Starting phenix.real_space_refine on Fri Jul 3 09:08:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k87_36946/07_2026/8k87_36946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k87_36946/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k87_36946/07_2026/8k87_36946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k87_36946/07_2026/8k87_36946.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k87_36946/07_2026/8k87_36946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k87_36946/07_2026/8k87_36946.map" } 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-dev-6108/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: 2.47, per 1000 atoms: 0.18 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: 0.76 Conformation dependent library (CDL) restraints added in 397.6 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: 1.25 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: 1.95 Time building geometry restraints manager: 1.12 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: 18945 2.91 - 5.82: 217 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 - 0.057: 1773 0.057 - 0.113: 324 0.113 - 0.170: 44 0.170 - 0.226: 5 0.226 - 0.283: 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 2.46 2.17 0.28 2.00e-01 2.50e+01 2.00e+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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.110 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:5.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- 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= 0.274 Angle : 0.787 14.548 19188 Z= 0.529 Chirality : 0.046 0.283 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 0.00440 / 0.27 (13868) covalent geometry : angle 0.78743 / 0.53 (19188) hydrogen bonds : bond 0.17360 / 19.12 ( 589) hydrogen bonds : angle 7.13231 / 8.28 ( 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 : 0.422 Fit side-chains revert: symmetry clash 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: 0.3718 time to fit residues: 112.6949 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 : 0.482 ------------------------------------------------------------------------------- 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: 8.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.101678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.087213 restraints weight = 26863.235| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.03 r_work: 0.3389 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13868 Z= 0.146 Angle : 0.642 7.932 19188 Z= 0.358 Chirality : 0.044 0.196 2148 Planarity : 0.006 0.065 2152 Dihedral : 19.645 167.318 2777 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.46 % Allowed : 30.23 % 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: 0.37 (0.22), residues: 1444 helix: 1.09 (0.24), residues: 474 sheet: 0.92 (0.29), residues: 328 loop : -0.73 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 527 TYR 0.019 0.002 TYR F 84 PHE 0.024 0.001 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 0.00307 / 0.15 (13868) covalent geometry : angle 0.64229 / 0.36 (19188) hydrogen bonds : bond 0.04847 / 5.32 ( 589) hydrogen bonds : angle 5.58489 / 6.60 ( 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 290 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8707 (mm) cc_final: 0.8461 (mt) REVERT: A 70 GLU cc_start: 0.8757 (tt0) cc_final: 0.8284 (tt0) REVERT: A 121 ASN cc_start: 0.8402 (t0) cc_final: 0.8187 (t0) REVERT: A 197 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6506 (mpp) REVERT: A 278 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7288 (pp30) REVERT: A 392 GLN cc_start: 0.8479 (tt0) cc_final: 0.8255 (tt0) REVERT: B 369 LYS cc_start: 0.8558 (mmpt) cc_final: 0.8208 (mmpt) REVERT: B 384 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: B 401 GLN cc_start: 0.8610 (pm20) cc_final: 0.8178 (pp30) REVERT: B 561 CYS cc_start: 0.7565 (t) cc_final: 0.6713 (p) REVERT: B 566 GLU cc_start: 0.8192 (tp30) cc_final: 0.7892 (pm20) REVERT: F 220 LYS cc_start: 0.8504 (ptpt) cc_final: 0.8190 (ptpt) REVERT: F 299 MET cc_start: 0.8773 (ptp) cc_final: 0.8029 (ppp) REVERT: F 370 THR cc_start: 0.8689 (t) cc_final: 0.8454 (p) REVERT: F 428 LEU cc_start: 0.8526 (mm) cc_final: 0.8210 (tp) REVERT: G 477 ASN