Starting phenix.real_space_refine on Sat Aug 23 16:27:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k87_36946/08_2025/8k87_36946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k87_36946/08_2025/8k87_36946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k87_36946/08_2025/8k87_36946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k87_36946/08_2025/8k87_36946.map" model { file = "/net/cci-nas-00/data/ceres_data/8k87_36946/08_2025/8k87_36946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k87_36946/08_2025/8k87_36946.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 88 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 8248 2.51 5 N 2300 2.21 5 O 2690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13372 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain: "A" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439} Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2053 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "I" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain: "F" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439} Chain: "G" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2053 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.13, per 1000 atoms: 0.23 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: 0.98 Conformation dependent library (CDL) restraints added in 546.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.75 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: 2.04 Time building geometry restraints manager: 1.38 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=" CB PRO B 353 " pdb=" CG PRO B 353 " ideal model delta sigma weight residual 1.492 1.635 -0.143 5.00e-02 4.00e+02 8.14e+00 bond pdb=" N3 U I 10 " pdb=" C4 U I 10 " ideal model delta sigma weight residual 1.380 1.331 0.049 2.00e-02 2.50e+03 6.02e+00 bond pdb=" CB PRO F 17 " pdb=" CG PRO F 17 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.94e+00 bond pdb=" CB PRO A 179 " pdb=" CG PRO A 179 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.87e+00 bond pdb=" CB GLU G 432 " pdb=" CG GLU G 432 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.75e+00 ... (remaining 13863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 18944 2.91 - 5.82: 218 5.82 - 8.73: 21 8.73 - 11.64: 3 11.64 - 14.55: 2 Bond angle restraints: 19188 Sorted by residual: 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=" CA PRO F 17 " pdb=" N PRO F 17 " pdb=" CD PRO F 17 " ideal model delta sigma weight residual 112.00 104.72 7.28 1.40e+00 5.10e-01 2.70e+01 angle pdb=" CA PRO A 179 " pdb=" N PRO A 179 " pdb=" CD PRO A 179 " ideal model delta sigma weight residual 112.00 104.75 7.25 1.40e+00 5.10e-01 2.68e+01 angle pdb=" CA GLU G 432 " pdb=" CB GLU G 432 " pdb=" CG GLU G 432 " ideal model delta sigma weight residual 114.10 122.99 -8.89 2.00e+00 2.50e-01 1.98e+01 angle pdb=" CB MET A 383 " pdb=" CG MET A 383 " pdb=" SD MET A 383 " ideal model delta sigma weight residual 112.70 125.17 -12.47 3.00e+00 1.11e-01 1.73e+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: 1815 0.057 - 0.113: 291 0.113 - 0.170: 35 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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= 0.174 Angle : 0.766 14.548 19188 Z= 0.418 Chirality : 0.043 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 aren 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 covalent geometry : bond 0.00406 (13868) covalent geometry : angle 0.76629 (19188) hydrogen bonds : bond 0.17360 ( 589) hydrogen bonds : angle 7.13231 ( 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 : 0.322 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: 0.3987 time to fit residues: 120.5881 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 : 0.402 ------------------------------------------------------------------------------- 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: 4.