Starting phenix.real_space_refine on Thu Aug 6 03:41:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k87_36946/08_2026/8k87_36946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k87_36946/08_2026/8k87_36946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k87_36946/08_2026/8k87_36946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k87_36946/08_2026/8k87_36946.map" model { file = "/net/cci-nas-00/data/ceres_data/8k87_36946/08_2026/8k87_36946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k87_36946/08_2026/8k87_36946.cif" } resolution = 2.9 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= 0.005 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 88 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 8248 2.51 5 N 2300 2.21 5 O 2690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13372 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain: "A" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439} Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2053 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "I" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain: "F" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439} Chain: "G" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2053 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.21, per 1000 atoms: 0.24 Number of scatterers: 13372 At special positions: 0 Unit cell: (92.828, 107.963, 165.476, 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 44 16.00 P 88 15.00 Mg 2 11.99 O 2690 8.00 N 2300 7.00 C 8248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 576.5 milliseconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 38.2% alpha, 25.1% beta 33 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 60 through 73 removed outlier: 3.825A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.879A pdb=" N GLY A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 134 through 137 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 151 through 158 removed outlier: 5.004A pdb=" N LYS A 156 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.859A pdb=" N LEU A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 208 removed outlier: 3.748A pdb=" N VAL A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 295 Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.785A pdb=" N PHE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.337A pdb=" N THR A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 Processing helix chain 'A' and resid 460 through 463 removed outlier: 4.071A pdb=" N VAL A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'B' and resid 355 through 367 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.930A pdb=" N ILE B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 414 through 430 Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 458 through 465 Processing helix chain 'B' and resid 513 through 519 removed outlier: 4.829A pdb=" N GLU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 528 Processing helix chain 'B' and resid 532 through 549 Processing helix chain 'F' and resid 29 through 37 Processing helix chain 'F' and resid 39 through 43 removed outlier: 3.898A pdb=" N CYS F 43 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 73 removed outlier: 3.792A pdb=" N LEU F 64 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 95 Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 111 through 120 removed outlier: 3.816A pdb=" N GLY F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 133 Processing helix chain 'F' and resid 133 through 140 removed outlier: 3.761A pdb=" N PHE F 137 " --> pdb=" O MET F 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 143 No H-bonds generated for 'chain 'F' and resid 141 through 143' Processing helix chain 'F' and resid 151 through 158 removed outlier: 5.017A pdb=" N LYS F 156 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 174 Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.806A pdb=" N LEU F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 208 removed outlier: 3.905A pdb=" N VAL F 196 " --> pdb=" O CYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 294 Processing helix chain 'F' and resid 312 through 323 removed outlier: 4.094A pdb=" N PHE F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing helix chain 'F' and resid 417 through 428 removed outlier: 4.641A pdb=" N THR F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 459 Processing helix chain 'F' and resid 460 through 463 removed outlier: 4.215A pdb=" N VAL F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 460 through 463' Processing helix chain 'F' and resid 470 through 472 No H-bonds generated for 'chain 'F' and resid 470 through 472' Processing helix chain 'G' and resid 355 through 367 Processing helix chain 'G' and resid 383 through 391 removed outlier: 3.533A pdb=" N ILE G 387 " --> pdb=" O GLY G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 414 Processing helix chain 'G' and resid 414 through 430 Processing helix chain 'G' and resid 455 through 457 No H-bonds generated for 'chain 'G' and resid 455 through 457' Processing helix chain 'G' and resid 458 through 466 Processing helix chain 'G' and