Starting phenix.real_space_refine on Thu Jul 2 23:13:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kco_37106/07_2026/8kco_37106_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kco_37106/07_2026/8kco_37106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kco_37106/07_2026/8kco_37106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kco_37106/07_2026/8kco_37106.map" model { file = "/net/cci-nas-00/data/ceres_data/8kco_37106/07_2026/8kco_37106_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kco_37106/07_2026/8kco_37106_neut.cif" } resolution = 2.8 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= 0.058 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 P 2 5.49 5 S 40 5.16 5 C 7106 2.51 5 N 1708 2.21 5 O 1976 1.98 5 F 5 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10837 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2436 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" 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: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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: "H" 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: "I" 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: "J" 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'N60': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 2.86, per 1000 atoms: 0.26 Number of scatterers: 10837 At special positions: 0 Unit cell: (110.888, 94.4194, 131.748, 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) S 40 16.00 P 2 15.00 F 5 9.00 O 1976 8.00 N 1708 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.02 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.01 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 BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 395.3 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2470 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 58.3% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 80 through 87 removed outlier: 3.877A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.023A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.704A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.718A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.515A pdb=" N THR A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.774A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.607A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 481 through 503 removed outlier: 3.611A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.562A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.520A pdb=" N GLN A 535 " --> pdb=" O ASN A 531 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 531 through 536' Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.737A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.513A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 79 through 103 removed outlier: 3.546A pdb=" N LEU B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.545A pdb=" N ALA B 98 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 156 removed outlier: 3.719A pdb=" N ARG B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 189 removed outlier: 3.592A pdb=" N ILE B 162 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.742A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 277 Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.831A pdb=" N PHE B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 429 Processing helix chain 'B' and resid 435 through 451 Processing helix chain 'B' and resid 453 through 464 Processing helix chain 'C' and resid 3 through 24 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 removed outlier: 3.844A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 103 removed outlier: 3.630A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 135 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.786A pdb=" N LEU C 142 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.669A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 204 removed outlier: 3.890A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.685A pdb=" N ALA C 212 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.562A pdb=" N GLY D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.555A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 42 Processing helix chain 