Starting phenix.real_space_refine on Thu Jul 31 08:38:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k87_36946/07_2025/8k87_36946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k87_36946/07_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_36946/07_2025/8k87_36946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k87_36946/07_2025/8k87_36946.map" model { file = "/net/cci-nas-00/data/ceres_data/8k87_36946/07_2025/8k87_36946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k87_36946/07_2025/8k87_36946.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.03, per 1000 atoms: 0.68 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: 3.23 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.89 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: 4.99 Time building geometry restraints manager: 3.73 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.060 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP F 218 HIS 0.008 0.001 HIS A 114 PHE 0.027 0.002 PHE A 143 TYR 0.046 0.002 TYR F 84 ARG 0.014 0.001 ARG G 527 Details of bonding type rmsd hydrogen bonds : bond 0.17360 ( 589) hydrogen bonds : angle 7.13231 ( 1631) covalent geometry : bond 0.00406 (13868) covalent geometry : angle 0.76629 (19188) *********************** 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 : 1.315 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: 0.9736 time to fit residues: 294.1259 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 : 1.272 ------------------------------------------------------------------------------- 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 126 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 117 optimal weight: 0.0370 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.101943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.087428 restraints weight = 26647.668| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.03 r_work: 0.3387 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13868 Z= 0.138 Angle : 0.629 7.929 19188 Z= 0.332 Chirality : 0.042 0.167 2148 Planarity : 0.006 0.069 2152 Dihedral : 19.572 163.537 2777 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.02 % Allowed : 28.62 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1444 helix: 1.34 (0.24), residues: 456 sheet: 0.82 (0.28), residues: 352 loop : -0.65 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 510 HIS 0.023 0.001 HIS G 441 PHE 0.027 0.002 PHE A 143 TYR 0.024 0.002 TYR F 84 ARG 0.008 0.001 ARG G 527 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 589) hydrogen bonds : angle 5.25206 ( 1631) covalent geometry : bond 0.00307 (13868) covalent geometry : angle 0.62856 (19188) *********************** 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 308 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8696 (tt0) cc_final: 0.8316 (tt0) REVERT: A 221 ASP cc_start: 0.8164 (m-30) cc_final: 0.7893 (m-30) REVERT: A 385 VAL cc_start: 0.8713 (m) cc_final: 0.8428 (t) REVERT: A 392 GLN cc_start: 0.8464 (tt0) cc_final: 0.8227 (tt0) REVERT: B 360 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8407 (pptt) REVERT: B 369 LYS cc_start: 0.8587 (mmpt) cc_final: 0.8267 (mmpt) REVERT: B 384 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: B 401 GLN cc_start: 0.8574 (pm20) cc_final: 0.8125 (pp30) REVERT: B 561 CYS cc_start: 0.7561 (t) cc_final: 0.6734 (p) REVERT: F 61 MET cc_start: 0.8690 (mmt) cc_final: 0.8279 (mmt) REVERT: F 107 CYS cc_start: 0.8028 (t) cc_final: 0.7587 (p) REVERT: F 220 LYS cc_start: 0.8506 (ptpt) cc_final: 0.8220 (ptpt) REVERT: F 299 MET cc_start: 0.8695 (ptp) cc_final: 0.7989 (ppp) REVERT: F 370 THR cc_start: 0.8682 (t) cc_final: 0.8455 (p) REVERT: F 392 GLN cc_start: 0.8176 (tt0) cc_final: 0.7975 (tt0) REVERT: F 428 LEU cc_start: 0.8495 (mm) cc_final: 0.8189 (tp) REVERT: G 477 ASN cc_start: 0.8709 (m-40) cc_final: 0.8462 (t0) outliers start: 50 outliers final: 25 residues processed: 283 average time/residue: 1.1600 time to fit residues: 370.3685 Evaluate side-chains 265 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR 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 F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 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 18 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 121 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.6942 ------------------------------------------------------------------------------- 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** A 389 ASN F 195 ASN