cc_start: 0.8723 (m-40) cc_final: 0.8483 (t0) REVERT: G 504 MET cc_start: 0.9090 (mpt) cc_final: 0.8776 (mmp) REVERT: G 512 LYS cc_start: 0.9023 (tttt) cc_final: 0.8776 (tttp) outliers start: 43 outliers final: 25 residues processed: 271 average time/residue: 0.3716 time to fit residues: 113.4795 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 : 0.415 ------------------------------------------------------------------------------- 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: 7.9990 chunk 149 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 126 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.101164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.086700 restraints weight = 26853.733| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.02 r_work: 0.3375 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1236 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= 0.141 Angle : 0.607 7.885 19188 Z= 0.336 Chirality : 0.043 0.216 2148 Planarity : 0.005 0.054 2152 Dihedral : 19.496 163.240 2757 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.86 % Allowed : 29.42 % 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: 0.55 (0.22), residues: 1444 helix: 1.58 (0.25), residues: 440 sheet: 0.72 (0.28), residues: 354 loop : -0.66 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 527 TYR 0.025 0.002 TYR F 84 PHE 0.023 0.001 PHE A 143 TRP 0.012 0.001 TRP F 340 HIS 0.016 0.001 HIS G 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (13868) covalent geometry : angle 0.60676 / 0.34 (19188) hydrogen bonds : bond 0.04298 / 4.77 ( 589) hydrogen bonds : angle 5.12237 / 6.07 ( 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 300 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8774 (mm) cc_final: 0.8484 (mt) REVERT: A 70 GLU cc_start: 0.8665 (tt0) cc_final: 0.8107 (tt0) REVERT: A 121 ASN cc_start: 0.8426 (t0) cc_final: 0.8172 (t0) REVERT: A 197 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7257 (mpp) REVERT: A 221 ASP cc_start: 0.8147 (m-30) cc_final: 0.7655 (m-30) REVERT: B 360 LYS cc_start: 0.8835 (mtpm) cc_final: 0.8425 (pptt) REVERT: B 384 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: B 401 GLN cc_start: 0.8626 (pm20) cc_final: 0.8180 (pp30) REVERT: B 442 ARG cc_start: 0.8663 (ttm110) cc_final: 0.8265 (mtp-110) REVERT: B 561 CYS cc_start: 0.7560 (t) cc_final: 0.6734 (p) REVERT: F 61 MET cc_start: 0.8646 (mmt) cc_final: 0.8192 (mmt) REVERT: F 107 CYS cc_start: 0.8051 (t) cc_final: 0.7655 (p) REVERT: F 220 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8207 (ptpt) REVERT: F 392 GLN cc_start: 0.8137 (tt0) cc_final: 0.7925 (tt0) REVERT: F 428 LEU cc_start: 0.8512 (mm) cc_final: 0.8222 (tp) REVERT: G 477 ASN cc_start: 0.8717 (m-40) cc_final: 0.8482 (t0) REVERT: G 504 MET cc_start: 0.9042 (mpt) cc_final: 0.8672 (mmp) REVERT: G 506 LYS cc_start: 0.8767 (mttp) cc_final: 0.8397 (tptt) REVERT: G 512 LYS cc_start: 0.8961 (tttt) cc_final: 0.8713 (tttp) outliers start: 48 outliers final: 31 residues processed: 282 average time/residue: 0.3694 time to fit residues: 117.1202 Evaluate side-chains 271 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 0.6980 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.100647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.086243 restraints weight = 26788.306| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.01 r_work: 0.3368 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13868 Z= 0.141 Angle : 0.596 8.139 19188 Z= 0.329 Chirality : 0.042 0.214 2148 Planarity : 0.005 0.054 2152 Dihedral : 19.436 165.020 2757 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.50 % Allowed : 29.50 % Favored : 66.00 % 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: 0.51 (0.22), residues: 1444 helix: 1.56 (0.25), residues: 442 sheet: 0.67 (0.28), residues: 354 loop : -0.69 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 62 TYR 0.048 0.002 TYR F 84 PHE 0.023 0.001 PHE A 143 TRP 0.011 0.001 TRP G 543 HIS 0.007 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (13868) covalent geometry : angle 0.59615 / 0.33 (19188) hydrogen bonds : bond 0.04106 / 4.60 ( 589) hydrogen bonds : angle 4.92299 / 5.89 ( 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 308 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 