'D' and resid 49 through 82 removed outlier: 4.163A pdb=" N ILE D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.360A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.834A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 275 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL A 363 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU A 365 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 279 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.871A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.673A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 288 through 289 583 hydrogen bonds defined for protein. 1686 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: 1.53 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1635 1.27 - 1.41: 2843 1.41 - 1.54: 6457 1.54 - 1.67: 121 1.67 - 1.81: 61 Bond restraints: 11117 Sorted by residual: bond pdb=" C LYS A 261 " pdb=" N PRO A 262 " ideal model delta sigma weight residual 1.332 1.510 -0.178 1.30e-02 5.92e+03 1.88e+02 bond pdb=" C ILE C 135 " pdb=" O ILE C 135 " ideal model delta sigma weight residual 1.239 1.140 0.099 1.13e-02 7.83e+03 7.67e+01 bond pdb=" C27 N60 B 501 " pdb=" C29 N60 B 501 " ideal model delta sigma weight residual 1.398 1.543 -0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" C26 N60 B 501 " pdb=" C31 N60 B 501 " ideal model delta sigma weight residual 1.392 1.534 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C31 N60 B 501 " pdb=" C32 N60 B 501 " ideal model delta sigma weight residual 1.401 1.543 -0.142 2.00e-02 2.50e+03 5.06e+01 ... (remaining 11112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 14715 2.96 - 5.91: 387 5.91 - 8.87: 55 8.87 - 11.82: 10 11.82 - 14.78: 3 Bond angle restraints: 15170 Sorted by residual: angle pdb=" C LYS A 261 " pdb=" N PRO A 262 " pdb=" CA PRO A 262 " ideal model delta sigma weight residual 119.76 132.30 -12.54 1.03e+00 9.43e-01 1.48e+02 angle pdb=" CA VAL C 134 " pdb=" C VAL C 134 " pdb=" O VAL C 134 " ideal model delta sigma weight residual 119.97 114.25 5.72 9.10e-01 1.21e+00 3.95e+01 angle pdb=" CA LYS A 261 " pdb=" C LYS A 261 " pdb=" N PRO A 262 " ideal model delta sigma weight residual 118.81 126.70 -7.89 1.29e+00 6.01e-01 3.74e+01 angle pdb=" C VAL C 134 " pdb=" N ILE C 135 " pdb=" CA ILE C 135 " ideal model delta sigma weight residual 121.52 112.96 8.56 1.44e+00 4.82e-01 3.53e+01 angle pdb=" N LYS B 80 " pdb=" CA LYS B 80 " pdb=" C LYS B 80 " ideal model delta sigma weight residual 111.69 104.94 6.75 1.23e+00 6.61e-01 3.02e+01 ... (remaining 15165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.59: 6625 23.59 - 47.17: 231 47.17 - 70.75: 43 70.75 - 94.34: 27 94.34 - 117.92: 17 Dihedral angle restraints: 6943 sinusoidal: 3110 harmonic: 3833 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 159 " pdb=" CB CYS A 159 " ideal model delta sinusoidal sigma weight residual -86.00 -172.00 86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -170.91 84.91 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CA ASN B 279 " pdb=" C ASN B 279 " pdb=" N GLU B 280 " pdb=" CA GLU B 280 " ideal model delta harmonic sigma weight residual -180.00 -143.84 -36.16 0 5.00e+00 4.00e-02 5.23e+01 ... (remaining 6940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1455 0.074 - 0.148: 308 0.148 - 0.222: 35 0.222 - 0.296: 7 0.296 - 0.371: 4 Chirality restraints: 1809 Sorted by residual: chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.14 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 1806 not shown) Planarity restraints: 1843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 260 " 0.018 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C LEU A 260 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU A 260 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS A 261 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.025 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP C 227 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 79 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ALA B 79 " 0.055 2.00e-02 2.50e+03 pdb=" O ALA B 79 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS B 80 " -0.019 2.00e-02 2.50e+03 ... (remaining 1840 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 623 2.72 - 3.27: 10517 3.27 - 3.81: 17665 3.81 - 4.36: 21672 4.36 - 4.90: 36656 Nonbonded interactions: 87133 Sorted by model distance: nonbonded pdb=" O THR B 291 " pdb=" OG1 THR B 291 " model vdw 2.180 3.040 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.229 3.040 nonbonded pdb=" CG2 THR B 291 " pdb=" CA GLY B 378 " model vdw 2.263 3.860 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP B 194 " pdb=" NE1 TRP D 74 " model vdw 2.283 3.120 ... (remaining 87128 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 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.220 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.810 Find NCS groups from input model: 0.070 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:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 : 0.010 0.178 11142 Z= 0.482 Angle : 1.200 14.777 15241 Z= 0.641 Chirality : 0.063 0.371 1809 Planarity : 0.008 0.077 1831 Dihedral : 14.742 117.924 4461 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.80 % Allowed : 2.22 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.39 % Twisted General : 0.24 % 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: -3.30 (0.19), residues: 1303 helix: -1.79 (0.16), residues: 710 sheet: -1.27 (0.47), residues: 107 loop : -2.85 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 342 TYR 0.030 0.003 TYR C 90 PHE 0.040 0.004 PHE A 448 TRP 0.052 0.004 TRP C 227 HIS 0.016 0.003 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00979 / 0.48 (11117) covalent geometry : angle 1.16864 / 0.64 (15170) SS BOND : bond 0.01192 / 0.59 ( 4) SS BOND : angle 3.35088 / 1.93 ( 8) hydrogen bonds : bond 0.16957 / 12.36 ( 583) hydrogen bonds : angle 6.69433 / 4.57 ( 1686) link_BETA1-3 : bond 0.00074 / 0.04 ( 1) link_BETA1-3 : angle 1.45430 / 0.91 ( 3) link_BETA1-4 : bond 0.00531 / 0.28 ( 7) link_BETA1-4 : angle 2.87909 / 2.20 ( 21) link_BETA1-6 : bond 0.00246 / 0.13 ( 1) link_BETA1-6 : angle 1.36511 / 1.01 ( 3) link_NAG-ASN : bond 0.01034 / 0.57 ( 12) link_NAG-ASN : angle 5.15903 / 3.60 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 231 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 ASP cc_start: 0.7794 (t70) cc_final: 0.7479 (t0) outliers start: 9 outliers final: 3 residues processed: 238 average time/residue: 0.5203 time to fit residues: 134.2487 Evaluate side-chains 126 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain C residue 135 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN A 305 GLN A 385 GLN A 444 HIS A 691 ASN B 81 HIS B 204 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077921 restraints weight = 19941.976| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.32 r_work: 0.2942 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11142 Z= 0.148 Angle : 0.742 10.494 15241 Z= 0.357 Chirality : 0.045 0.289 1809 Planarity : 0.005 0.058 1831 Dihedral : 12.532 104.163 2157 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.84 % Allowed : 11.01 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.97 (0.23), residues: 1303 helix: 0.49 (0.19), residues: 713 sheet: -1.15 (0.43), residues: 135 loop : -2.29 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 241 TYR 0.016 0.002 TYR B 256 PHE 0.033 0.002 PHE A 302 TRP 0.019 0.002 TRP D 36 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (11117) covalent geometry : angle 0.71994 / 0.35 (15170) SS BOND : bond 0.00438 / 0.22 ( 4) SS BOND : angle 1.14933 / 0.52 ( 8) hydrogen bonds : bond 0.04977 / 3.42 ( 583) hydrogen bonds : angle 4.33209 / 2.98 ( 1686) link_BETA1-3 : bond 0.00736 / 0.39 ( 1) link_BETA1-3 : angle 1.96529 / 1.49 ( 3) link_BETA1-4 : bond 0.00486 / 0.28 ( 7) link_BETA1-4 : angle 2.10602 / 1.52 ( 21) link_BETA1-6 : bond 0.01511 / 0.80 ( 1) link_BETA1-6 : angle 2.75721 / 2.55 ( 3) link_NAG-ASN : bond 0.00545 / 0.28 ( 12) link_NAG-ASN : angle 3.27014 / 2.