G 437 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.101219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.086815 restraints weight = 26729.452| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.01 r_work: 0.3375 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13868 Z= 0.137 Angle : 0.603 8.143 19188 Z= 0.315 Chirality : 0.041 0.172 2148 Planarity : 0.005 0.054 2152 Dihedral : 19.470 167.669 2759 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.46 % Allowed : 29.74 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1444 helix: 1.57 (0.25), residues: 442 sheet: 0.75 (0.28), residues: 354 loop : -0.58 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 340 HIS 0.006 0.001 HIS A 114 PHE 0.026 0.001 PHE A 143 TYR 0.024 0.002 TYR F 84 ARG 0.008 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 589) hydrogen bonds : angle 4.84594 ( 1631) covalent geometry : bond 0.00309 (13868) covalent geometry : angle 0.60267 (19188) *********************** 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 297 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 1.698 Fit side-chains revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8390 (t0) cc_final: 0.8184 (t0) REVERT: A 392 GLN cc_start: 0.8471 (tt0) cc_final: 0.8199 (tt0) REVERT: B 360 LYS cc_start: 0.8799 (mtpm) cc_final: 0.8404 (pptt) REVERT: B 384 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: B 401 GLN cc_start: 0.8650 (pm20) cc_final: 0.8187 (pp30) REVERT: B 442 ARG cc_start: 0.8640 (ttm110) cc_final: 0.8253 (mtp-110) REVERT: B 519 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: B 561 CYS cc_start: 0.7442 (t) cc_final: 0.6580 (p) REVERT: F 61 MET cc_start: 0.8780 (mmt) cc_final: 0.8373 (mmt) REVERT: F 107 CYS cc_start: 0.8054 (t) cc_final: 0.7601 (p) REVERT: F 220 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8139 (ptmt) REVERT: F 232 LYS cc_start: 0.9048 (ttpp) cc_final: 0.8719 (tttm) REVERT: F 370 THR cc_start: 0.8710 (t) cc_final: 0.8510 (p) REVERT: F 392 GLN cc_start: 0.8248 (tt0) cc_final: 0.8010 (tt0) REVERT: F 428 LEU cc_start: 0.8538 (mm) cc_final: 0.8259 (tp) REVERT: G 377 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8149 (mptt) REVERT: G 477 ASN cc_start: 0.8682 (m-40) cc_final: 0.8444 (t0) REVERT: G 506 LYS cc_start: 0.8772 (mttp) cc_final: 0.8429 (tptt) REVERT: G 512 LYS cc_start: 0.8879 (tttt) cc_final: 0.8663 (tttp) REVERT: G 530 TYR cc_start: 0.9020 (m-80) cc_final: 0.8808 (m-80) outliers start: 43 outliers final: 28 residues processed: 281 average time/residue: 1.1196 time to fit residues: 353.3393 Evaluate side-chains 268 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 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 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 329 ILE Chi-restraints excluded: chain F residue 337 SER 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 377 LYS Chi-restraints excluded: chain G residue 396 ILE 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 47 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 147 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.100842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.086502 restraints weight = 26502.858| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.00 r_work: 0.3370 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13868 Z= 0.137 Angle : 0.597 8.856 19188 Z= 0.312 Chirality : 0.041 0.159 2148 Planarity : 0.005 0.050 2152 Dihedral : 19.268 168.200 2755 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.34 % Allowed : 29.10 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1444 helix: 1.77 (0.25), residues: 430 sheet: 0.70 (0.28), residues: 354 loop : -0.45 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 340 HIS 0.006 0.001 HIS A 114 PHE 0.025 0.001 PHE A 143 TYR 0.026 0.002 TYR F 84 ARG 0.009 0.000 ARG F 269 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 589) hydrogen bonds : angle 4.69112 ( 1631) covalent geometry : bond 0.00312 (13868) covalent geometry : angle 0.59692 (19188) *********************** 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 316 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 262 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8647 (tt0) cc_final: 0.8060 (tt0) REVERT: A 121 ASN cc_start: 0.8385 (t0) cc_final: 0.8137 (t0) REVERT: A 197 MET cc_start: 0.7645 (mpp) cc_final: 0.7171 (mpp) REVERT: A 221 ASP cc_start: 0.8001 (m-30) cc_final: 0.7526 (p0) REVERT: A 222 GLU cc_start: 0.6421 (mm-30) cc_final: 0.6189 (mm-30) REVERT: A 375 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 392 GLN cc_start: 0.8482 (tt0) cc_final: 0.8221 (tt0) REVERT: B 360 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8383 (pptt) REVERT: B 384 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: B 401 GLN cc_start: 0.8615 (pm20) cc_final: 0.8182 (pp30) REVERT: B 440 ARG cc_start: 0.8965 (ttt-90) cc_final: 0.8628 (ttt-90) REVERT: B 561 CYS cc_start: 0.7464 (t) cc_final: 0.6579 (p) REVERT: F 61 MET cc_start: 0.8804 (mmt) cc_final: 0.8404 (mmt) REVERT: F 107 CYS cc_start: 0.8077 (t) cc_final: 0.7601 (p) REVERT: F 214 LYS cc_start: 0.9100 (ptmm) cc_final: 0.8624 (ptmm) REVERT: F 220 LYS cc_start: 0.8553 (ptpt) cc_final: 0.8159 (ptmt) REVERT: F 232 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8702 (tttp) REVERT: F 370 THR cc_start: 0.8706 (t) cc_final: 0.8500 (p) REVERT: F 392 GLN cc_start: 0.8272 (tt0) cc_final: 0.7998 (tt0) REVERT: F 428 LEU cc_start: 0.8554 (mm) cc_final: 0.8250 (tp) REVERT: G 342 SER cc_start: 0.8359 (p) cc_final: 0.8078 (m) REVERT: G 377 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8105 (mptt) REVERT: G 401 GLN cc_start: 0.7828 (pp30) cc_final: 0.7606 (pp30) REVERT: G 477 ASN cc_start: 0.8669 (m-40) cc_final: 0.8427 (t0) REVERT: G 512 LYS cc_start: 0.8864 (tttt) cc_final: 0.8653 (tttp) outliers start: 54 outliers final: 34 residues processed: 298 average time/residue: 1.0230 time to fit residues: 343.7736 Evaluate side-chains 287 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 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 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 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 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 534 GLN F 195 ASN F 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.096714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.082354 restraints weight = 27210.607| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.00 r_work: 0.3293 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13868 Z= 0.214 Angle : 0.643 9.444 19188 Z= 0.338 Chirality : 0.043 0.218 2148 Planarity : 0.005 0.052 2152 Dihedral : 19.166 172.698 2753 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.82 % Allowed : 29.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1444 helix: 1.51 (0.25), residues: 442 sheet: 0.67 (0.29), residues: 342 loop : -0.72 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 340 HIS 0.005 0.001 HIS A 114 PHE 0.023 0.002 PHE A 143 TYR 0.029 0.002 TYR F 84 ARG 0.009 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 589) hydrogen bonds : angle 4.70379 ( 1631) covalent geometry : bond 0.00493 (13868) covalent geometry : angle 0.64280 (19188) *********************** 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 314 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 254 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8678 (tp) REVERT: A 70 GLU cc_start: 0.8650 (tt0) cc_final: 0.8156 (tt0) REVERT: A 121 ASN cc_start: 0.8525 (t0) cc_final: 0.8238 (t0) REVERT: A 197 MET cc_start: 0.7785 (mpp) cc_final: 0.7503 (mpp) REVERT: A 285 SER cc_start: 0.8330 (m) cc_final: 0.7947 (p) REVERT: A 392 GLN cc_start: 0.8510 (tt0) cc_final: 0.8251 (tt0) REVERT: B 384 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: B 401 GLN cc_start: 0.8624 (pm20) cc_final: 0.8151 (pp30) REVERT: B 440 ARG cc_start: 0.8988 (ttt-90) cc_final: 0.8646 (ttt-90) REVERT: B 442 ARG cc_start: 0.8793 (ttm110) cc_final: 0.8341 (mtp-110) REVERT: F 46 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8549 (pp) REVERT: F 55 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7657 (tp) REVERT: F 61 MET cc_start: 0.8856 (mmt) cc_final: 0.8411 (mmt) REVERT: F 214 LYS cc_start: 0.9122 (ptmm) cc_final: 0.8647 (ptmm) REVERT: F 220 LYS cc_start: 0.8620 (ptpt) cc_final: 0.8302 (ptpt) REVERT: F 370 THR cc_start: 0.8783 (t) cc_final: 0.8568 (p) REVERT: G 342 SER cc_start: 0.8379 (p) cc_final: 0.8088 (m) REVERT: G 357 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.9111 (p) REVERT: G 377 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8079 (mptt) REVERT: G 401 GLN cc_start: 0.7890 (pp30) cc_final: 0.7650 (pp30) REVERT: G 441 HIS cc_start: 0.7951 (t-90) cc_final: 0.7695 (t70) outliers start: 60 outliers final: 36 residues processed: 290 average time/residue: 0.8537 time to fit residues: 280.2446 Evaluate side-chains 293 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 64 LEU 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 