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 392 GLN F 184 ASN F 310 HIS G 441 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.102633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.088102 restraints weight = 26714.833| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.04 r_work: 0.3399 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13868 Z= 0.133 Angle : 0.624 8.101 19188 Z= 0.329 Chirality : 0.042 0.167 2148 Planarity : 0.005 0.070 2152 Dihedral : 19.557 163.051 2777 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.10 % Allowed : 28.30 % Favored : 67.60 % 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 aren not related in a simple way. whole: 0.52 (0.22), residues: 1444 helix: 1.36 (0.24), residues: 456 sheet: 0.80 (0.29), residues: 342 loop : -0.61 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 527 TYR 0.023 0.002 TYR F 84 PHE 0.025 0.002 PHE A 143 TRP 0.010 0.001 TRP G 510 HIS 0.022 0.001 HIS G 441 Details of bonding type rmsd covalent geometry : bond 0.00295 (13868) covalent geometry : angle 0.62400 (19188) hydrogen bonds : bond 0.04120 ( 589) hydrogen bonds : angle 5.19931 ( 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 313 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8663 (tt0) cc_final: 0.8401 (tt0) REVERT: A 376 LEU cc_start: 0.8746 (tm) cc_final: 0.8543 (tt) REVERT: A 385 VAL cc_start: 0.8724 (m) cc_final: 0.8447 (t) REVERT: A 392 GLN cc_start: 0.8459 (tt0) cc_final: 0.8176 (tt0) REVERT: B 360 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8427 (pptt) REVERT: B 369 LYS cc_start: 0.8568 (mmpt) cc_final: 0.8249 (mmpt) REVERT: B 384 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8476 (mp0) REVERT: B 401 GLN cc_start: 0.8556 (pm20) cc_final: 0.8104 (pp30) REVERT: B 519 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: B 561 CYS cc_start: 0.7547 (t) cc_final: 0.6735 (p) REVERT: F 61 MET cc_start: 0.8724 (mmt) cc_final: 0.8314 (mmt) REVERT: F 107 CYS cc_start: 0.8017 (t) cc_final: 0.7582 (p) REVERT: F 220 LYS cc_start: 0.8489 (ptpt) cc_final: 0.8065 (ptmt) REVERT: F 232 LYS cc_start: 0.9103 (ttpp) cc_final: 0.8893 (ttpp) REVERT: F 299 MET cc_start: 0.8717 (ptp) cc_final: 0.7979 (ppp) REVERT: F 370 THR cc_start: 0.8685 (t) cc_final: 0.8476 (p) REVERT: F 392 GLN cc_start: 0.8229 (tt0) cc_final: 0.7990 (tt0) REVERT: F 428 LEU cc_start: 0.8472 (mm) cc_final: 0.8176 (tp) outliers start: 51 outliers final: 25 residues processed: 288 average time/residue: 0.4514 time to fit residues: 144.3674 Evaluate side-chains 265 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 197 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 265 PHE 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 360 LYS 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 501 LEU Chi-restraints excluded: chain B residue 519 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 403 LEU Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 459 LEU 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: 3.9990 chunk 45 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 126 optimal weight: 0.0010 chunk 7 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 389 ASN F 195 ASN ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.098881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.084483 restraints weight = 26897.261| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.01 r_work: 0.3330 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13868 Z= 0.165 Angle : 0.616 8.663 19188 Z= 0.324 Chirality : 0.042 0.157 2148 Planarity : 0.005 0.057 2152 Dihedral : 19.434 171.091 2759 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.70 % Allowed : 29.66 % Favored : 66.64 % 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 aren not related in a simple way. whole: 0.53 (0.22), residues: 1444 helix: 1.49 (0.24), residues: 442 sheet: 0.70 (0.28), residues: 354 loop : -0.62 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 69 TYR 0.030 0.002 TYR F 84 PHE 0.025 0.002 PHE A 143 TRP 0.013 0.001 TRP F 340 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00378 (13868) covalent geometry : angle 0.61642 (19188) hydrogen bonds : bond 0.04126 ( 589) hydrogen bonds : angle 4.82150 ( 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: 46 poor density : 254 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8464 (t0) cc_final: 0.8228 (t0) REVERT: A 375 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8406 (mp) REVERT: A 392 GLN cc_start: 0.8532 (tt0) cc_final: 0.8223 (tt0) REVERT: B 360 LYS cc_start: 0.8815 (mtpm) cc_final: 0.8376 (pptt) REVERT: B 384 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8465 (mp0) REVERT: B 401 GLN cc_start: 0.8640 (pm20) cc_final: 0.8210 (pp30) REVERT: B 442 ARG cc_start: 0.8736 (ttm110) cc_final: 0.8290 (mtp-110) REVERT: B 561 CYS cc_start: 0.7523 (t) cc_final: 0.6645 (p) REVERT: F 61 MET cc_start: 0.8808 (mmt) cc_final: 0.8395 (mmt) REVERT: F 107 CYS cc_start: 0.8142 (t) cc_final: 0.7579 (p) REVERT: F 220 LYS cc_start: 0.8535 (ptpt) cc_final: 0.8243 (ptpt) REVERT: F 232 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8725 (tttm) REVERT: F 370 THR cc_start: 0.8735 (t) cc_final: 0.8523 (p) REVERT: G 401 GLN cc_start: 0.7829 (pp30) cc_final: 0.7617 (pp30) outliers start: 46 outliers final: 25 residues processed: 283 average time/residue: 0.3888 time to fit residues: 123.4405 Evaluate side-chains 262 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 375 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU 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 262 THR Chi-restraints excluded: chain F residue 327 THR 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 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 485 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 71 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 13 optimal weight: 0.0170 chunk 30 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 0.0060 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN G 437 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.101989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087483 restraints weight = 26555.805| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.97 r_work: 0.3393 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13868 Z= 0.124 Angle : 0.593 9.039 19188 Z= 0.310 Chirality : 0.041 0.189 2148 Planarity : 0.005 0.050 2152 Dihedral : 19.223 166.751 2753 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.02 % Allowed : 29.26 % 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 aren not related in a simple way. whole: 0.73 (0.22), residues: 1444 helix: 1.76 (0.25), residues: 432 sheet: 0.68 (0.28), residues: 354 loop : -0.46 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 62 TYR 0.023 0.002 TYR F 84 PHE 0.027 0.001 PHE A 143 TRP 0.009 0.001 TRP G 510 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00278 (13868) covalent geometry : angle 0.59280 (19188) hydrogen bonds : bond 0.03450 ( 589) hydrogen bonds : angle 4.67409 ( 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 315 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8539 (tt0) cc_final: 0.8245 (tt0) REVERT: A 121 ASN cc_start: 0.8391 (t0) cc_final: 0.8140 (t0) REVERT: A 392 GLN cc_start: 0.8481 (tt0) cc_final: 0.8201 (tt0) REVERT: B 360 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8348 (pptt) REVERT: B 384 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8443 (mp0) REVERT: B 401 GLN cc_start: 0.8645 (pm20) cc_final: 0.8225 (pp30) REVERT: B 442 ARG cc_start: 0.8728 (ttm110) cc_final: 0.8297 (mtp-110) REVERT: B 561 CYS cc_start: 0.7450 (t) cc_final: 0.6574 (p) REVERT: F 61 MET cc_start: 0.8704 (mmt) cc_final: 0.8317 (mmt) REVERT: F 107 CYS cc_start: 0.8017 (t) cc_final: 0.7571 (p) REVERT: F 220 LYS cc_start: 0.8532 (ptpt) cc_final: 0.8150 (ptmt) REVERT: F 330 GLU cc_start: 0.8135 (tp30) cc_final: 0.7933 (mm-30) REVERT: F 370 THR cc_start: 0.8697 (t) cc_final: 0.8490 (p) REVERT: F 413 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8389 (p) REVERT: G 342 SER cc_start: 0.8293 (p) cc_final: 0.7991 (m) REVERT: G 357 SER cc_start: 0.9345 (OUTLIER) cc_final: 0.9124 (p) REVERT: G 401 GLN cc_start: 0.7804 (pp30) cc_final: 0.7525 (pp30) REVERT: G 477 ASN cc_start: 0.8656 (m-40) cc_final: 0.8435 (t0) REVERT: G 512 LYS cc_start: 0.8837 (tttt) cc_final: 0.8633 (tttp) outliers start: 50 outliers final: 31 residues processed: 294 average time/residue: 0.3790 time to fit residues: 126.3884 Evaluate side-chains 282 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE 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 360 LYS 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 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 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 56 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 58 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 278 GLN A 415 ASN B 534 GLN G 441 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.098791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.084424 restraints weight = 26979.760| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.02 r_work: 0.3335 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13868 Z= 0.168 Angle : 0.613 9.223 19188 Z= 0.322 Chirality : 0.041 0.172 2148 Planarity : 0.005 0.049 2152 Dihedral : 19.130 170.877 2753 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.06 % Allowed : 28.94 % 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 aren not related in a simple way. whole: 0.67 (0.22), residues: 1444 helix: 1.75 (0.25), residues: 430 sheet: 