252 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8759 (mm) cc_final: 0.8511 (mt) REVERT: A 121 ASN cc_start: 0.8495 (t0) cc_final: 0.8242 (t0) REVERT: A 220 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7875 (mttt) REVERT: B 360 LYS cc_start: 0.8860 (mtpm) cc_final: 0.8419 (pptt) REVERT: B 371 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8657 (pp) REVERT: B 384 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: B 401 GLN cc_start: 0.8574 (pm20) cc_final: 0.8138 (pp30) REVERT: B 442 ARG cc_start: 0.8658 (ttm110) cc_final: 0.8373 (mtp-110) REVERT: B 561 CYS cc_start: 0.7448 (t) cc_final: 0.6607 (p) REVERT: F 61 MET cc_start: 0.8758 (mmt) cc_final: 0.8464 (mmt) REVERT: F 107 CYS cc_start: 0.8067 (t) cc_final: 0.7685 (p) REVERT: F 220 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8237 (ptpt) REVERT: F 269 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.7818 (tpp-160) REVERT: F 328 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: F 392 GLN cc_start: 0.8168 (tt0) cc_final: 0.7934 (tt0) REVERT: F 428 LEU cc_start: 0.8542 (mm) cc_final: 0.8262 (tp) REVERT: G 401 GLN cc_start: 0.7838 (pp30) cc_final: 0.7598 (pp30) REVERT: G 477 ASN cc_start: 0.8728 (m-40) cc_final: 0.8488 (t0) REVERT: G 512 LYS cc_start: 0.8916 (tttt) cc_final: 0.8694 (tttp) outliers start: 56 outliers final: 37 residues processed: 280 average time/residue: 0.3631 time to fit residues: 114.8338 Evaluate side-chains 273 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 220 LYS 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 371 LEU Chi-restraints excluded: chain B residue 384 GLU 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 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 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 Chi-restraints excluded: chain G residue 509 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.0020 chunk 82 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 80 optimal weight: 0.2980 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3733 r_free = 0.3733 target = 0.099407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.084987 restraints weight = 27058.027| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.02 r_work: 0.3346 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13868 Z= 0.166 Angle : 0.610 8.490 19188 Z= 0.336 Chirality : 0.043 0.204 2148 Planarity : 0.005 0.057 2152 Dihedral : 19.351 165.859 2751 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.50 % Allowed : 30.47 % Favored : 65.03 % 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: 1.52 (0.25), residues: 442 sheet: 0.58 (0.28), residues: 354 loop : -0.70 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 527 TYR 0.034 0.002 TYR A 439 PHE 0.018 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 0.00367 / 0.17 (13868) covalent geometry : angle 0.60975 / 0.34 (19188) hydrogen bonds : bond 0.04102 / 4.59 ( 589) hydrogen bonds : angle 4.87122 / 5.84 ( 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 307 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 251 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8791 (mm) cc_final: 0.8513 (mt) REVERT: A 70 GLU cc_start: 0.8642 (tt0) cc_final: 0.8067 (tt0) REVERT: A 121 ASN cc_start: 0.8529 (t0) cc_final: 0.8242 (t0) REVERT: A 197 MET cc_start: 0.7698 (mpp) cc_final: 0.7201 (mpp) REVERT: A 220 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7815 (mttt) REVERT: A 439 TYR cc_start: 0.7913 (p90) cc_final: 0.7471 (p90) REVERT: B 384 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8540 (mp0) REVERT: B 401 GLN cc_start: 0.8630 (pm20) cc_final: 0.8200 (pp30) REVERT: B 442 ARG cc_start: 0.8723 (ttm110) cc_final: 0.8253 (mtp-110) REVERT: B 561 CYS cc_start: 0.7383 (t) cc_final: 0.6559 (p) REVERT: F 55 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7579 (tp) REVERT: F 61 MET cc_start: 0.8775 (mmt) cc_final: 0.8447 (mmt) REVERT: F 220 LYS cc_start: 0.8595 (ptpt) cc_final: 0.8276 (ptpt) REVERT: F 269 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.7970 (tpp-160) REVERT: F 328 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: F 392 GLN cc_start: 0.8208 (tt0) cc_final: 0.7996 (tt0) REVERT: F 428 LEU cc_start: 0.8593 (mm) cc_final: 0.8260 (tp) REVERT: G 377 LYS