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 246 GLN Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 355 THR Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 87 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 135 optimal weight: 0.3980 chunk 42 optimal weight: 0.0000 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.099256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.084837 restraints weight = 26973.292| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.04 r_work: 0.3346 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13868 Z= 0.138 Angle : 0.618 10.174 19188 Z= 0.324 Chirality : 0.042 0.187 2148 Planarity : 0.005 0.051 2152 Dihedral : 19.136 169.462 2752 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.10 % Allowed : 30.23 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1444 helix: 1.77 (0.25), residues: 430 sheet: 0.59 (0.29), residues: 342 loop : -0.51 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 340 HIS 0.005 0.001 HIS A 114 PHE 0.026 0.002 PHE A 143 TYR 0.026 0.002 TYR F 240 ARG 0.013 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 589) hydrogen bonds : angle 4.65222 ( 1631) covalent geometry : bond 0.00314 (13868) covalent geometry : angle 0.61817 (19188) *********************** 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 311 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 260 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8666 (tp) REVERT: A 70 GLU cc_start: 0.8612 (tt0) cc_final: 0.8152 (tt0) REVERT: A 121 ASN cc_start: 0.8534 (t0) cc_final: 0.8223 (t0) REVERT: A 233 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8281 (mmpt) REVERT: A 285 SER cc_start: 0.8426 (m) cc_final: 0.8032 (p) REVERT: A 392 GLN cc_start: 0.8481 (tt0) cc_final: 0.8229 (tt0) REVERT: B 371 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8598 (pp) REVERT: B 384 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: B 401 GLN cc_start: 0.8609 (pm20) cc_final: 0.8152 (pp30) REVERT: B 440 ARG cc_start: 0.8959 (ttt-90) cc_final: 0.8628 (ttt-90) REVERT: B 442 ARG cc_start: 0.8785 (ttm110) cc_final: 0.8268 (mtp-110) REVERT: B 561 CYS cc_start: 0.7567 (t) cc_final: 0.6656 (p) REVERT: F 46 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8504 (pp) REVERT: F 61 MET cc_start: 0.8763 (mmt) cc_final: 0.8384 (mmt) REVERT: F 69 ARG cc_start: 0.8560 (mtp-110) cc_final: 0.8310 (ptm-80) REVERT: F 107 CYS cc_start: 0.8079 (t) cc_final: 0.7607 (p) REVERT: F 214 LYS cc_start: 0.9113 (ptmm) cc_final: 0.8609 (ptmm) REVERT: F 220 LYS cc_start: 0.8578 (ptpt) cc_final: 0.8186 (ptmt) REVERT: F 328 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7877 (mm-30) REVERT: F 370 THR cc_start: 0.8734 (t) cc_final: 0.8507 (p) REVERT: G 342 SER cc_start: 0.8286 (p) cc_final: 0.7986 (m) REVERT: G 357 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.9106 (p) REVERT: G 377 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8218 (mppt) REVERT: G 401 GLN cc_start: 0.7912 (pp30) cc_final: 0.7567 (pp30) REVERT: G 441 HIS cc_start: 0.7912 (t-90) cc_final: 0.7645 (t70) REVERT: G 477 ASN cc_start: 0.8601 (m-40) cc_final: 0.8332 (t0) outliers start: 51 outliers final: 31 residues processed: 289 average time/residue: 0.9639 time to fit residues: 314.7107 Evaluate side-chains 284 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 143 PHE Chi-restraints excluded: chain A residue 289 HIS 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 371 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 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 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 39 optimal weight: 0.4980 chunk 129 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.097619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.083269 restraints weight = 27022.391| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.01 r_work: 0.3314 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13868 Z= 0.172 Angle : 0.644 10.192 19188 Z= 0.337 Chirality : 0.043 0.194 2148 Planarity : 0.005 0.054 2152 Dihedral : 19.079 171.581 2750 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.50 % Allowed : 30.87 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.22), residues: 1444 helix: 1.63 (0.25), residues: 442 sheet: 0.57 (0.29), residues: 342 loop : -0.68 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 340 HIS 0.012 0.001 HIS A 289 PHE 0.024 0.001 PHE A 143 TYR 0.038 0.002 TYR F 84 ARG 0.012 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 589) hydrogen