.00263 ( 2) link_NAG-ASN : angle 0.91708 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 GLU cc_start: 0.7505 (tt0) cc_final: 0.7046 (mt-10) REVERT: B 463 MET cc_start: 0.8626 (mtp) cc_final: 0.8387 (mtp) REVERT: B 534 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6743 (mt-10) REVERT: C 50 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6534 (tt0) REVERT: A 33 ARG cc_start: 0.7711 (mmm160) cc_final: 0.7312 (mpt180) REVERT: A 50 MET cc_start: 0.7778 (tpp) cc_final: 0.7478 (mmm) REVERT: A 517 GLU cc_start: 0.8183 (tt0) cc_final: 0.7949 (tt0) REVERT: A 541 LYS cc_start: 0.8239 (mttt) cc_final: 0.7882 (mtmt) REVERT: A 579 HIS cc_start: 0.6993 (m-70) cc_final: 0.6665 (m-70) REVERT: D 42 ARG cc_start: 0.7561 (ttp80) cc_final: 0.7250 (ttp80) REVERT: D 68 LYS cc_start: 0.7787 (mmmt) cc_final: 0.7232 (mmmt) REVERT: D 76 GLU cc_start: 0.8007 (tt0) cc_final: 0.7661 (tt0) outliers start: 7 outliers final: 7 residues processed: 169 average time/residue: 0.1900 time to fit residues: 48.4481 Evaluate side-chains 169 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain D residue 37 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 97 optimal weight: 0.3980 chunk 125 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.156760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114863 restraints weight = 33705.457| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.47 r_work: 0.3003 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10556 Z= 0.099 Angle : 0.460 4.741 14382 Z= 0.236 Chirality : 0.039 0.183 1696 Planarity : 0.004 0.043 1802 Dihedral : 3.951 16.686 1504 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.82 % Allowed : 9.89 % Favored : 89.29 % 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: 1.43 (0.24), residues: 1336 helix: 2.00 (0.19), residues: 782 sheet: 0.79 (0.49), residues: 118 loop : -0.97 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 237 TYR 0.010 0.001 TYR D 37 PHE 0.016 0.001 PHE B 270 TRP 0.008 0.001 TRP A 241 HIS 0.002 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00234 (10552) covalent geometry : angle 0.45986 (14372) SS BOND : bond 0.00056 ( 2) SS BOND : angle 0.47695 ( 4) hydrogen bonds : bond 0.03007 ( 633) hydrogen bonds : angle 3.76886 ( 1905) link_NAG-ASN : bond 0.00284 ( 2) link_NAG-ASN : angle 0.70341 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 GLU cc_start: 0.7475 (tt0) cc_final: 0.7036 (mt-10) REVERT: B 534 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6726 (mt-10) REVERT: C 50 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6467 (tt0) REVERT: A 33 ARG cc_start: 0.7662 (mmm160) cc_final: 0.7284 (mpt180) REVERT: A 50 MET cc_start: 0.7720 (tpp) cc_final: 0.7428 (mmm) REVERT: A 517 GLU cc_start: 0.8159 (tt0) cc_final: 0.7932 (tt0) REVERT: A 541 LYS cc_start: 0.8188 (mttt) cc_final: 0.7844 (mtmt) REVERT: A 579 HIS cc_start: 0.6956 (m-70) cc_final: 0.6691 (m-70) REVERT: D 42 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7342 (ttp80) REVERT: D 68 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7209 (mmmt) REVERT: D 76 GLU cc_start: 0.7982 (tt0) cc_final: 0.7642 (tt0) outliers start: 9 outliers final: 7 residues processed: 166 average time/residue: 0.1966 time to fit residues: 48.6569 Evaluate side-chains 168 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain D residue 37 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 122 optimal weight: 0.0020 chunk 119 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.157431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.115491 restraints weight = 33778.977| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.49 r_work: 0.2999 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10556 Z= 0.094 Angle : 0.455 4.678 14382 Z= 0.234 Chirality : 0.038 0.177 1696 Planarity : 0.004 0.066 1802 Dihedral : 3.872 16.452 1504 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.73 % Allowed : 10.07 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1336 helix: 2.11 (0.20), residues: 782 sheet: 0.79 (0.48), residues: 118 loop : -0.91 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 33 TYR 0.010 0.001 TYR D 37 PHE 0.017 0.001 PHE B 270 TRP 0.008 0.001 TRP A 241 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00219 (10552) covalent geometry : angle 0.45528 (14372) SS BOND : bond 0.00034 ( 2) SS BOND : angle 0.46045 ( 4) hydrogen bonds : bond 0.02952 ( 633) hydrogen bonds : angle 3.72043 ( 1905) link_NAG-ASN : bond 0.00264 ( 2) link_NAG-ASN : angle 0.63255 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5171.18 seconds wall clock time: 88 minutes 11.05 seconds (5291.05 seconds total)