cc_start: 0.8558 (mptt) cc_final: 0.8142 (mptt) REVERT: G 401 GLN cc_start: 0.7901 (pp30) cc_final: 0.7614 (pp30) REVERT: G 512 LYS cc_start: 0.8918 (tttt) cc_final: 0.8691 (tttp) outliers start: 56 outliers final: 35 residues processed: 283 average time/residue: 0.3485 time to fit residues: 111.7903 Evaluate side-chains 279 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 384 GLU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 135 optimal weight: 0.0870 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3735 r_free = 0.3735 target = 0.099502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.085239 restraints weight = 26796.188| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.99 r_work: 0.3353 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13868 Z= 0.150 Angle : 0.616 8.883 19188 Z= 0.337 Chirality : 0.043 0.199 2148 Planarity : 0.005 0.067 2152 Dihedral : 19.290 166.392 2751 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.18 % Allowed : 31.35 % Favored : 64.47 % 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: 0.59 (0.22), residues: 1444 helix: 1.71 (0.25), residues: 430 sheet: 0.48 (0.29), residues: 354 loop : -0.50 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 527 TYR 0.029 0.002 TYR F 84 PHE 0.024 0.001 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 0.00331 / 0.15 (13868) covalent geometry : angle 0.61584 / 0.34 (19188) hydrogen bonds : bond 0.03978 / 4.48 ( 589) hydrogen bonds : angle 4.76930 / 5.68 ( 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 303 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8772 (mm) cc_final: 0.8519 (mt) REVERT: A 70 GLU cc_start: 0.8625 (tt0) cc_final: 0.7941 (tt0) REVERT: A 121 ASN cc_start: 0.8543 (t0) cc_final: 0.8260 (t0) REVERT: A 133 MET cc_start: 0.8252 (ptt) cc_final: 0.7949 (ptp) REVERT: A 197 MET cc_start: 0.7713 (mpp) cc_final: 0.7127 (mpp) REVERT: B 360 LYS cc_start: 0.8871 (mtpm) cc_final: 0.8387 (pptt) REVERT: B 384 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: B 401 GLN cc_start: 0.8660 (pm20) cc_final: 0.8136 (pp30) REVERT: B 519 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: B 561 CYS cc_start: 0.7490 (t) cc_final: 0.6667 (p) REVERT: F 46 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8611 (pp) REVERT: F 55 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7618 (tp) REVERT: F 61 MET cc_start: 0.8770 (mmt) cc_final: 0.8515 (mmt) REVERT: F 220 LYS cc_start: 0.8620 (ptpt) cc_final: 0.8300 (ptpt) REVERT: F 269 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8009 (tpp-160) REVERT: F 328 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: F 392 GLN cc_start: 0.8237 (tt0) cc_final: 0.8001 (tt0) REVERT: G 377 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8084 (mptt) REVERT: G 401 GLN cc_start: 0.7899 (pp30) cc_final: 0.7545 (pp30) REVERT: G 512 LYS cc_start: 0.8919 (tttt) cc_final: 0.8689 (tttp) outliers start: 52 outliers final: 35 residues processed: 282 average time/residue: 0.3804 time to fit residues: 120.7865 Evaluate side-chains 282 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 384 GLU 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 519 GLU 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 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 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 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 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: 0.7980 chunk 9 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.099918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.085537 restraints weight = 26832.646| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.00 r_work: 0.3357 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13868 Z= 0.143 Angle : 0.614 10.158 19188 Z= 0.337 Chirality : 0.043 0.206 2148 Planarity : 0.005 0.050 2152 Dihedral : 19.217 165.749 2751 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.58 % Allowed : 31.19 % Favored : 64.23 % 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: 0.60 (0.22), residues: 1444 helix: 1.76 (0.25), residues: 430 sheet: 0.56 (0.29), residues: 342 loop : -0.56 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 527 TYR 0.024 0.002 TYR F 84 PHE 0.031 0.002 PHE A 143 TRP 0.011 0.001 TRP A 340 HIS 