0.59 (0.28), residues: 354 loop : -0.48 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 69 TYR 0.023 0.002 TYR A 439 PHE 0.026 0.002 PHE A 143 TRP 0.014 0.001 TRP A 340 HIS 0.019 0.001 HIS G 441 Details of bonding type rmsd covalent geometry : bond 0.00388 (13868) covalent geometry : angle 0.61263 (19188) hydrogen bonds : bond 0.03751 ( 589) hydrogen bonds : angle 4.62465 ( 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 327 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 264 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8669 (tp) REVERT: A 70 GLU cc_start: 0.8609 (tt0) cc_final: 0.8252 (tt0) REVERT: A 121 ASN cc_start: 0.8466 (t0) cc_final: 0.8187 (t0) REVERT: A 220 LYS cc_start: 0.7896 (mttt) cc_final: 0.7606 (ttmt) REVERT: A 248 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7103 (p90) REVERT: A 285 SER cc_start: 0.8358 (m) cc_final: 0.7909 (p) REVERT: A 392 GLN cc_start: 0.8510 (tt0) cc_final: 0.8229 (tt0) REVERT: B 384 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: B 401 GLN cc_start: 0.8632 (pm20) cc_final: 0.8054 (pp30) REVERT: B 442 ARG cc_start: 0.8806 (ttm110) cc_final: 0.8329 (mtp-110) REVERT: B 518 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8423 (tm-30) REVERT: F 46 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8574 (pp) REVERT: F 61 MET cc_start: 0.8794 (mmt) cc_final: 0.8383 (mmt) REVERT: F 107 CYS cc_start: 0.8141 (t) cc_final: 0.7563 (p) REVERT: F 220 LYS cc_start: 0.8568 (ptpt) cc_final: 0.8183 (ptmt) REVERT: F 328 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: F 330 GLU cc_start: 0.8158 (tp30) cc_final: 0.7925 (mm-30) REVERT: F 370 THR cc_start: 0.8724 (t) cc_final: 0.8497 (p) REVERT: F 413 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8344 (p) REVERT: G 342 SER cc_start: 0.8292 (p) cc_final: 0.7986 (m) REVERT: G 357 SER cc_start: 0.9348 (OUTLIER) cc_final: 0.9108 (p) REVERT: G 377 LYS cc_start: 0.8527 (mptt) cc_final: 0.8317 (mppt) REVERT: G 401 GLN cc_start: 0.7905 (pp30) cc_final: 0.7648 (pp30) REVERT: G 477 ASN cc_start: 0.8655 (m-40) cc_final: 0.8426 (t0) REVERT: G 512 LYS cc_start: 0.8871 (tttt) cc_final: 0.8664 (tttp) outliers start: 63 outliers final: 35 residues processed: 299 average time/residue: 0.3960 time to fit residues: 132.9716 Evaluate side-chains 292 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 143 PHE Chi-restraints excluded: chain A residue 248 PHE 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 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 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 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 355 THR Chi-restraints excluded: chain G residue 357 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 0.1980 chunk 55 optimal weight: 0.0000 chunk 59 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 135 optimal weight: 0.3980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 246 GLN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN G 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.100269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.085872 restraints weight = 26620.329| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.01 r_work: 0.3364 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13868 Z= 0.135 Angle : 0.614 9.842 19188 Z= 0.322 Chirality : 0.041 0.176 2148 Planarity : 0.005 0.052 2152 Dihedral : 19.105 168.974 2752 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.06 % Allowed : 29.18 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.22), residues: 1444 helix: 1.77 (0.25), residues: 432 sheet: 0.64 (0.29), residues: 342 loop : -0.46 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 69 TYR 0.040 0.002 TYR F 84 PHE 0.026 0.001 PHE A 143 TRP 0.011 0.001 TRP A 340 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00309 (13868) covalent geometry : angle 0.61424 (19188) hydrogen bonds : bond 0.03506 ( 589) hydrogen bonds : angle 4.58244 ( 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 324 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8667 (tp) REVERT: A 70 GLU cc_start: 0.8589 (tt0) cc_final: 0.8127 (tt0) REVERT: A 121 ASN cc_start: 0.8486 (t0) cc_final: 0.8171 (t0) REVERT: A 220 LYS cc_start: 0.7868 (mttt) cc_final: 0.7620 (tppt) REVERT: A 221 ASP cc_start: 0.8036 (m-30) cc_final: 0.7493 (p0) REVERT: A 249 ASP cc_start: 0.7507 (p0) cc_final: 0.7290 (p0) REVERT: A 285 SER cc_start: 0.8311 (m) cc_final: 0.7871 (p) REVERT: A 392 GLN cc_start: 0.8490 (tt0) cc_final: 0.8241 (tt0) REVERT: B 384 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8459 (mp0) REVERT: B 401 GLN cc_start: 0.8644 (pm20) cc_final: 0.8039 (pp30) REVERT: B 442 ARG cc_start: 0.8791 (ttm110) cc_final: 0.8297 (mtp-110) REVERT: B 518 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8373 (tm-30) REVERT: F 46 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8546 (pp) REVERT: F 61 MET cc_start: 0.8761 (mmt) cc_final: 0.8388 (mmt) REVERT: F 69 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8241 (ptm-80) REVERT: F 107 CYS cc_start: 0.8111 (t) cc_final: 0.7533 (p) REVERT: F 133 MET cc_start: 0.8381 (ptp) cc_final: 0.8163 (ttp) REVERT: F 220 LYS cc_start: 0.8571 (ptpt) cc_final: 0.8193 (ptmt) REVERT: F 328 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: F 330 GLU cc_start: 0.8151 (tp30) cc_final: 0.7905 (mm-30) REVERT: F 370 THR cc_start: 0.8734 (t) cc_final: 0.8518 (p) REVERT: F 413 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8325 (p) REVERT: F 454 ASP cc_start: 0.7510 (t0) cc_final: 0.7263 (t0) REVERT: G 342 SER cc_start: 0.8263 (p) cc_final: 0.7975 (m) REVERT: G 357 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9105 (p) REVERT: G 377 LYS cc_start: 0.8508 (mptt) cc_final: 0.8284 (mppt) REVERT: G 401 GLN cc_start: 0.7900 (pp30) cc_final: 0.7669 (pp30) REVERT: G 477 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8427 (t0) outliers start: 63 outliers final: 35 residues processed: 297 average time/residue: 0.4193 time to fit residues: 140.2875 Evaluate side-chains 294 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 143 PHE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 246 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 A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 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 69 ARG 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 403 LEU Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 421 THR 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 357 SER Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 477 ASN 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: 0.4980 chunk 38 optimal weight: 0.0470 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 130 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 278 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 = 0.3766 r_free = 0.3766 target = 0.101569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.087135 restraints weight = 26758.001| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.04 r_work: 0.3387 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13868 Z= 0.128 Angle : 0.629 10.429 19188 Z= 0.328 Chirality : 0.041 0.193 2148 Planarity : 0.005 0.055 2152 Dihedral : 19.074 168.833 2750 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.10 % Allowed : 30.71 % Favored : 65.19 % 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 aren not related in a simple way. whole: 0.72 (0.22), residues: 1444 helix: 1.86 (0.25), residues: 432 sheet: 0.61 (0.29), residues: 342 loop : -0.48 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 69 TYR 0.021 0.002 TYR F 240 PHE 0.027 0.001 PHE A 143 TRP 0.010 0.001 TRP F 340 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00292 (13868) covalent geometry : angle 0.62899 (19188) hydrogen bonds : bond 0.03366 ( 589) hydrogen bonds : angle 4.47246 ( 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 317 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 266 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8666 (tp) REVERT: A 121 ASN cc_start: 0.8482 (t0) cc_final: 0.8205 (t0) REVERT: A 220 LYS cc_start: 0.7882 (mttt) cc_final: 0.7587 (tppt) REVERT: A 221 ASP cc_start: 0.8059 (m-30) cc_final: 0.7526 (p0) REVERT: A 222 GLU cc_start: 0.6320 (mm-30) cc_final: 0.6037 (mm-30) REVERT: A 285 SER cc_start: 0.8315 (m) cc_final: 0.7864 (p) REVERT: A 392 GLN cc_start: 0.8461 (tt0) cc_final: 0.8232 (tt0) REVERT: B 384 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: B 401 GLN cc_start: 0.8652 (pm20) cc_final: 0.8062 (pp30) REVERT: B 411 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8141 (t) REVERT: B 442 ARG cc_start: 0.8780 (ttm110) cc_final: 0.8278 (mtp-110) REVERT: B 518 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8386 (tm-30) REVERT: F 46 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8544 (pp) REVERT: F 61 MET cc_start: 0.8749 (mmt) cc_final: 0.8378 (mmt) REVERT: F 69 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8246 (ptm-80) REVERT: F 