bonds : angle 4.63000 ( 1631) covalent geometry : bond 0.00397 (13868) covalent geometry : angle 0.64389 (19188) *********************** 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 303 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 247 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8688 (tp) REVERT: A 70 GLU cc_start: 0.8647 (tt0) cc_final: 0.8279 (tt0) REVERT: A 121 ASN cc_start: 0.8580 (t0) cc_final: 0.8283 (t0) REVERT: A 248 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.7145 (p90) REVERT: A 285 SER cc_start: 0.8409 (m) cc_final: 0.8076 (p) REVERT: A 392 GLN cc_start: 0.8501 (tt0) cc_final: 0.8224 (tt0) REVERT: B 371 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8633 (pp) REVERT: B 384 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: B 401 GLN cc_start: 0.8613 (pm20) cc_final: 0.8165 (pp30) REVERT: B 440 ARG cc_start: 0.8954 (ttt-90) cc_final: 0.8654 (ttt-90) REVERT: B 442 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8370 (mtp-110) REVERT: F 61 MET cc_start: 0.8781 (mmt) cc_final: 0.8408 (mmt) REVERT: F 69 ARG cc_start: 0.8576 (mtp-110) cc_final: 0.8327 (ptm-80) REVERT: F 107 CYS cc_start: 0.8103 (t) cc_final: 0.7617 (p) REVERT: F 214 LYS cc_start: 0.9120 (ptmm) cc_final: 0.8605 (ptmm) REVERT: F 220 LYS cc_start: 0.8640 (ptpt) cc_final: 0.8322 (ptpt) REVERT: F 328 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7898 (mm-30) REVERT: F 370 THR cc_start: 0.8753 (t) cc_final: 0.8517 (p) REVERT: G 342 SER cc_start: 0.8270 (p) cc_final: 0.7962 (m) REVERT: G 357 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.9106 (p) REVERT: G 377 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8065 (mptt) REVERT: G 401 GLN cc_start: 0.7869 (pp30) cc_final: 0.7499 (pp30) REVERT: G 441 HIS cc_start: 0.7974 (t-90) cc_final: 0.7707 (t70) REVERT: G 477 ASN cc_start: 0.8615 (m-40) cc_final: 0.8348 (t0) outliers start: 56 outliers final: 34 residues processed: 283 average time/residue: 0.9746 time to fit residues: 313.4016 Evaluate side-chains 283 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 248 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 371 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 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 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.097684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.083337 restraints weight = 27201.389| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.03 r_work: 0.3317 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2290 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= 0.171 Angle : 0.655 11.557 19188 Z= 0.344 Chirality : 0.043 0.206 2148 Planarity : 0.005 0.051 2152 Dihedral : 19.035 171.990 2750 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.34 % Allowed : 31.03 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.22), residues: 1444 helix: 1.59 (0.25), residues: 442 sheet: 0.51 (0.29), residues: 342 loop : -0.70 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 340 HIS 0.005 0.001 HIS A 114 PHE 0.027 0.002 PHE A 143 TYR 0.030 0.002 TYR F 240 ARG 0.014 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 589) hydrogen bonds : angle 4.57359 ( 1631) covalent geometry : bond 0.00396 (13868) covalent geometry : angle 0.65463 (19188) *********************** 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 314 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 260 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8609 (t0) cc_final: 0.8312 (t0) REVERT: A 285 SER cc_start: 0.8569 (m) cc_final: 0.8149 (p) REVERT: A 374 CYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7772 (t) REVERT: A 392 GLN cc_start: 0.8447 (tt0) cc_final: 0.8207 (tt0) REVERT: B 371 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8633 (pp) REVERT: B 384 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: B 401 GLN cc_start: 0.8623 (pm20) cc_final: 0.8152 (pp30) REVERT: B 440 ARG cc_start: 0.8951 (ttt-90) cc_final: 0.8656 (ttt-90) REVERT: B 442 ARG cc_start: 0.8836 (ttm110) cc_final: 0.8308 (mtp-110) REVERT: B 561 CYS cc_start: 0.7613 (t) cc_final: 0.6725 (p) REVERT: F 46 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8466 (pp) REVERT: F 61 MET cc_start: 0.8797 (mmt) cc_final: 0.8277 (mmt) REVERT: F 69 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.8315 (ptm-80) REVERT: F 107 CYS cc_start: 0.8093 (t) cc_final: 0.7579 (p) REVERT: F 214 LYS cc_start: 0.9130 (ptmm) cc_final: 0.8619 (ptmm) REVERT: F 220 LYS cc_start: 0.8668 (ptpt) cc_final: 