0.020 0.001 HIS G 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13868) covalent geometry : angle 0.61405 / 0.34 (19188) hydrogen bonds : bond 0.03844 / 4.30 ( 589) hydrogen bonds : angle 4.72764 / 5.62 ( 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 310 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8635 (tt0) cc_final: 0.7902 (tt0) REVERT: A 121 ASN cc_start: 0.8553 (t0) cc_final: 0.8257 (t0) REVERT: A 133 MET cc_start: 0.8198 (ptt) cc_final: 0.7921 (ptp) REVERT: A 197 MET cc_start: 0.7728 (mpp) cc_final: 0.7096 (mpp) REVERT: A 221 ASP cc_start: 0.8016 (m-30) cc_final: 0.7500 (p0) REVERT: A 222 GLU cc_start: 0.6408 (mm-30) cc_final: 0.6052 (mm-30) REVERT: A 233 LYS cc_start: 0.8414 (mmpt) cc_final: 0.8176 (mmpt) REVERT: A 285 SER cc_start: 0.8313 (m) cc_final: 0.7853 (p) REVERT: A 309 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8445 (p) REVERT: B 384 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: B 401 GLN cc_start: 0.8664 (pm20) cc_final: 0.8154 (pp30) REVERT: B 442 ARG cc_start: 0.8710 (ttm110) cc_final: 0.8409 (mtp-110) REVERT: B 519 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: B 561 CYS cc_start: 0.7503 (t) cc_final: 0.6653 (p) REVERT: F 46 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8568 (pp) REVERT: F 61 MET cc_start: 0.8763 (mmt) cc_final: 0.8517 (mmt) REVERT: F 107 CYS cc_start: 0.8086 (t) cc_final: 0.7678 (p) REVERT: F 220 LYS cc_start: 0.8634 (ptpt) cc_final: 0.8331 (ptpt) REVERT: F 269 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8030 (tpp-160) REVERT: F 328 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7889 (mm-30) REVERT: F 392 GLN cc_start: 0.8236 (tt0) cc_final: 0.7992 (tt0) REVERT: G 342 SER cc_start: 0.8357 (p) cc_final: 0.8121 (m) REVERT: G 377 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8075 (mptt) REVERT: G 401 GLN cc_start: 0.7937 (pp30) cc_final: 0.7663 (pp30) REVERT: G 477 ASN cc_start: 0.8691 (m-40) cc_final: 0.8461 (t0) REVERT: G 512 LYS cc_start: 0.8916 (tttt) cc_final: 0.8692 (tttp) outliers start: 57 outliers final: 33 residues processed: 288 average time/residue: 0.3512 time to fit residues: 114.6495 Evaluate side-chains 281 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 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 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 309 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 384 GLU 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 519 GLU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 0.0870 chunk 77 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.098901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.084487 restraints weight = 26858.266| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.00 r_work: 0.3341 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13868 Z= 0.165 Angle : 0.637 11.760 19188 Z= 0.348 Chirality : 0.043 0.211 2148 Planarity : 0.005 0.076 2152 Dihedral : 19.155 166.286 2750 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.26 % Allowed : 32.23 % Favored : 63.50 % 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: 0.47 (0.22), residues: 1444 helix: 1.61 (0.25), residues: 442 sheet: 0.43 (0.29), residues: 354 loop : -0.63 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 62 TYR 0.026 0.002 TYR F 84 PHE 0.030 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 0.00369 / 0.17 (13868) covalent geometry : angle 0.63661 / 0.35 (19188) hydrogen bonds : bond 0.03914 / 4.39 ( 589) hydrogen bonds : angle 4.72765 / 5.62 ( 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 303 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 250 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8690 (tp) REVERT: A 70 GLU cc_start: 0.8639 (tt0) cc_final: 0.8122 (tt0) REVERT: A 121 ASN cc_start: 0.8598 (t0) cc_final: 0.8285 (t0) REVERT: A 133 MET cc_start: 0.8145 (ptt) cc_final: 0.7916 (ptp) REVERT: A 285 SER cc_start: 0.8356 (m) cc_final: 0.7895 (p) REVERT: A 309 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8414 (p) REVERT: B 384 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: B 401 GLN cc_start: 0.8676 (pm20) cc_final: 0.8161 (pp30) REVERT: B 442 ARG cc_start: 0.8747 (ttm110) cc_final: 0.8416 (mtp-110) REVERT: B 519 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: B 561 CYS cc_start: 0.7508 (t) cc_final: 0.6649 (p) REVERT: F 46 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8538 (pp) REVERT: F 61 MET cc_start: 0.8801 (mmt) cc_final: 0.8481 (mmt) REVERT: F 107 CYS cc_start: 0.8132 (t) cc_final: 0.7692 (p) REVERT: F 133 MET cc_start: 0.8417 (ptp) cc_final: 0.8185 (ttp) REVERT: F 197 MET cc_start: 0.7479 (mpp) cc_final: 0.7243 (mmt) REVERT: F 220 LYS cc_start: 0.8670 (ptpt) cc_final: 0.8345 (ptpt) REVERT: F 269 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.7996 (tpp-160) REVERT: F 328 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: F 392 GLN cc_start: 0.8226 (tt0) cc_final: 0.8011 (tt0) REVERT: G 342 SER cc_start: 0.8329 (p) cc_final: 0.8088 (m) REVERT: G 377 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8232 (mppt) REVERT: G 401 GLN cc_start: 0.7926 (pp30) cc_final: 0.7644 (pp30) REVERT: G 477 ASN cc_start: 0.8689 (m-40) cc_final: 0.8452 (t0) REVERT: G 512 LYS cc_start: 0.8931 (tttt) cc_final: 0.8705 (tttp) outliers start: 53 outliers final: 32 residues processed: 282 average time/residue: 0.3468 time to fit residues: 110.5911 Evaluate side-chains 284 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 309 THR 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 384 GLU 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 B residue 519 GLU 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 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: 1.9990 chunk 97 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 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 = 0.3713 r_free = 0.3713 target = 0.098209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.083854 restraints weight = 27077.999| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.01 r_work: 0.3327 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13868 Z= 0.177 Angle : 0.657 11.154 19188 Z= 0.359 Chirality : 0.044 0.231 2148 Planarity : 0.005 0.049 2152 Dihedral : 19.126 167.356 2750 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.70 % Allowed : 32.56 % 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: 0.42 (0.22), residues: 1444 helix: 1.60 (0.25), residues: 438 sheet: 0.50 (0.29), residues: 342 loop : -0.73 (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 0.031 0.002 PHE A 143 TRP 0.015 0.001 TRP F 340 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (13868) covalent geometry : angle 0.65729 / 0.36 (19188) hydrogen bonds : bond 0.04037 / 4.51 ( 589) hydrogen bonds : angle 4.74244 / 5.64 ( 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 291 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 245 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8679 (tp) REVERT: A 70 GLU cc_start: 0.8616 (tt0) cc_final: 0.8124 (tt0) REVERT: A 121 ASN cc_start: 0.8612 (t0) cc_final: 0.8297 (t0) REVERT: A 133 MET cc_start: 0.8203 (ptt) cc_final: 0.7977 (ptp) REVERT: A 285 SER cc_start: 0.8380 (m) cc_final: 0.7933 (p) REVERT: B 384 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: B 401 GLN cc_start: 0.8684 (pm20) cc_final: 0.8171 (pp30) REVERT: B 442 ARG cc_start: 0.8775 (ttm110) cc_final: 0.8440 (mtp-110) REVERT: B 561 CYS cc_start: 0.7561 (t) cc_final: 0.6700 (p) REVERT: F 46 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8539 (pp) REVERT: F 61 MET cc_start: 0.8802 (mmt) cc_final: 0.8462 (mmt) REVERT: F 107 CYS cc_start: 0.8148 (t) cc_final: 0.7687 (p) REVERT: F 197 MET cc_start: 0.7507 (mpp) cc_final: 0.7270 (mmt) REVERT: F 220 LYS cc_start: 0.8710 (ptpt) cc_final: 0.8380 (ptpt) REVERT: F 269 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.8007 (tpp-160) REVERT: F 328 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7859 (mm-30) REVERT: F 392 GLN cc_start: 0.8236 (tt0) cc_final: 0.8031 (tt0) REVERT: G 342 SER cc_start: 0.8331 (p) cc_final: 0.8088 (m) REVERT: G 377 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8239 (mppt) REVERT: G 401 GLN cc_start: 0.7930 (pp30) cc_final: 0.7650 (pp30) REVERT: G 512 LYS cc_start: 0.8954 (tttt) cc_final: 0.8732 (tttp) outliers start: 46 outliers final: 34 residues processed: 272 average time/residue: 0.3587 time to fit residues: 110.5037 Evaluate side-chains 283 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 384 GLU 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 