107 CYS cc_start: 0.8124 (t) cc_final: 0.7547 (p) REVERT: F 220 LYS cc_start: 0.8605 (ptpt) cc_final: 0.8234 (ptmt) REVERT: F 328 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: F 330 GLU cc_start: 0.8174 (tp30) cc_final: 0.7928 (mm-30) REVERT: F 370 THR cc_start: 0.8716 (t) cc_final: 0.8503 (p) REVERT: F 413 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8328 (p) REVERT: F 454 ASP cc_start: 0.7504 (t0) cc_final: 0.7257 (t0) REVERT: G 342 SER cc_start: 0.8249 (p) cc_final: 0.7968 (m) REVERT: G 357 SER cc_start: 0.9340 (OUTLIER) cc_final: 0.9113 (p) REVERT: G 377 LYS cc_start: 0.8493 (mptt) cc_final: 0.8262 (mppt) REVERT: G 401 GLN cc_start: 0.7898 (pp30) cc_final: 0.7561 (pp30) REVERT: G 477 ASN cc_start: 0.8591 (m-40) cc_final: 0.8374 (t0) outliers start: 51 outliers final: 33 residues processed: 295 average time/residue: 0.4134 time to fit residues: 137.4093 Evaluate side-chains 296 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 99 VAL 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 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 411 VAL 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 69 ARG Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 143 PHE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 355 THR Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3742 r_free = 0.3742 target = 0.100182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.085844 restraints weight = 26735.122| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.02 r_work: 0.3363 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13868 Z= 0.151 Angle : 0.650 10.774 19188 Z= 0.339 Chirality : 0.042 0.244 2148 Planarity : 0.005 0.057 2152 Dihedral : 19.026 170.191 2749 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.66 % Allowed : 30.47 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.22), residues: 1444 helix: 1.83 (0.25), residues: 432 sheet: 0.58 (0.29), residues: 342 loop : -0.51 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 62 TYR 0.027 0.002 TYR F 341 PHE 0.028 0.001 PHE A 143 TRP 0.012 0.001 TRP A 340 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00351 (13868) covalent geometry : angle 0.65011 (19188) hydrogen bonds : bond 0.03533 ( 589) hydrogen bonds : angle 4.48310 ( 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 319 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 261 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8570 (tt0) cc_final: 0.8325 (tt0) REVERT: A 121 ASN cc_start: 0.8502 (t0) cc_final: 0.8206 (t0) REVERT: A 220 LYS cc_start: 0.7889 (mttt) cc_final: 0.7646 (tppt) REVERT: A 285 SER cc_start: 0.8406 (m) cc_final: 0.7944 (p) REVERT: A 392 GLN cc_start: 0.8489 (tt0) cc_final: 0.8247 (tt0) REVERT: B 384 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: B 401 GLN cc_start: 0.8687 (pm20) cc_final: 0.8110 (pp30) REVERT: B 411 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8194 (t) REVERT: B 442 ARG cc_start: 0.8825 (ttm110) cc_final: 0.8319 (mtp-110) REVERT: F 46 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8508 (pp) REVERT: F 61 MET cc_start: 0.8763 (mmt) cc_final: 0.8382 (mmt) REVERT: F 69 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8256 (ptm-80) REVERT: F 70 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8512 (pp20) REVERT: F 107 CYS cc_start: 0.8113 (t) cc_final: 0.7555 (p) REVERT: F 220 LYS cc_start: 0.8637 (ptpt) cc_final: 0.8261 (ptmt) REVERT: F 328 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7899 (mm-30) REVERT: F 330 GLU cc_start: 0.8155 (tp30) cc_final: 0.7893 (mm-30) REVERT: F 370 THR cc_start: 0.8736 (t) cc_final: 0.8521 (p) REVERT: F 413 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8307 (p) REVERT: F 454 ASP cc_start: 0.7609 (t0) cc_final: 0.7243 (t0) REVERT: G 342 SER cc_start: 0.8256 (p) cc_final: 0.7959 (m) REVERT: G 357 SER cc_start: 0.9348 (OUTLIER) cc_final: 0.9112 (p) REVERT: G 377 LYS cc_start: 0.8483 (mptt) cc_final: 0.8077 (mptt) REVERT: G 401 GLN cc_start: 0.7925 (pp30) cc_final: 0.7494 (pp30) REVERT: G 477 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8404 (t0) outliers start: 58 outliers final: 31 residues processed: 294 average time/residue: 0.4001 time to fit residues: 133.1780 Evaluate side-chains 291 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 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 411 VAL 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 69 ARG Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 355 