0.8362 (ptpt) REVERT: F 328 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: F 370 THR cc_start: 0.8753 (t) cc_final: 0.8512 (p) REVERT: G 342 SER cc_start: 0.8258 (p) cc_final: 0.7952 (m) REVERT: G 357 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9104 (p) REVERT: G 377 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8064 (mptt) REVERT: G 401 GLN cc_start: 0.7891 (pp30) cc_final: 0.7605 (pp30) REVERT: G 441 HIS cc_start: 0.7984 (t-90) cc_final: 0.7694 (t70) REVERT: G 477 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8340 (t0) outliers start: 54 outliers final: 38 residues processed: 292 average time/residue: 1.0070 time to fit residues: 331.7850 Evaluate side-chains 299 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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 64 LEU 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 221 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 LEU 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 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 372 LEU Chi-restraints excluded: chain G residue 377 LYS 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 546 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 134 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN F 405 ASN G 334 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.099314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.084980 restraints weight = 26673.731| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.00 r_work: 0.3349 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13868 Z= 0.149 Angle : 0.664 11.904 19188 Z= 0.348 Chirality : 0.042 0.217 2148 Planarity : 0.005 0.061 2152 Dihedral : 19.012 170.780 2750 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.10 % Allowed : 31.43 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1444 helix: 1.69 (0.25), residues: 438 sheet: 0.50 (0.29), residues: 342 loop : -0.68 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 340 HIS 0.005 0.001 HIS A 114 PHE 0.027 0.001 PHE F 323 TYR 0.025 0.002 TYR F 341 ARG 0.014 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 589) hydrogen bonds : angle 4.56330 ( 1631) covalent geometry : bond 0.00344 (13868) covalent geometry : angle 0.66404 (19188) *********************** 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: 51 poor density : 249 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8594 (tt0) cc_final: 0.8197 (tt0) REVERT: A 121 ASN cc_start: 0.8552 (t0) cc_final: 0.8250 (t0) REVERT: A 221 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7461 (p0) REVERT: A 285 SER cc_start: 0.8542 (m) cc_final: 0.8123 (p) REVERT: A 374 CYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7801 (t) REVERT: A 385 VAL cc_start: 0.8749 (m) cc_final: 0.8457 (t) REVERT: A 392 GLN cc_start: 0.8411 (tt0) cc_final: 0.8173 (tt0) REVERT: B 371 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8453 (pp) REVERT: B 401 GLN cc_start: 0.8595 (pm20) cc_final: 0.8037 (pp30) REVERT: B 411 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8130 (t) REVERT: B 442 ARG cc_start: 0.8811 (ttm110) cc_final: 0.8353 (mtp-110) REVERT: F 46 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8433 (pp) REVERT: F 61 MET cc_start: 0.8833 (mmt) cc_final: 0.8450 (mmt) REVERT: F 69 ARG cc_start: 0.8487 (mtp-110) cc_final: 0.8216 (ppp80) REVERT: F 107 CYS cc_start: 0.8100 (t) cc_final: 0.7602 (p) REVERT: F 197 MET cc_start: 0.7366 (mpt) cc_final: 0.6975 (mmt) REVERT: F 214 LYS cc_start: 0.9136 (ptmm) cc_final: 0.8617 (ptmm) REVERT: F 220 LYS cc_start: 0.8671 (ptpt) cc_final: 0.8354 (ptpt) REVERT: F 328 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7958 (mm-30) REVERT: F 370 THR cc_start: 0.8739 (t) cc_final: 0.8498 (p) REVERT: G 342 SER cc_start: 0.8245 (p) cc_final: 0.7942 (m) REVERT: G 357 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.9102 (p) REVERT: G 377 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7994 (mptt) REVERT: G 401 GLN cc_start: 0.7892 (pp30) cc_final: 0.7514 (pp30) REVERT: G 441 HIS cc_start: 0.7979 (t-90) cc_final: 0.7697 (t70) REVERT: G 477 ASN cc_start: 0.8582 (m-40) cc_final: 0.8302 (t0) outliers start: 51 outliers final: 34 residues processed: 280 average time/residue: 0.9002 time to fit residues: 283.7638 Evaluate side-chains 288 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 99 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 411 VAL 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 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 