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.413 Fit side-chains REVERT: A 82 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8809 (mp) REVERT: A 391 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8196 (ttp80) REVERT: B 257 ASP cc_start: 0.8639 (t70) cc_final: 0.8136 (t0) REVERT: B 276 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8176 (tp-100) REVERT: C 180 ASP cc_start: 0.9051 (t70) cc_final: 0.8594 (t0) REVERT: C 237 ARG cc_start: 0.7559 (mmm160) cc_final: 0.7263 (tpp80) REVERT: D 10 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: D 11 LYS cc_start: 0.8478 (mtpt) cc_final: 0.8062 (mtmt) outliers start: 32 outliers final: 14 residues processed: 165 average time/residue: 0.5324 time to fit residues: 95.3674 Evaluate side-chains 131 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain D residue 10 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 0.1980 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 ASN B 127 GLN C 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.095388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.072140 restraints weight = 19996.180| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.29 r_work: 0.2830 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11142 Z= 0.250 Angle : 0.770 10.732 15241 Z= 0.376 Chirality : 0.048 0.320 1809 Planarity : 0.005 0.059 1831 Dihedral : 10.861 117.023 2152 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.44 % Allowed : 12.52 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.20 (0.24), residues: 1303 helix: 1.25 (0.19), residues: 712 sheet: -1.12 (0.44), residues: 136 loop : -2.09 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 184 TYR 0.020 0.002 TYR A 173 PHE 0.033 0.003 PHE A 302 TRP 0.021 0.002 TRP C 209 HIS 0.007 0.002 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 (11117) covalent geometry : angle 0.74962 / 0.37 (15170) SS BOND : bond 0.00707 / 0.35 ( 4) SS BOND : angle 1.74344 / 0.92 ( 8) hydrogen bonds : bond 0.05323 / 3.69 ( 583) hydrogen bonds : angle 4.09700 / 2.82 ( 1686) link_BETA1-3 : bond 0.00659 / 0.35 ( 1) link_BETA1-3 : angle 1.74331 / 1.14 ( 3) link_BETA1-4 : bond 0.00392 / 0.22 ( 7) link_BETA1-4 : angle 2.39320 / 1.71 ( 21) link_BETA1-6 : bond 0.01425 / 0.75 ( 1) link_BETA1-6 : angle 2.27726 / 1.90 ( 3) link_NAG-ASN : bond 0.00461 / 0.22 ( 12) link_NAG-ASN : angle 3.13666 / 2.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 117 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8987 (mmm) REVERT: A 115 THR cc_start: 0.8544 (p) cc_final: 0.8263 (t) REVERT: A 212 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 310 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8486 (tp30) REVERT: A 367 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8605 (mt0) REVERT: B 257 ASP cc_start: 0.8642 (t70) cc_final: 0.8077 (t0) REVERT: B 273 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8254 (mt-10) REVERT: B 277 GLU cc_start: 0.8722 (pp20) cc_final: 0.8270 (pp20) REVERT: B 454 GLN cc_start: 0.8809 (tp40) cc_final: 0.8577 (tp40) REVERT: C 10 THR cc_start: 0.9264 (t) cc_final: 0.9035 (p) REVERT: C 180 ASP cc_start: 0.9062 (t70) cc_final: 0.8682 (t0) REVERT: D 10 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: D 11 LYS cc_start: 0.8432 (mtpt) cc_final: 0.8211 (mtmt) REVERT: D 40 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: D 47 TYR cc_start: 0.7175 (m-80) cc_final: 0.6672 (m-80) REVERT: D 65 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8809 (tp) outliers start: 50 outliers final: 23 residues processed: 153 average time/residue: 0.5034 time to fit residues: 83.6513 Evaluate side-chains 138 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 0.0670 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN B 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.074620 restraints weight = 20429.629| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.37 r_work: 0.2871 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11142 Z= 0.138 Angle : 0.658 9.614 15241 Z= 0.323 Chirality : 0.044 0.283 1809 Planarity : 0.004 0.056 1831 Dihedral : 10.031 115.202 2152 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.64 % Allowed : 13.68 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.35 (0.24), residues: 1303 helix: 1.81 (0.19), residues: 708 sheet: -0.88 (0.45), residues: 131 loop : -2.02 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 184 TYR 0.014 0.001 TYR A 569 PHE 0.030 0.002 PHE A 302 TRP 0.012 0.001 TRP D 36 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (11117) covalent geometry : angle 0.64121 / 0.32 (15170) SS BOND : bond 0.00432 / 0.22 ( 4) SS BOND : angle 1.27557 / 0.62 ( 8) hydrogen bonds : bond 0.04370 / 3.01 ( 583) hydrogen bonds : angle 3.93550 / 2.71 ( 1686) link_BETA1-3 : bond 0.00686 / 0.36 ( 1) link_BETA1-3 : angle 1.53759 / 0.99 ( 3) link_BETA1-4 : bond 0.00406 / 0.23 ( 7) link_BETA1-4 : angle 1.99993 / 1.40 ( 21) link_BETA1-6 : bond 0.01246 / 0.66 ( 1) link_BETA1-6 : angle 2.72509 / 2.48 ( 3) link_NAG-ASN : bond 0.00474 / 0.24 ( 12) link_NAG-ASN : angle 2.56917 / 1.