resid 513 through 519 removed outlier: 4.938A pdb=" N GLU G 518 " --> pdb=" O ASP G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 520 through 529 Processing helix chain 'G' and resid 532 through 549 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.535A pdb=" N SER A 12 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 331 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 303 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL A 332 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A 305 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A 334 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS A 307 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 223 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N HIS A 306 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 225 " --> pdb=" O HIS A 306 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 232 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 248 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU A 256 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.688A pdb=" N VAL A 50 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N CYS A 107 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR A 54 " --> pdb=" O CYS A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.688A pdb=" N VAL A 50 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG A 51 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU A 147 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 53 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N TYR A 149 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A 55 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 146 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE A 183 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 148 " --> pdb=" O ILE A 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA7, first strand: chain 'B' and resid 335 through 338 removed outlier: 4.816A pdb=" N LEU B 501 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS B 444 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 338 removed outlier: 4.816A pdb=" N LEU B 501 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 371 through 374 removed outlier: 3.584A pdb=" N LEU B 371 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 378 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 346 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 556 through 561 removed outlier: 3.607A pdb=" N ALA B 569 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 13 removed outlier: 6.626A pdb=" N LEU F 331 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA F 223 " --> pdb=" O PHE F 304 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS F 306 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE F 225 " --> pdb=" O HIS F 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 25 through 27 removed outlier: 3.581A pdb=" N LYS F 214 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 98 through 99 removed outlier: 7.073A pdb=" N VAL F 50 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N CYS F 107 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR F 54 " --> pdb=" O CYS F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 98 through 99 removed outlier: 7.073A pdb=" N VAL F 50 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG F 51 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU F 147 " --> pdb=" O ARG F 51 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA F 53 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR F 149 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 55 " --> pdb=" O TYR F 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 355 through 356 removed outlier: 3.562A pdb=" N ALA F 355 " --> pdb=" O ASP F 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 381 through 382 removed outlier: 3.523A pdb=" N VAL F 394 " --> pdb=" O VAL F 382 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 335 through 337 removed outlier: 3.979A pdb=" N HIS G 444 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 335 through 337 Processing sheet with id=AC1, first strand: chain 'G' and resid 371 through 374 removed outlier: 3.569A pdb=" N VAL G 378 " --> pdb=" O VAL G 348 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER G 398 " --> pdb=" O THR G 349 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 556 through 561 removed outlier: 3.694A pdb=" N ALA G 569 " --> pdb=" O CYS G 561 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3304 1.33 - 1.45: 3132 1.45 - 1.57: 7192 1.57 - 1.69: 176 1.69 - 1.81: 64 Bond restraints: 13868 Sorted by residual: bond pdb=" N3 U I 10 " pdb=" C4 U I 10 " ideal model delta sigma weight residual 1.380 1.331 0.049 9.00e-03 1.23e+04 2.97e+01 bond pdb=" C3' DA H 15 " pdb=" C2' DA H 15 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3' DC C 20 " pdb=" C2' DC C 20 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.57e+00 bond pdb=" C3' DT H 24 " pdb=" C2' DT H 24 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.23e+00 bond pdb=" C3' DC H 21 " pdb=" C2' DC H 21 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.19e+00 ... (remaining 13863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 