401 THR 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 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 93 optimal weight: 0.1980 chunk 14 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 246 GLN G 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.099820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.085513 restraints weight = 26698.579| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.02 r_work: 0.3358 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13868 Z= 0.150 Angle : 0.679 12.104 19188 Z= 0.356 Chirality : 0.042 0.229 2148 Planarity : 0.005 0.060 2152 Dihedral : 18.983 170.955 2748 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.54 % Allowed : 32.64 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1444 helix: 1.82 (0.25), residues: 426 sheet: 0.43 (0.29), residues: 342 loop : -0.52 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 340 HIS 0.004 0.001 HIS A 114 PHE 0.027 0.002 PHE A 143 TYR 0.018 0.002 TYR F 341 ARG 0.016 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 589) hydrogen bonds : angle 4.59981 ( 1631) covalent geometry : bond 0.00348 (13868) covalent geometry : angle 0.67927 (19188) ********************** 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 298 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8547 (t0) cc_final: 0.8247 (t0) REVERT: A 285 SER cc_start: 0.8563 (m) cc_final: 0.8145 (p) REVERT: A 385 VAL cc_start: 0.8785 (m) cc_final: 0.8515 (t) REVERT: A 392 GLN cc_start: 0.8408 (tt0) cc_final: 0.8178 (tt0) REVERT: B 371 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8467 (pp) REVERT: B 401 GLN cc_start: 0.8583 (pm20) cc_final: 0.8015 (pp30) REVERT: B 411 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8143 (t) REVERT: B 442 ARG cc_start: 0.8800 (ttm110) cc_final: 0.8278 (mtp-110) REVERT: F 46 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8491 (pp) REVERT: F 61 MET cc_start: 0.8850 (mmt) cc_final: 0.8464 (mmt) REVERT: F 69 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.8212 (ppp80) REVERT: F 107 CYS cc_start: 0.8101 (t) cc_final: 0.7638 (p) REVERT: F 214 LYS cc_start: 0.9133 (ptmm) cc_final: 0.8605 (ptmm) REVERT: F 220 LYS cc_start: 0.8696 (ptpt) cc_final: 0.8378 (ptpt) REVERT: F 370 THR cc_start: 0.8731 (t) cc_final: 0.8488 (p) REVERT: G 342 SER cc_start: 0.8238 (p) cc_final: 0.7936 (m) REVERT: G 357 SER cc_start: 0.9345 (OUTLIER) cc_final: 0.9109 (p) REVERT: G 377 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8031 (mptt) REVERT: G 401 GLN cc_start: 0.7916 (pp30) cc_final: 0.7538 (pp30) REVERT: G 441 HIS cc_start: 0.7994 (t-90) cc_final: 0.7720 (t70) REVERT: G 477 ASN cc_start: 0.8570 (m-40) cc_final: 0.8290 (t0) REVERT: G 484 LEU cc_start: 0.9051 (mt) cc_final: 0.8816 (mt) outliers start: 44 outliers final: 36 residues processed: 279 average time/residue: 0.8519 time to fit residues: 269.0551 Evaluate side-chains 292 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 64 LEU 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 173 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 411 VAL 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 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 337 SER Chi-restraints excluded: chain F residue 401 THR 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 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 124 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 G 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.099662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.085299 restraints weight = 26980.044| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.04 r_work: 0.3352 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13868 Z= 0.156 Angle : 0.689 12.970 19188 Z= 0.360 Chirality : 0.043 0.205 2148 Planarity : 0.005 0.059 2152 Dihedral : 18.961 171.383 2748 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.30 % Allowed : 32.88 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1444 helix: 1.74 (0.25), residues: 428 sheet: 0.44 (0.29), residues: 340 loop : -0.51 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 340 HIS 0.004 0.001 HIS A 114 PHE 0.028 0.001 PHE A 143 TYR 0.025 0.002 TYR F 341 ARG 0.016 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 589) hydrogen bonds : angle 4.61199 ( 1631) covalent geometry : bond 0.00365 (13868) covalent geometry : angle 0.68915 (19188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10110.98 seconds wall clock time: 180 minutes 29.02 seconds (10829.02 seconds total)