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8879 (mmm) REVERT: A 115 THR cc_start: 0.8466 (p) cc_final: 0.8214 (t) REVERT: A 310 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8468 (tp30) REVERT: A 391 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8062 (ttp80) REVERT: A 583 ARG cc_start: 0.7706 (ttt90) cc_final: 0.7487 (ttt90) REVERT: B 257 ASP cc_start: 0.8560 (t70) cc_final: 0.8044 (t0) REVERT: B 269 ARG cc_start: 0.8478 (ttt-90) cc_final: 0.7853 (ttp80) REVERT: C 24 THR cc_start: 0.9203 (m) cc_final: 0.8911 (p) REVERT: C 180 ASP cc_start: 0.9080 (t70) cc_final: 0.8724 (t0) REVERT: D 10 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: D 40 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: D 47 TYR cc_start: 0.7156 (m-80) cc_final: 0.6650 (m-80) outliers start: 41 outliers final: 17 residues processed: 145 average time/residue: 0.4298 time to fit residues: 67.9254 Evaluate side-chains 130 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.096818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.073529 restraints weight = 20416.456| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.37 r_work: 0.2851 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11142 Z= 0.170 Angle : 0.663 9.571 15241 Z= 0.326 Chirality : 0.044 0.272 1809 Planarity : 0.004 0.054 1831 Dihedral : 9.688 113.451 2152 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.55 % Allowed : 14.21 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.56 (0.24), residues: 1303 helix: 1.99 (0.19), residues: 710 sheet: -0.84 (0.45), residues: 131 loop : -1.92 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 241 TYR 0.015 0.001 TYR A 569 PHE 0.030 0.002 PHE A 302 TRP 0.015 0.001 TRP D 36 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (11117) covalent geometry : angle 0.64674 / 0.32 (15170) SS BOND : bond 0.00522 / 0.26 ( 4) SS BOND : angle 1.42730 / 0.72 ( 8) hydrogen bonds : bond 0.04438 / 3.07 ( 583) hydrogen bonds : angle 3.90083 / 2.69 ( 1686) link_BETA1-3 : bond 0.00677 / 0.36 ( 1) link_BETA1-3 : angle 1.59738 / 0.98 ( 3) link_BETA1-4 : bond 0.00329 / 0.19 ( 7) link_BETA1-4 : angle 1.93282 / 1.37 ( 21) link_BETA1-6 : bond 0.01248 / 0.66 ( 1) link_BETA1-6 : angle 2.75471 / 2.50 ( 3) link_NAG-ASN : bond 0.00421 / 0.22 ( 12) link_NAG-ASN : angle 2.52053 / 1.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8869 (mmm) REVERT: A 115 THR cc_start: 0.8453 (p) cc_final: 0.8207 (t) REVERT: A 212 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8271 (mp) REVERT: A 310 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8423 (tp30) REVERT: A 367 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8602 (mt0) REVERT: A 391 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8027 (ttp80) REVERT: A 677 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8591 (m-80) REVERT: B 257 ASP cc_start: 0.8486 (t70) cc_final: 0.8040 (t0) REVERT: B 269 ARG cc_start: 0.8660 (ttt-90) cc_final: 0.7840 (ttp80) REVERT: B 273 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8376 (mt-10) REVERT: B 277 GLU cc_start: 0.8580 (pp20) cc_final: 0.8168 (pp20) REVERT: C 10 THR cc_start: 0.9210 (t) cc_final: 0.8969 (p) REVERT: C 59 VAL cc_start: 0.9113 (t) cc_final: 0.8725 (m) REVERT: D 54 LYS cc_start: 0.8728 (tppt) cc_final: 0.8431 (tppp) outliers start: 40 outliers final: 23 residues processed: 144 average time/residue: 0.4574 time to fit residues: 72.1206 Evaluate side-chains 135 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 25 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 17 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075593 restraints weight = 20307.137| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.35 r_work: 0.2892 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11142 Z= 0.119 Angle : 0.619 9.416 15241 Z= 0.303 Chirality : 0.042 0.259 1809 Planarity : 0.004 0.052 1831 Dihedral : 9.169 105.065 2152 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.55 % Allowed : 14.92 