18942 2.91 - 5.82: 220 5.82 - 8.73: 21 8.73 - 11.64: 3 11.64 - 14.55: 2 Bond angle restraints: 19188 Sorted by residual: angle pdb=" O4 U I 10 " pdb=" C4 U I 10 " pdb=" C5 U I 10 " ideal model delta sigma weight residual 125.90 132.99 -7.09 6.00e-01 2.78e+00 1.39e+02 angle pdb=" CA PRO B 353 " pdb=" N PRO B 353 " pdb=" CD PRO B 353 " ideal model delta sigma weight residual 112.00 97.45 14.55 1.40e+00 5.10e-01 1.08e+02 angle pdb=" C4 U I 10 " pdb=" C5 U I 10 " pdb=" C6 U I 10 " ideal model delta sigma weight residual 119.70 124.03 -4.33 6.00e-01 2.78e+00 5.20e+01 angle pdb=" N3 U I 10 " pdb=" C4 U I 10 " pdb=" C5 U I 10 " ideal model delta sigma weight residual 114.60 110.59 4.01 6.00e-01 2.78e+00 4.47e+01 angle pdb=" C1' U I 10 " pdb=" N1 U I 10 " pdb=" C2 U I 10 " ideal model delta sigma weight residual 117.70 124.91 -7.21 1.20e+00 6.94e-01 3.61e+01 ... (remaining 19183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 7710 35.24 - 70.48: 492 70.48 - 105.72: 25 105.72 - 140.96: 2 140.96 - 176.20: 5 Dihedral angle restraints: 8234 sinusoidal: 4014 harmonic: 4220 Sorted by residual: dihedral pdb=" O4' U I 10 " pdb=" C1' U I 10 " pdb=" N1 U I 10 " pdb=" C2 U I 10 " ideal model delta sinusoidal sigma weight residual 200.00 23.80 176.20 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U I 8 " pdb=" C1' U I 8 " pdb=" N1 U I 8 " pdb=" C2 U I 8 " ideal model delta sinusoidal sigma weight residual 200.00 30.20 169.80 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U I 2 " pdb=" C1' U I 2 " pdb=" N1 U I 2 " pdb=" C2 U I 2 " ideal model delta sinusoidal sigma weight residual -160.00 -1.21 -158.79 1 1.50e+01 4.44e-03 8.24e+01 ... (remaining 8231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1762 0.059 - 0.119: 307 0.119 - 0.178: 73 0.178 - 0.237: 4 0.237 - 0.296: 2 Chirality restraints: 2148 Sorted by residual: chirality pdb=" C1' G D 7 " pdb=" O4' G D 7 " pdb=" C2' G D 7 " pdb=" N9 G D 7 " both_signs ideal model delta sigma weight residual False 2.47 2.17 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA PRO B 353 " pdb=" N PRO B 353 " pdb=" C PRO B 353 " pdb=" CB PRO B 353 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CG LEU A 46 " pdb=" CB LEU A 46 " pdb=" CD1 LEU A 46 " pdb=" CD2 LEU A 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2145 not shown) Planarity restraints: 2152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 352 " 0.094 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO B 353 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO B 353 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO B 353 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 178 " -0.085 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO A 179 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 367 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO B 368 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO B 368 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 368 " -0.056 5.00e-02 4.00e+02 ... (remaining 2149 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 125 2.52 - 3.12: 9715 3.12 - 3.71: 21751 3.71 - 4.31: 29834 4.31 - 4.90: 48733 Nonbonded interactions: 110158 Sorted by model distance: nonbonded pdb=" OP2 A D 1 " pdb="MG MG A 501 " model vdw 1.929 2.170 nonbonded pdb=" OXT MET A 473 " pdb="MG MG A 501 " model vdw 1.969 2.170 nonbonded pdb=" ND2 ASN A 434 " pdb="MG MG A 501 " model vdw 2.001 2.250 nonbonded pdb=" OG1 THR F 312 " pdb=" OD1 ASP F 314 " model vdw 2.122 3.040 nonbonded pdb=" O LEU A 426 " pdb=" OG1 THR A 429 " model vdw 2.133 3.040 ... (remaining 110153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } 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: 1.580 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.670 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.004 0.143 13868 Z= 0.276 Angle : 0.808 14.548 19188 Z= 0.554 Chirality : 0.049 0.296 2148 Planarity : 0.007 0.130 2152 Dihedral : 20.688 176.198 5522 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.09 % Allowed : 36.90 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.22), residues: 1444 helix: 1.50 (0.25), residues: 430 sheet: 0.98 (0.30), residues: 314 loop : -0.86 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 527 TYR 0.046 0.002 TYR F 84 PHE 0.027 0.002 PHE A 143 TRP 0.012 0.001 TRP F 218 HIS 0.008 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.28 (13868) covalent geometry : angle 0.80843 / 0.55 (19188) hydrogen bonds : bond 0.17360 / 19.48 ( 589) hydrogen bonds : angle 7.13231 / 8.55 ( 1631) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8858 (mm) cc_final: 0.8585 (mt) REVERT: A 70 GLU cc_start: 0.8822 (tt0) cc_final: 0.8214 (tt0) REVERT: A 133 MET cc_start: 0.8162 (ptt) cc_final: 0.7912 (ptp) REVERT: A 197 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6245 (mpp) REVERT: A 439 TYR cc_start: 0.7710 (p90) cc_final: 0.7326 (p90) REVERT: B 360 LYS cc_start: 0.8839 (mtpm) cc_final: 0.8469 (pptt) REVERT: B 561 CYS cc_start: 0.7575 (t) cc_final: 0.6489 (p) REVERT: F 214 LYS cc_start: 0.8627 (ptmm) cc_final: 0.8393 (ptpp) REVERT: F 220 LYS cc_start: 0.8374 (ptpt) cc_final: 0.7950 (ptmt) REVERT: F 264 GLU cc_start: 0.8204 (tt0) cc_final: 0.7962 (tp30) REVERT: F 299 MET cc_start: 0.8531 (ptp) cc_final: 0.7886 (ppp) REVERT: F 428 LEU cc_start: 0.8768 (mm) cc_final: 0.8416 (tp) REVERT: F 467 TYR cc_start: 0.7944 (m-80) cc_final: 0.7692 (m-80) REVERT: G 506 LYS cc_start: 0.8825 (mttp) cc_final: 0.8558 (tptp) outliers start: 26 outliers final: 22 residues processed: 270 average time/residue: 0.4386 time to fit residues: 132.9825 Evaluate side-chains 251 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 478 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN F 184 ASN F 310 HIS G 441 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.101413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.086989 restraints weight = 26875.725| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.01 r_work: 0.3384 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13868 Z= 0.148 Angle : 0.649 7.897 19188 Z= 0.360 Chirality : 0.044 0.204 2148 Planarity : 0.006 0.066 2152 Dihedral : 19.561 167.503 2777 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.54 % Allowed : 30.14 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.22), residues: 1444 helix: 1.08 (0.24), residues: 474 sheet: 0.91 (0.29), residues: 328 loop : -0.74 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 527 TYR 0.020 0.002 TYR F 84 PHE 0.023 0.002 PHE A 143 TRP 0.009 0.001 TRP F 340 HIS 0.026 0.001 HIS G 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (13868) covalent geometry : angle 0.64941 / 0.36 (19188) hydrogen bonds : bond 0.04945 / 5.48 ( 589) hydrogen bonds : angle 5.59910 / 6.80 ( 1631) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8709 (mm) cc_final: 0.8463 (mt) REVERT: A 70 GLU cc_start: 0.8762 (tt0) cc_final: 0.8288 (tt0) REVERT: A 121 ASN cc_start: 0.8409 (t0) cc_final: 0.8198 (t0) REVERT: A 197 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6496 (mpp) REVERT: A 278 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7294 (pp30) REVERT: A 392 GLN cc_start: 0.8485 (tt0) cc_final: 0.8268 (tt0) REVERT: B 369 LYS cc_start: 0.8566 (mmpt) cc_final: 0.8215 (mmpt) REVERT: B 384 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: B 401 GLN cc_start: 0.8613 (pm20) cc_final: 0.8156 (pp30) REVERT: B 561 CYS cc_start: 0.7570 (t) cc_final: 0.6717 (p) REVERT: B 566 GLU cc_start: 0.8191 (tp30) cc_final: 0.7899 (pm20) REVERT: F 220 LYS cc_start: 0.8505 (ptpt) cc_final: 0.8186 (ptpt) REVERT: F 299 MET cc_start: 0.8774 (ptp) cc_final: 0.8032 (ppp) REVERT: F 370 THR cc_start: 0.8695 (t) cc_final: 0.8460 (p) REVERT: F 428 LEU cc_start: 0.8537 (mm) cc_final: 0.8217 (tp) REVERT: G 477 ASN cc_start: 0.8725 (m-40) cc_final: 0.8485 (t0) REVERT: G 504 MET cc_start: 0.9093 (mpt) cc_final: 0.8782 (mmp) REVERT: G 512 LYS cc_start: 0.9031 (tttt) cc_final: 0.8785 (tttp) outliers start: 44 outliers final: 25 residues processed: 273 average time/residue: 0.4155 time to fit residues: 127.8267 Evaluate side-chains 262 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 509 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 126 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 ASN F 195 ASN G 437 HIS G 441 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.101377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.086904 restraints weight = 26802.036| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.02 r_work: 0.3380 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13868 Z= 0.136 Angle : 0.612 7.901 19188 Z= 0.337 Chirality : 0.043 0.210 2148 Planarity : 0.005 0.053 2152 Dihedral : 19.398 163.246 2757 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.70 % Allowed : 29.58 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.22), residues: 1444 helix: 1.60 (0.25), residues: 440 sheet: 0.73 (0.28), residues: 354 loop : -0.67 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 527 TYR 0.025 0.002 TYR F 84 PHE 0.023 0.001 PHE A 143 TRP 0.011 0.001 TRP F 340 HIS 0.017 0.001 HIS G 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (13868) covalent geometry : angle 0.61200 / 0.34 (19188) hydrogen bonds : bond 0.04322 / 4.86 ( 589) hydrogen bonds : angle 5.14374 / 6.27 ( 1631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8773 (mm) cc_final: 0.8482 (mt) REVERT: A 70 GLU cc_start: 0.8666 (tt0) cc_final: 0.8100 (tt0) REVERT: A 121 ASN cc_start: 0.8425 (t0) cc_final: 0.8169 (t0) REVERT: A 133 MET cc_start: 0.8313 (ptt) cc_final: 0.8039 (ptp) REVERT: A 197 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7189 (mpp) REVERT: A 221 ASP cc_start: 0.8131 (m-30) cc_final: 0.7884 (m-30) REVERT: B 360 LYS cc_start: 0.8831 (mtpm) cc_final: 0.8420 (pptt) REVERT: B 371 LEU cc_start: 0.8857 (pt) cc_final: 0.8550 (pp) REVERT: B 384 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8472 (mp0) REVERT: B 401 GLN cc_start: 0.8625 (pm20) cc_final: 0.8180 (pp30) REVERT: B 561 CYS cc_start: 0.7561 (t) cc_final: 0.6733 (p) REVERT: F 61 MET cc_start: 0.8669 (mmt) cc_final: 0.8215 (mmt) REVERT: F 107 CYS cc_start: 0.8047 (t) cc_final: 0.7652 (p) REVERT: F 220 LYS cc_start: 0.8519 (ptpt) cc_final: 0.8199 (ptpt) REVERT: F 299 MET cc_start: 0.8731 (ptp) cc_final: 0.8016 (ppp) REVERT: F 392 GLN cc_start: 0.8134 (tt0) cc_final: 0.7924 (tt0) REVERT: F 428 LEU cc_start: 0.8518 (mm) cc_final: 0.8228 (tp) REVERT: G 477 ASN cc_start: 0.8715 (m-40) cc_final: 0.8481 (t0) REVERT: G 506 LYS cc_start: 0.8758 (mttp) cc_final: 0.8388 (tptt) REVERT: G 512 LYS cc_start: 0.8961 (tttt) cc_final: 0.8715 (tttp) outliers start: 46 outliers final: 31 residues processed: 279 average time/residue: 0.4265 time to fit residues: 133.3369 Evaluate side-chains 270 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN A 392 GLN B 334 ASN B 534 GLN ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.100868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.086392 restraints weight = 26797.240| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.02 r_work: 0.3372 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13868 Z= 0.141 Angle : 0.599 7.774 19188 Z= 0.329 Chirality : 0.042 0.212 2148 Planarity : 0.005 0.054 2152 Dihedral : 19.336 165.226 2757 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.50 % Allowed : 29.74 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.22), residues: 1444 helix: 1.56 (0.25), residues: 442 sheet: 0.68 (0.29), residues: 354 loop : -0.67 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 62 TYR 0.050 0.002 TYR F 84 PHE 0.024 0.002 PHE A 143 TRP 0.012 0.001 TRP G 543 HIS 0.007 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (13868) covalent geometry : angle 0.59870 / 0.33 (19188) hydrogen bonds : bond 0.04124 / 4.68 ( 589) hydrogen bonds : angle 4.93670 / 6.04 ( 1631) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 249 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8758 (mm) cc_final: 0.8506 (mt) REVERT: A 121 ASN cc_start: 0.8470 (t0) cc_final: 0.8190 (t0) REVERT: A 220 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7898 (mttm) REVERT: A 248 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7366 (p90) REVERT: B 360 LYS cc_start: 0.8843 (mtpm) cc_final: 0.8425 (pptt) REVERT: B 401 GLN cc_start: 0.8565 (pm20) cc_final: 0.8122 (pp30) REVERT: B 561 CYS cc_start: 0.7430 (t) cc_final: 0.6592 (p) REVERT: F 61 MET cc_start: 0.8794 (mmt) cc_final: 0.8502 (mmt) REVERT: F 107 CYS cc_start: 0.8051 (t) cc_final: 0.7680 (p) REVERT: F 220 LYS cc_start: 0.8541 (ptpt) cc_final: 0.8237 (ptpt) REVERT: F 232 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8756 (tttm) REVERT: F 269 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.7814 (tpp-160) REVERT: F 328 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: F 392 GLN cc_start: 0.8167 (tt0) cc_final: 0.7954 (tt0) REVERT: F 428 LEU cc_start: 0.8550 (mm) cc_final: 0.8254 (tp) REVERT: G 401 GLN cc_start: 0.7860 (pp30) cc_final: 0.7618 (pp30) REVERT: G 477 ASN cc_start: 0.8717 (m-40) cc_final: 0.8476 (t0) REVERT: G 504 MET cc_start: 0.9036 (mpt) cc_final: 0.8653 (mmp) REVERT: G 512 LYS cc_start: 0.8912 (tttt) cc_final: 0.8690 (tttp) outliers start: 56 outliers final: 37 residues processed: 279 average time/residue: 0.3713 time to fit residues: 117.1315 Evaluate side-chains 273 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 56 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN A 415 ASN ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.099454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.085033 restraints weight = 27065.278| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.02 r_work: 0.3348 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13868 Z= 0.163 Angle : 0.613 8.282 19188 Z= 0.336 Chirality : 0.043 0.210 2148 Planarity : 0.005 0.056 2152 Dihedral : 19.243 165.968 2753 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.34 % Allowed : 30.39 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1444 helix: 1.55 (0.25), residues: 442 sheet: 0.60 (0.28), residues: 354 loop : -0.67 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 527 TYR 0.031 0.002 TYR F 84 PHE 0.019 0.002 PHE A 143 TRP 0.011 0.001 TRP A 340 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (13868) covalent geometry : angle 0.61298 / 0.34 (19188) hydrogen bonds : bond 0.04109 / 4.66 ( 589) hydrogen bonds : angle 4.85895 / 5.95 ( 1631) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 249 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8797 (mm) cc_final: 0.8521 (mt) REVERT: A 70 GLU cc_start: 0.8637 (tt0) cc_final: 0.8078 (tt0) REVERT: A 121 ASN cc_start: 0.8520 (t0) cc_final: 0.8237 (t0) REVERT: A 197 MET cc_start: 0.7693 (mpp) cc_final: 0.7234 (mpp) REVERT: A 220 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7901 (mttt) REVERT: A 248 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.7303 (p90) REVERT: B 401 GLN cc_start: 0.8638 (pm20) cc_final: 0.8202 (pp30) REVERT: B 561 CYS cc_start: 0.7364 (t) cc_final: 0.6533 (p) REVERT: F 55 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7592 (tp) REVERT: F 61 MET cc_start: 0.8791 (mmt) cc_final: 0.8506 (mmt) REVERT: F 220 LYS cc_start: 0.8594 (ptpt) cc_final: 0.8271 (ptpt) REVERT: F 232 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8762 (tttm) REVERT: F 269 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.7949 (tpp-160) REVERT: F 328 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: F 392 GLN cc_start: 0.8208 (tt0) cc_final: 0.7997 (tt0) REVERT: F 428 LEU cc_start: 0.8596 (mm) cc_final: 0.8263 (tp) REVERT: G 377 LYS cc_start: 0.8539 (mptt) cc_final: 0.8119 (mptt) REVERT: G 401 GLN cc_start: 0.7900 (pp30) cc_final: 0.7692 (pp30) REVERT: G 512 LYS cc_start: 0.8926 (tttt) cc_final: 0.8696 (tttp) outliers start: 54 outliers final: 37 residues processed: 279 average time/residue: 0.3750 time to fit residues: 119.0162 Evaluate side-chains 279 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 509 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN A 392 GLN ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.099944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.085524 restraints weight = 26747.784| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.01 r_work: 0.3358 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13868 Z= 0.143 Angle : 0.609 9.140 19188 Z= 0.333 Chirality : 0.043 0.199 2148 Planarity : 0.005 0.059 2152 Dihedral : 19.187 166.414 2753 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.10 % Allowed : 31.03 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1444 helix: 1.75 (0.25), residues: 430 sheet: 0.53 (0.29), residues: 354 loop : -0.51 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 527 TYR 0.027 0.002 TYR F 84 PHE 0.022 0.002 PHE A 143 TRP 0.011 0.001 TRP A 340 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13868) covalent geometry : angle 0.60930 / 0.33 (19188) hydrogen bonds : bond 0.03958 / 4.51 ( 589) hydrogen bonds : angle 4.77787 / 5.82 ( 1631) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 253 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8771 (mm) cc_final: 0.8521 (mt) REVERT: A 70 GLU cc_start: 0.8629 (tt0) cc_final: 0.7952 (tt0) REVERT: A 121 ASN cc_start: 0.8527 (t0) cc_final: 0.8247 (t0) REVERT: A 197 MET cc_start: 0.7712 (mpp) cc_final: 0.7143 (mpp) REVERT: B 360 LYS cc_start: 0.8870 (mtpm) cc_final: 0.8390 (pptt) REVERT: B 401 GLN cc_start: 0.8665 (pm20) cc_final: 0.8137 (pp30) REVERT: B 561 CYS cc_start: 0.7454 (t) cc_final: 0.6647 (p) REVERT: F 46 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8616 (pp) REVERT: F 55 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7579 (tp) REVERT: F 61 MET cc_start: 0.8806 (mmt) cc_final: 0.8457 (mmt) REVERT: F 83 TYR cc_start: 0.8181 (t80) cc_final: 0.7903 (t80) REVERT: F 220 LYS cc_start: 0.8621 (ptpt) cc_final: 0.8280 (ptpt) REVERT: F 269 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.7975 (tpp-160) REVERT: F 328 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: F 392 GLN cc_start: 0.8224 (tt0) cc_final: 0.7989 (tt0) REVERT: F 428 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8235 (tp) REVERT: G 377 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8133 (mptt) REVERT: G 401 GLN cc_start: 0.7886 (pp30) cc_final: 0.7582 (pp30) REVERT: G 512 LYS cc_start: 0.8916 (tttt) cc_final: 0.8685 (tttp) outliers start: 51 outliers final: 36 residues processed: 281 average time/residue: 0.3670 time to fit residues: 116.1747 Evaluate side-chains 281 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 410 SER Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 509 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 9 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN F 195 ASN ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.097549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083152 restraints weight = 27179.515| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.01 r_work: 0.3311 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13868 Z= 0.202 Angle : 0.658 9.867 19188 Z= 0.358 Chirality : 0.044 0.214 2148 Planarity : 0.005 0.050 2152 Dihedral : 19.103 167.179 2753 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.66 % Allowed : 31.59 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.22), residues: 1444 helix: 1.64 (0.25), residues: 430 sheet: 0.47 (0.29), residues: 354 loop : -0.60 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 301 TYR 0.024 0.002 TYR F 84 PHE 0.029 0.002 PHE A 143 TRP 0.014 0.001 TRP A 340 HIS 0.021 0.001 HIS G 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (13868) covalent geometry : angle 0.65757 / 0.36 (19188) hydrogen bonds : bond 0.04300 / 4.88 ( 589) hydrogen bonds : angle 4.79981 / 5.85 ( 1631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8813 (mm) cc_final: 0.8580 (mt) REVERT: A 70 GLU cc_start: 0.8670 (tt0) cc_final: 0.8176 (tt0) REVERT: A 121 ASN cc_start: 0.8589 (t0) cc_final: 0.8295 (t0) REVERT: A 285 SER cc_start: 0.8258 (m) cc_final: 0.7787 (p) REVERT: B 371 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8626 (pp) REVERT: B 401 GLN cc_start: 0.8688 (pm20) cc_final: 0.8183 (pp30) REVERT: B 561 CYS cc_start: 0.7460 (t) cc_final: 0.6626 (p) REVERT: F 46 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8550 (pp) REVERT: F 55 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7291 (tp) REVERT: F 61 MET cc_start: 0.8794 (mmt) cc_final: 0.8405 (mmt) REVERT: F 107 CYS cc_start: 0.8121 (t) cc_final: 0.7675 (p) REVERT: F 220 LYS cc_start: 0.8677 (ptpt) cc_final: 0.8358 (ptpt) REVERT: F 269 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8004 (tpp-160) REVERT: F 328 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: F 330 GLU cc_start: 0.8212 (tp30) cc_final: 0.7998 (tp30) REVERT: F 392 GLN cc_start: 0.8253 (tt0) cc_final: 0.8049 (tt0) REVERT: F 413 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8615 (p) REVERT: G 342 SER cc_start: 0.8368 (p) cc_final: 0.8107 (m) REVERT: G 377 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8264 (mppt) REVERT: G 401 GLN cc_start: 0.7941 (pp30) cc_final: 0.7602 (pp30) REVERT: G 512 LYS cc_start: 0.8942 (tttt) cc_final: 0.8714 (tttp) outliers start: 58 outliers final: 38 residues processed: 281 average time/residue: 0.3824 time to fit residues: 122.0385 Evaluate side-chains 284 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 509 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 0.0020 chunk 77 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN F 246 GLN G 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.099030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.084601 restraints weight = 26683.812| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.91 r_work: 0.3343 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13868 Z= 0.156 Angle : 0.650 11.740 19188 Z= 0.353 Chirality : 0.043 0.223 2148 Planarity : 0.005 0.060 2152 Dihedral : 19.078 167.955 2752 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.78 % Allowed : 32.48 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.22), residues: 1444 helix: 1.53 (0.25), residues: 438 sheet: 0.53 (0.29), residues: 342 loop : -0.71 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 62 TYR 0.023 0.002 TYR F 84 PHE 0.032 0.002 PHE A 143 TRP 0.013 0.001 TRP A 340 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (13868) covalent geometry : angle 0.65004 / 0.35 (19188) hydrogen bonds : bond 0.04000 / 4.55 ( 589) hydrogen bonds : angle 4.76618 / 5.80 ( 1631) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8684 (tp) REVERT: A 64 LEU cc_start: 0.8768 (mm) cc_final: 0.8496 (mt) REVERT: A 70 GLU cc_start: 0.8561 (tt0) cc_final: 0.8077 (tt0) REVERT: A 121 ASN cc_start: 0.8552 (t0) cc_final: 0.8249 (t0) REVERT: A 285 SER cc_start: 0.8359 (m) cc_final: 0.7918 (p) REVERT: B 401 GLN cc_start: 0.8684 (pm20) cc_final: 0.8176 (pp30) REVERT: B 561 CYS cc_start: 0.7440 (t) cc_final: 0.6728 (p) REVERT: F 46 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8539 (pp) REVERT: F 61 MET cc_start: 0.8725 (mmt) cc_final: 0.8452 (mmt) REVERT: F 107 CYS cc_start: 0.8076 (t) cc_final: 0.7665 (p) REVERT: F 133 MET cc_start: 0.8429 (ptp) cc_final: 0.8195 (ttp) REVERT: F 220 LYS cc_start: 0.8697 (ptpt) cc_final: 0.8364 (ptpt) REVERT: F 269 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.8020 (tpp-160) REVERT: F 328 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: F 330 GLU cc_start: 0.8167 (tp30) cc_final: 0.7961 (mm-30) REVERT: F 413 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8449 (p) REVERT: G 342 SER cc_start: 0.8368 (p) cc_final: 0.8136 (m) REVERT: G 377 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8262 (mppt) REVERT: G 401 GLN cc_start: 0.7898 (pp30) cc_final: 0.7610 (pp30) REVERT: G 512 LYS cc_start: 0.8924 (tttt) cc_final: 0.8709 (tttp) outliers start: 47 outliers final: 31 residues processed: 276 average time/residue: 0.3918 time to fit residues: 122.1173 Evaluate side-chains 276 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 17 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN A 392 GLN G 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.098401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.083998 restraints weight = 27038.836| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.01 r_work: 0.3332 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13868 Z= 0.164 Angle : 0.668 11.319 19188 Z= 0.363 Chirality : 0.044 0.212 2148 Planarity : 0.005 0.048 2152 Dihedral : 19.032 166.742 2750 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.54 % Allowed : 33.12 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.22), residues: 1444 helix: 1.55 (0.25), residues: 438 sheet: 0.45 (0.29), residues: 342 loop : -0.72 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 69 TYR 0.030 0.002 TYR F 341 PHE 0.030 0.002 PHE A 143 TRP 0.014 0.001 TRP F 340 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (13868) covalent geometry : angle 0.66814 / 0.36 (19188) hydrogen bonds : bond 0.04018 / 4.55 ( 589) hydrogen bonds : angle 4.73699 / 5.75 ( 1631) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8675 (tp) REVERT: A 64 LEU cc_start: 0.8794 (mm) cc_final: 0.8560 (mt) REVERT: A 70 GLU cc_start: 0.8622 (tt0) cc_final: 0.8102 (tt0) REVERT: A 121 ASN cc_start: 0.8596 (t0) cc_final: 0.8283 (t0) REVERT: A 133 MET cc_start: 0.8165 (ptt) cc_final: 0.7897 (ptp) REVERT: A 285 SER cc_start: 0.8370 (m) cc_final: 0.7929 (p) REVERT: A 374 CYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7793 (t) REVERT: B 401 GLN cc_start: 0.8680 (pm20) cc_final: 0.8155 (pp30) REVERT: B 561 CYS cc_start: 0.7541 (t) cc_final: 0.6714 (p) REVERT: F 46 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8517 (pp) REVERT: F 61 MET cc_start: 0.8794 (mmt) cc_final: 