THR Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain G residue 478 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 17 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 119 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 GLN F 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.095763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.081531 restraints weight = 27130.324| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.91 r_work: 0.3316 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13868 Z= 0.239 Angle : 0.728 11.259 19188 Z= 0.380 Chirality : 0.045 0.217 2148 Planarity : 0.005 0.054 2152 Dihedral : 19.016 176.737 2749 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.02 % Allowed : 31.59 % Favored : 64.39 % 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 aren not related in a simple way. whole: 0.25 (0.22), residues: 1444 helix: 1.39 (0.25), residues: 440 sheet: 0.42 (0.29), residues: 342 loop : -0.79 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 69 TYR 0.039 0.002 TYR F 341 PHE 0.026 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 covalent geometry : bond 0.00558 (13868) covalent geometry : angle 0.72751 (19188) hydrogen bonds : bond 0.04368 ( 589) hydrogen bonds : angle 4.67582 ( 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 300 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 250 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8719 (tp) REVERT: A 70 GLU cc_start: 0.8623 (tt0) cc_final: 0.8303 (tt0) REVERT: A 121 ASN cc_start: 0.8637 (t0) cc_final: 0.8377 (t0) REVERT: A 220 LYS cc_start: 0.7975 (mttt) cc_final: 0.7769 (tppt) REVERT: A 278 GLN cc_start: 0.7689 (pp30) cc_final: 0.7335 (tm-30) REVERT: A 285 SER cc_start: 0.8491 (m) cc_final: 0.8089 (p) REVERT: A 376 LEU cc_start: 0.8871 (tm) cc_final: 0.8630 (tt) REVERT: A 392 GLN cc_start: 0.8530 (tt0) cc_final: 0.8274 (tt0) REVERT: B 384 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: B 401 GLN cc_start: 0.8714 (pm20) cc_final: 0.8135 (pp30) REVERT: B 442 ARG cc_start: 0.8847 (ttm110) cc_final: 0.8646 (ttm110) REVERT: B 561 CYS cc_start: 0.7615 (t) cc_final: 0.6746 (p) REVERT: F 55 LEU cc_start: 0.7885 (tp) cc_final: 0.7298 (mt) REVERT: F 61 MET cc_start: 0.8882 (mmt) cc_final: 0.8425 (mmt) REVERT: F 69 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8358 (ptm-80) REVERT: F 107 CYS cc_start: 0.8193 (t) cc_final: 0.7563 (p) REVERT: F 220 LYS cc_start: 0.8724 (ptpt) cc_final: 0.8423 (ptpt) REVERT: F 328 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7877 (mm-30) REVERT: F 330 GLU cc_start: 0.8156 (tp30) cc_final: 0.7880 (mm-30) REVERT: F 370 THR cc_start: 0.8780 (t) cc_final: 0.8532 (p) REVERT: F 392 GLN cc_start: 0.8496 (tt0) cc_final: 0.8214 (tt0) REVERT: F 413 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8062 (p) REVERT: F 454 ASP cc_start: 0.7698 (t0) cc_final: 0.7313 (t0) REVERT: G 342 SER cc_start: 0.8286 (p) cc_final: 0.8011 (m) REVERT: G 357 SER cc_start: 0.9348 (OUTLIER) cc_final: 0.9109 (p) REVERT: G 377 LYS cc_start: 0.8478 (mptt) cc_final: 0.8064 (mptt) REVERT: G 401 GLN cc_start: 0.8014 (pp30) cc_final: 0.7795 (pp30) REVERT: G 477 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8452 (t0) outliers start: 50 outliers final: 35 residues processed: 283 average time/residue: 0.3615 time to fit residues: 116.0059 Evaluate side-chains 291 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 143 PHE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain 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 415 THR Chi-restraints excluded: chain B residue 471 LEU 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 69 ARG Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain 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 355 THR Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 477 ASN 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: 0.9990 chunk 99 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 85 optimal weight: 0.0270 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 49 GLN A 246 GLN ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN G 441 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.098785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.084459 restraints weight = 26897.079| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.02 r_work: 0.3339 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13868 Z= 0.153 Angle : 0.698 13.318 19188 Z= 0.364 Chirality : 0.043 0.202 2148 Planarity : 0.005 0.063 2152 