B residue 508 GLU 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 246 GLN 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 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: 2.9990 chunk 146 optimal weight: 0.6980 chunk 85 optimal weight: 0.0870 chunk 84 optimal weight: 0.0570 chunk 22 optimal weight: 0.0870 chunk 77 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.100547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.086125 restraints weight = 26747.319| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.01 r_work: 0.3372 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13868 Z= 0.138 Angle : 0.667 12.201 19188 Z= 0.363 Chirality : 0.043 0.221 2148 Planarity : 0.005 0.076 2152 Dihedral : 19.142 166.386 2750 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.81 % Allowed : 33.60 % Favored : 63.59 % 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: 1.68 (0.25), residues: 438 sheet: 0.48 (0.29), residues: 342 loop : -0.65 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 62 TYR 0.035 0.002 TYR F 240 PHE 0.032 0.002 PHE F 323 TRP 0.011 0.001 TRP F 340 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (13868) covalent geometry : angle 0.66692 / 0.36 (19188) hydrogen bonds : bond 0.03760 / 4.20 ( 589) hydrogen bonds : angle 4.72651 / 5.62 ( 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 291 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8664 (tp) REVERT: A 121 ASN cc_start: 0.8560 (t0) cc_final: 0.8236 (t0) REVERT: A 133 MET cc_start: 0.8084 (ptt) cc_final: 0.7876 (ptp) REVERT: A 285 SER cc_start: 0.8342 (m) cc_final: 0.7887 (p) REVERT: B 384 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: B 401 GLN cc_start: 0.8678 (pm20) cc_final: 0.8167 (pp30) REVERT: B 442 ARG cc_start: 0.8720 (ttm110) cc_final: 0.8203 (mtp-110) REVERT: B 561 CYS cc_start: 0.7507 (t) cc_final: 0.6634 (p) REVERT: F 46 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8519 (pp) REVERT: F 61 MET cc_start: 0.8756 (mmt) cc_final: 0.8462 (mmt) REVERT: F 107 CYS cc_start: 0.8094 (t) cc_final: 0.7711 (p) REVERT: F 220 LYS cc_start: 0.8702 (ptpt) cc_final: 0.8360 (ptpt) REVERT: F 269 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.8069 (tpp-160) REVERT: F 328 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: G 342 SER cc_start: 0.8300 (p) cc_final: 0.8065 (m) REVERT: G 377 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8066 (mptt) REVERT: G 401 GLN cc_start: 0.7932 (pp30) cc_final: 0.7656 (pp30) REVERT: G 477 ASN cc_start: 0.8641 (m-40) cc_final: 0.8423 (t0) REVERT: G 508 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7353 (tm-30) REVERT: G 512 LYS cc_start: 0.8896 (tttt) cc_final: 0.8679 (tttp) outliers start: 35 outliers final: 28 residues processed: 277 average time/residue: 0.3523 time to fit residues: 110.3055 Evaluate side-chains 281 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 508 GLU 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 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 377 LYS 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: 0.3980 chunk 31 optimal weight: 0.5980 chunk 103 optimal weight: 0.0040 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.101085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.086622 restraints weight = 26814.796| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.03 r_work: 0.3380 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13868 Z= 0.141 Angle : 0.666 12.270 19188 Z= 0.363 Chirality : 0.043 0.229 2148 Planarity : 0.005 0.047 2152 Dihedral : 19.098 164.489 2750 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.97 % Allowed : 33.68 % 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: 0.45 (0.22), residues: 1444 helix: 1.65 (0.25), residues: 438 sheet: 0.46 (0.29), residues: 342 loop : -0.68 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 69 TYR 0.047 0.002 TYR F 84 PHE 0.029 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 0.00310 / 0.14 (13868) covalent geometry : angle 0.66624 / 0.36 (19188) hydrogen bonds : bond 0.03686 / 4.12 ( 589) hydrogen bonds : angle 4.69958 / 5.58 ( 1631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3681.78 seconds wall clock time: 63 minutes 34.82 seconds (3814.82 seconds total)