0.8488 (mmt) REVERT: F 107 CYS cc_start: 0.8135 (t) cc_final: 0.7663 (p) REVERT: F 133 MET cc_start: 0.8447 (ptp) cc_final: 0.8235 (ttp) REVERT: F 220 LYS cc_start: 0.8705 (ptpt) cc_final: 0.8363 (ptpt) REVERT: F 269 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.7949 (tpp-160) REVERT: F 302 LYS cc_start: 0.8902 (tttt) cc_final: 0.8675 (tmtp) REVERT: F 328 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: F 330 GLU cc_start: 0.8172 (tp30) cc_final: 0.7911 (mm-30) REVERT: F 358 SER cc_start: 0.9022 (p) cc_final: 0.8821 (t) REVERT: F 392 GLN cc_start: 0.8243 (tt0) cc_final: 0.7911 (tt0) REVERT: F 413 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8319 (p) REVERT: G 342 SER cc_start: 0.8335 (p) cc_final: 0.8091 (m) REVERT: G 377 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8248 (mppt) REVERT: G 401 GLN cc_start: 0.7874 (pp30) cc_final: 0.7576 (pp30) REVERT: G 512 LYS cc_start: 0.8943 (tttt) cc_final: 0.8724 (tttp) outliers start: 44 outliers final: 30 residues processed: 272 average time/residue: 0.4039 time to fit residues: 124.0333 Evaluate side-chains 275 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 84 optimal weight: 0.0050 chunk 22 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.099680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.085214 restraints weight = 26861.366| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.02 r_work: 0.3355 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13868 Z= 0.144 Angle : 0.673 12.529 19188 Z= 0.365 Chirality : 0.043 0.220 2148 Planarity : 0.005 0.059 2152 Dihedral : 19.031 166.683 2750 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.97 % Allowed : 33.76 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1444 helix: 1.57 (0.25), residues: 438 sheet: 0.46 (0.29), residues: 342 loop : -0.67 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 62 TYR 0.038 0.002 TYR F 84 PHE 0.031 0.002 PHE A 143 TRP 0.012 0.001 TRP F 340 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13868) covalent geometry : angle 0.67337 / 0.36 (19188) hydrogen bonds : bond 0.03827 / 4.34 ( 589) hydrogen bonds : angle 4.72134 / 5.72 ( 1631) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8685 (tp) REVERT: A 70 GLU cc_start: 0.8591 (tt0) cc_final: 0.8086 (tt0) REVERT: A 121 ASN cc_start: 0.8575 (t0) cc_final: 0.8263 (t0) REVERT: A 133 MET cc_start: 0.8136 (ptt) cc_final: 0.7930 (ptp) REVERT: A 285 SER cc_start: 0.8376 (m) cc_final: 0.7922 (p) REVERT: A 374 CYS cc_start: 0.8185 (t) cc_final: 0.7696 (t) REVERT: B 401 GLN cc_start: 0.8634 (pm20) cc_final: 0.8117 (pp30) REVERT: B 561 CYS cc_start: 0.7546 (t) cc_final: 0.6713 (p) REVERT: F 46 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8502 (pp) REVERT: F 61 MET cc_start: 0.8790 (mmt) cc_final: 0.8501 (mmt) REVERT: F 107 CYS cc_start: 0.8132 (t) cc_final: 0.7677 (p) REVERT: F 133 MET cc_start: 0.8413 (ptp) cc_final: 0.8187 (ttp) REVERT: F 220 LYS cc_start: 0.8708 (ptpt) cc_final: 0.8359 (ptpt) REVERT: F 269 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.7965 (tpp-160) REVERT: F 302 LYS cc_start: 0.8892 (tttt) cc_final: 0.8680 (tmtp) REVERT: F 328 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: F 330 GLU cc_start: 0.8163 (tp30) cc_final: 0.7897 (mm-30) REVERT: F 392 GLN cc_start: 0.8286 (tt0) cc_final: 0.7946 (tt0) REVERT: F 413 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8309 (p) REVERT: G 342 SER cc_start: 0.8334 (p) cc_final: 0.8093 (m) REVERT: G 377 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8088 (mptt) REVERT: G 401 GLN cc_start: 0.7863 (pp30) cc_final: 0.7562 (pp30) REVERT: G 512 LYS cc_start: 0.8907 (tttt) cc_final: 0.8687 (tttp) outliers start: 37 outliers final: 29 residues processed: 272 average time/residue: 0.3828 time to fit residues: 117.7619 Evaluate side-chains 278 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 76 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 103 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 0.0770 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN G 334 ASN G 437 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.101220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.086691 restraints weight = 26741.626| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.04 r_work: 0.3383 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13868 Z= 0.139 Angle : 0.674 12.689 19188 Z= 0.365 Chirality : 0.043 0.231 2148 Planarity : 0.005 0.060 2152 Dihedral : 19.004 165.015 2750 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.97 % Allowed : 34.24 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.22), residues: 1444 helix: 1.64 (0.25), residues: 438 sheet: 0.43 (0.29), residues: 342 loop : -0.67 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 25 TYR 0.024 0.002 TYR F 83 PHE 0.040 0.002 PHE F 323 TRP 0.014 0.001 TRP G 543 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (13868) covalent geometry : angle 0.67440 / 0.37 (19188) hydrogen bonds : bond 0.03737 / 4.22 ( 589) hydrogen bonds : angle 4.66926 / 5.65 ( 1631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3861.29 seconds wall clock time: 66 minutes 44.48 seconds (4004.48 seconds total)