Dihedral : 19.013 170.809 2749 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.05 % Allowed : 32.88 % Favored : 64.07 % 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 aren not related in a simple way. whole: 0.35 (0.22), residues: 1444 helix: 1.53 (0.25), residues: 440 sheet: 0.40 (0.29), residues: 342 loop : -0.73 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 62 TYR 0.039 0.002 TYR F 240 PHE 0.028 0.001 PHE A 143 TRP 0.011 0.001 TRP F 340 HIS 0.020 0.001 HIS G 441 Details of bonding type rmsd covalent geometry : bond 0.00355 (13868) covalent geometry : angle 0.69832 (19188) hydrogen bonds : bond 0.03764 ( 589) hydrogen bonds : angle 4.62155 ( 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 290 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 252 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8585 (tt0) cc_final: 0.8220 (tt0) REVERT: A 121 ASN cc_start: 0.8563 (t0) cc_final: 0.8259 (t0) REVERT: A 220 LYS cc_start: 0.7937 (mttt) cc_final: 0.7681 (tppt) REVERT: A 278 GLN cc_start: 0.7598 (pp30) cc_final: 0.7286 (tm-30) REVERT: A 285 SER cc_start: 0.8473 (m) cc_final: 0.8067 (p) REVERT: A 376 LEU cc_start: 0.8814 (tm) cc_final: 0.8586 (tt) REVERT: A 392 GLN cc_start: 0.8488 (tt0) cc_final: 0.8224 (tt0) REVERT: B 384 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: B 401 GLN cc_start: 0.8688 (pm20) cc_final: 0.8101 (pp30) REVERT: B 411 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8196 (t) REVERT: B 442 ARG cc_start: 0.8811 (ttm110) cc_final: 0.8284 (mtp-110) REVERT: B 561 CYS cc_start: 0.7599 (t) cc_final: 0.6726 (p) REVERT: F 61 MET cc_start: 0.8758 (mmt) cc_final: 0.8404 (mmt) REVERT: F 69 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8277 (ptm-80) REVERT: F 107 CYS cc_start: 0.8106 (t) cc_final: 0.7538 (p) REVERT: F 220 LYS cc_start: 0.8717 (ptpt) cc_final: 0.8384 (ptpt) REVERT: F 328 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: F 330 GLU cc_start: 0.8158 (tp30) cc_final: 0.7881 (mm-30) REVERT: F 370 THR cc_start: 0.8743 (t) cc_final: 0.8492 (p) REVERT: F 392 GLN cc_start: 0.8413 (tt0) cc_final: 0.8092 (tt0) REVERT: F 413 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8232 (p) REVERT: F 454 ASP cc_start: 0.7629 (t0) cc_final: 0.7227 (t0) REVERT: G 342 SER cc_start: 0.8236 (p) cc_final: 0.7952 (m) REVERT: G 357 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9106 (p) REVERT: G 377 LYS cc_start: 0.8456 (mptt) cc_final: 0.8046 (mptt) REVERT: G 401 GLN cc_start: 0.8000 (pp30) cc_final: 0.7586 (pp30) REVERT: G 477 ASN cc_start: 0.8643 (m-40) cc_final: 0.8407 (t0) outliers start: 38 outliers final: 27 residues processed: 275 average time/residue: 0.4719 time to fit residues: 145.8729 Evaluate side-chains 280 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 143 PHE Chi-restraints excluded: chain A residue 173 VAL 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 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 411 VAL Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 421 THR 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 355 THR Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 103 optimal weight: 0.0370 chunk 47 optimal weight: 0.0770 chunk 69 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 119 ASN A 246 GLN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.102023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.087625 restraints weight = 26669.017| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.04 r_work: 0.3395 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2626 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= 0.137 Angle : 0.684 12.583 19188 Z= 0.358 Chirality : 0.042 0.233 2148 Planarity : 0.005 0.066 2152 Dihedral : 18.996 169.549 2749 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.73 % Allowed : 33.36 % Favored : 63.91 % 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 aren not related in a simple way. whole: 0.54 (0.22), residues: 1444 helix: 1.83 (0.25), residues: 416 sheet: 0.38 (0.29), residues: 342 loop : -0.55 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 69 TYR 0.022 0.002 TYR F 341 PHE 0.028 0.002 PHE F 323 TRP 0.011 0.001 TRP G 543 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00317 (13868) covalent geometry : angle 0.68447 (19188) hydrogen bonds : bond 0.03444 ( 589) hydrogen bonds : angle 4.60098 ( 1631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4103.33 seconds wall clock time: 70 minutes 52.18 seconds (4252.18 seconds total)