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.84 (0.24), residues: 1303 helix: 2.25 (0.20), residues: 709 sheet: -0.79 (0.45), residues: 131 loop : -1.84 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 241 TYR 0.013 0.001 TYR A 569 PHE 0.029 0.001 PHE A 302 TRP 0.011 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (11117) covalent geometry : angle 0.60593 / 0.30 (15170) SS BOND : bond 0.00369 / 0.18 ( 4) SS BOND : angle 1.12209 / 0.55 ( 8) hydrogen bonds : bond 0.03847 / 2.65 ( 583) hydrogen bonds : angle 3.80148 / 2.61 ( 1686) link_BETA1-3 : bond 0.00731 / 0.38 ( 1) link_BETA1-3 : angle 1.30366 / 0.88 ( 3) link_BETA1-4 : bond 0.00403 / 0.22 ( 7) link_BETA1-4 : angle 1.64597 / 1.15 ( 21) link_BETA1-6 : bond 0.01498 / 0.79 ( 1) link_BETA1-6 : angle 3.17889 / 2.80 ( 3) link_NAG-ASN : bond 0.00387 / 0.20 ( 12) link_NAG-ASN : angle 2.16275 / 1.59 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8752 (mmm) REVERT: A 115 THR cc_start: 0.8462 (p) cc_final: 0.8241 (t) REVERT: A 310 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8399 (tp30) REVERT: A 391 ARG cc_start: 0.8380 (ttp80) cc_final: 0.8041 (ttp80) REVERT: A 677 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8567 (m-80) REVERT: B 257 ASP cc_start: 0.8346 (t70) cc_final: 0.7931 (t0) REVERT: B 269 ARG cc_start: 0.8685 (ttt-90) cc_final: 0.7899 (ttp80) REVERT: B 273 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8319 (mt-10) REVERT: B 277 GLU cc_start: 0.8534 (pp20) cc_final: 0.8135 (pp20) REVERT: C 10 THR cc_start: 0.9173 (t) cc_final: 0.8957 (p) REVERT: C 24 THR cc_start: 0.9128 (m) cc_final: 0.8822 (p) REVERT: C 59 VAL cc_start: 0.9097 (t) cc_final: 0.8668 (m) REVERT: D 54 LYS cc_start: 0.8711 (tppt) cc_final: 0.8398 (tppp) outliers start: 40 outliers final: 22 residues processed: 147 average time/residue: 0.4861 time to fit residues: 77.7754 Evaluate side-chains 133 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 313 GLN A 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.073892 restraints weight = 19922.208| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.29 r_work: 0.2857 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11142 Z= 0.187 Angle : 0.664 9.427 15241 Z= 0.327 Chirality : 0.044 0.258 1809 Planarity : 0.005 0.097 1831 Dihedral : 9.168 97.000 2152 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.64 % Allowed : 15.72 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1303 helix: 2.25 (0.19), residues: 710 sheet: -0.74 (0.46), residues: 131 loop : -1.85 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 583 TYR 0.015 0.001 TYR A 569 PHE 0.029 0.002 PHE A 302 TRP 0.014 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (11117) covalent geometry : angle 0.64867 / 0.32 (15170) SS BOND : bond 0.00550 / 0.27 ( 4) SS BOND : angle 1.46028 / 0.75 ( 8) hydrogen bonds : bond 0.04381 / 3.03 ( 583) hydrogen bonds : angle 3.84665 / 2.65 ( 1686) link_BETA1-3 : bond 0.00614 / 0.32 ( 1) link_BETA1-3 : angle 1.50409 / 0.98 ( 3) link_BETA1-4 : bond 0.00260 / 0.15 ( 7) link_BETA1-4 : angle 1.77592 / 1.27 ( 21) link_BETA1-6 : bond 0.01445 / 0.76 ( 1) link_BETA1-6 : angle 3.36629 / 2.91 ( 3) link_NAG-ASN : bond 0.00352 / 0.17 ( 12) link_NAG-ASN : angle 2.38767 / 1.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8928 (mmm) REVERT: A 212 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8327 (mp) REVERT: A 310 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8362 (tp30) REVERT: A 391 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8070 (ttp80) REVERT: A 677 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8565 (m-80) REVERT: B 139 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7490 (ttm) REVERT: B 257 ASP cc_start: 0.8353 (t70) cc_final: 0.7970 (t0) REVERT: B 269 ARG cc_start: 0.8725 (ttt-90) cc_final: 0.7993 (ttp80) REVERT: B 273 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8426 (mt-10) REVERT: B 276 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8514 (tp-100) REVERT: B 277 GLU cc_start: 0.8591 (pp20) cc_final: 0.8267 (pp20) REVERT: C 10 THR cc_start: 0.9221 (t) cc_final: 0.8984 (p) REVERT: C 59 VAL cc_start: 0.9219 (t) cc_final: 0.8784 (m) outliers start: 41 outliers final: 26 residues processed: 138 average time/residue: 0.5037 time to fit residues: 75.9360 Evaluate side-chains 134 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.095901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.072816 restraints weight = 19994.699| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.28 r_work: 0.2834 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11142 Z= 0.212 Angle : 0.698 9.471 15241 Z= 0.342 Chirality : 0.046 0.254 1809 Planarity : 0.005 0.097 1831 Dihedral : 9.136 88.915 2152 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.20 % Allowed : 16.43 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.77 (0.24), residues: 1303 helix: 2.13 (0.19), residues: 717 sheet: -0.74 (0.46), residues: 132 loop : -1.85 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 241 TYR 0.021 0.002 TYR D 47 PHE 0.030 0.002 PHE A 302 TRP 0.014 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (11117) covalent geometry : angle 0.68273 / 0.34 (15170) SS BOND : bond 0.00610 / 0.30 ( 4) SS BOND : angle 1.64992 / 0.85 ( 8) hydrogen bonds : bond 0.04713 / 3.26 ( 583) hydrogen bonds : angle 3.89777 / 2.69 ( 1686) link_BETA1-3 : bond 0.00563 / 0.30 ( 1) link_BETA1-3 : angle 1.40777 / 0.94 ( 3) link_BETA1-4 : bond 0.00198 / 0.11 ( 7) link_BETA1-4 : angle 1.78977 / 1.31 ( 21) link_BETA1-6 : bond 0.01180 / 0.62 ( 1) link_BETA1-6 : angle 3.15612 / 2.50 ( 3) link_NAG-ASN : bond 0.00379 / 0.18 ( 12) link_NAG-ASN : angle 2.52808 / 1.94 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8912 (mmm) REVERT: A 212 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8374 (mp) REVERT: A 310 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8447 (tp30) REVERT: A 677 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8581 (m-80) REVERT: B 139 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7476 (ttm) REVERT: B 257 ASP cc_start: 0.8429 (t70) cc_final: 0.8073 (t0) REVERT: B 269 ARG cc_start: 0.8710 (ttt-90) cc_final: 0.7961 (ttp80) REVERT: B 276 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8590 (tp-100) REVERT: B 277 GLU cc_start: 0.8665 (pp20) cc_final: 0.8381 (pp20) REVERT: C 59 VAL cc_start: 0.9206 (t) cc_final: 0.8763 (m) outliers start: 36 outliers final: 24 residues processed: 135 average time/residue: 0.4802 time to fit residues: 70.6401 Evaluate side-chains 134 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 123 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.074419 restraints weight = 20346.892| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.36 r_work: 0.2864 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11142 Z= 0.133 Angle : 0.635 9.470 15241 Z= 0.313 Chirality : 0.043 0.245 1809 Planarity : 0.005 0.082 1831 Dihedral : 8.629 88.824 2152 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.93 % Allowed : 16.70 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.98 (0.25), residues: 1303 helix: 2.37 (0.20), residues: 711 sheet: -0.75 (0.46), residues: 132 loop : -1.80 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 241 TYR 0.013 0.001 TYR D 47 PHE 0.029 0.001 PHE A 302 TRP 0.011 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11117) covalent geometry : angle 0.62276 / 0.31 (15170) SS BOND : bond 0.00407 / 0.20 ( 4) SS BOND : angle 1.29358 / 0.63 ( 8) hydrogen bonds : bond 0.04090 / 2.81 ( 583) hydrogen bonds : angle 3.82790 / 2.64 ( 1686) link_BETA1-3 : bond 0.00704 / 0.37 ( 1) link_BETA1-3 : angle 1.12687 / 0.83 ( 3) link_BETA1-4 : bond 0.00337 / 0.18 ( 7) link_BETA1-4 : angle 1.51349 / 1.11 ( 21) link_BETA1-6 : bond 0.00935 / 0.49 ( 1) link_BETA1-6 : angle 3.28237 / 2.46 ( 3) link_NAG-ASN : bond 0.00365 / 0.19 ( 12) link_NAG-ASN : angle 2.18903 / 1.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8745 (mmm) REVERT: A 310 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8444 (tp30) REVERT: A 677 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: B 139 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7552 (ttm) REVERT: B 257 ASP cc_start: 0.8416 (t70) cc_final: 0.8064 (t0) REVERT: B 269 ARG cc_start: 0.8670 (ttt-90) cc_final: 0.7824 (ttp80) REVERT: B 273 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8253 (mt-10) REVERT: B 276 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8549 (tp-100) REVERT: B 277 GLU cc_start: 0.8666 (pp20) cc_final: 0.8363 (pp20) REVERT: C 10 THR cc_start: 0.9219 (t) cc_final: 0.9002 (p) REVERT: C 24 THR cc_start: 0.9158 (m) cc_final: 0.8814 (p) REVERT: C 59 VAL cc_start: 0.9095 (t) cc_final: 0.8588 (m) REVERT: C 184 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.7978 (mtm-85) REVERT: D 40 GLU cc_start: 0.8456 (tp30) cc_final: 0.8035 (tm-30) outliers start: 33 outliers final: 26 residues processed: 134 average time/residue: 0.4571 time to fit residues: 66.7105 Evaluate side-chains 131 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 92 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.074798 restraints weight = 19756.367| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.30 r_work: 0.2874 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11142 Z= 0.149 Angle : 0.644 9.475 15241 Z= 0.317 Chirality : 0.043 0.246 1809 Planarity : 0.005 0.082 1831 Dihedral : 8.521 88.802 2152 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.49 % Allowed : 17.41 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.96 (0.24), residues: 1303 helix: 2.31 (0.19), residues: 717 sheet: -0.76 (0.47), residues: 131 loop : -1.78 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 241 TYR 0.020 0.001 TYR D 47 PHE 0.029 0.002 PHE A 302 TRP 0.011 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (11117) covalent geometry : angle 0.63078 / 0.31 (15170) SS BOND : bond 0.00454 / 0.23 ( 4) SS BOND : angle 1.36425 / 0.68 ( 8) hydrogen bonds : bond 0.04166 / 2.85 ( 583) hydrogen bonds : angle 3.82104 / 2.63 ( 1686) link_BETA1-3 : bond 0.00693 / 0.36 ( 1) link_BETA1-3 : angle 1.18763 / 0.87 ( 3) link_BETA1-4 : bond 0.00280 / 0.15 ( 7) link_BETA1-4 : angle 1.55786 / 1.13 ( 21) link_BETA1-6 : bond 0.00882 / 0.46 ( 1) link_BETA1-6 : angle 3.22016 / 2.42 ( 3) link_NAG-ASN : bond 0.00341 / 0.17 ( 12) link_NAG-ASN : angle 2.21714 / 1.67 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8842 (mmm) REVERT: A 310 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8402 (tp30) REVERT: A 677 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8515 (m-80) REVERT: B 139 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7525 (ttm) REVERT: B 257 ASP cc_start: 0.8395 (t70) cc_final: 0.7990 (t0) REVERT: B 269 ARG cc_start: 0.8676 (ttt-90) cc_final: 0.7873 (ttp80) REVERT: B 273 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8253 (mt-10) REVERT: B 276 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8514 (tp-100) REVERT: B 277 GLU cc_start: 0.8677 (pp20) cc_final: 0.8388 (pp20) REVERT: C 10 THR cc_start: 0.9238 (t) cc_final: 0.9028 (p) REVERT: C 24 THR cc_start: 0.9175 (m) cc_final: 0.8835 (p) REVERT: C 59 VAL cc_start: 0.9145 (t) cc_final: 0.8630 (m) outliers start: 28 outliers final: 23 residues processed: 125 average time/residue: 0.4870 time to fit residues: 66.4826 Evaluate side-chains 130 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.1980 chunk 115 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.072074 restraints weight = 19990.543| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.29 r_work: 0.2821 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11142 Z= 0.238 Angle : 0.715 9.499 15241 Z= 0.352 Chirality : 0.046 0.250 1809 Planarity : 0.005 0.090 1831 Dihedral : 8.742 88.476 2152 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.93 % Allowed : 17.32 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.72 (0.24), residues: 1303 helix: 2.09 (0.19), residues: 716 sheet: -0.88 (0.46), residues: 130 loop : -1.84 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 241 TYR 0.026 0.002 TYR D 47 PHE 0.029 0.002 PHE A 302 TRP 0.013 0.001 TRP D 36 HIS 0.005 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (11117) covalent geometry : angle 0.70001 / 0.35 (15170) SS BOND : bond 0.00651 / 0.32 ( 4) SS BOND : angle 1.71377 / 0.89 ( 8) hydrogen bonds : bond 0.04943 / 3.40 ( 583) hydrogen bonds : angle 3.93933 / 2.72 ( 1686) link_BETA1-3 : bond 0.00576 / 0.30 ( 1) link_BETA1-3 : angle 1.42052 / 0.97 ( 3) link_BETA1-4 : bond 0.00261 / 0.13 ( 7) link_BETA1-4 : angle 1.84779 / 1.35 ( 21) link_BETA1-6 : bond 0.00785 / 0.41 ( 1) link_BETA1-6 : angle 2.90225 / 2.15 ( 3) link_NAG-ASN : bond 0.00399 / 0.19 ( 12) link_NAG-ASN : angle 2.57327 / 1.98 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.03 seconds wall clock time: 57 minutes 58.78 seconds (3478.78 seconds total)