Starting phenix.real_space_refine on Thu Sep 18 04:07:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhn_61488/09_2025/9jhn_61488.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhn_61488/09_2025/9jhn_61488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jhn_61488/09_2025/9jhn_61488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhn_61488/09_2025/9jhn_61488.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jhn_61488/09_2025/9jhn_61488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhn_61488/09_2025/9jhn_61488.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 Mn 4 7.51 5 P 70 5.49 5 S 40 5.16 5 C 8488 2.51 5 N 2230 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13512 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, D, F Time building chain proxies: 5.27, per 1000 atoms: 0.39 Number of scatterers: 13512 At special positions: 0 Unit cell: (89.38, 118.9, 103.32, 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) Mn 4 24.99 S 40 16.00 P 70 15.00 O 2680 8.00 N 2230 7.00 C 8488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 499.6 milliseconds Enol-peptide restraints added in 14.3 microseconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 28 sheets defined 31.4% alpha, 17.2% beta 22 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 97 through 115 removed outlier: 4.078A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.745A pdb=" N MET A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 253 through 256 Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.662A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.585A pdb=" N LEU A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.106A pdb=" N TYR A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 603 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.567A pdb=" N ALA A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'B' and resid 43 through 54 Processing helix chain 'B' and resid 97 through 115 removed outlier: 4.078A pdb=" N LYS B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.744A pdb=" N MET B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 253 through 256 Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.662A pdb=" N LYS B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.586A pdb=" N LEU B 339 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 388 through 404 Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.105A pdb=" N TYR B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 603 Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 698 through 711 removed outlier: 3.566A pdb=" N ALA B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 166 removed outlier: 4.697A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.347A pdb=" N GLN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.732A pdb=" N LEU A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA8, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.830A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 259 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL A 219 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN A 261 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 215 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 214 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.679A pdb=" N ILE A 637 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 609 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE A 638 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE A 611 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 640 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG A 613 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS A 539 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS A 612 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 541 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA A 614 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU A 543 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP A 562 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU A 567 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 358 through 359 removed outlier: 4.807A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 529 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.775A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 382 through 385 removed outlier: 5.976A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AB6, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'B' and resid 163 through 166 removed outlier: 4.697A pdb=" N VAL B 172 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.346A pdb=" N GLN B 28 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 62 Processing sheet with id=AC1, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AC2, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.731A pdb=" N LEU B 134 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AC4, first strand: chain 'B' and resid 268 through 271 removed outlier: 3.829A pdb=" N TYR B 271 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 260 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 259 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL B 219 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN B 261 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 215 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.680A pdb=" N ILE B 637 " --> pdb=" O SER B 693 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 609 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE B 638 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE B 611 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 640 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG B 613 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS B 539 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS B 612 " --> pdb=" O CYS B 539 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 541 " --> pdb=" O HIS B 612 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA B 614 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU B 543 " --> pdb=" O ALA B 614 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 562 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU B 567 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 358 through 359 removed outlier: 4.806A pdb=" N LEU B 352 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 529 " --> pdb=" O MET B 353 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.774A pdb=" N VAL B 378 " --> pdb=" O GLU B 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 382 through 385 removed outlier: 5.976A pdb=" N VAL B 382 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR B 435 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR B 384 " --> pdb=" O TYR B 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AD1, first strand: chain 'B' and resid 462 through 463 442 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.43 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: 2891 1.33 - 1.45: 3309 1.45 - 1.57: 7520 1.57 - 1.69: 136 1.69 - 1.81: 70 Bond restraints: 13926 Sorted by residual: bond pdb=" O5' DT D 6 " pdb=" C5' DT D 6 " ideal model delta sigma weight residual 1.423 1.357 0.066 3.00e-02 1.11e+03 4.80e+00 bond pdb=" O5' DT C 6 " pdb=" C5' DT C 6 " ideal model delta sigma weight residual 1.423 1.357 0.066 3.00e-02 1.11e+03 4.79e+00 bond pdb=" CG1 ILE B 678 " pdb=" CD1 ILE B 678 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.73e+00 bond pdb=" CG1 ILE A 678 " pdb=" CD1 ILE A 678 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.65e+00 bond pdb=" CG MET B 491 " pdb=" SD MET B 491 " ideal model delta sigma weight residual 1.803 1.750 0.053 2.50e-02 1.60e+03 4.56e+00 ... (remaining 13921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 17946 1.87 - 3.73: 973 3.73 - 5.60: 109 5.60 - 7.47: 31 7.47 - 9.34: 13 Bond angle restraints: 19072 Sorted by residual: angle pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 120.54 127.93 -7.39 1.35e+00 5.49e-01 3.00e+01 angle pdb=" C LYS B 63 " pdb=" N ASP B 64 " pdb=" CA ASP B 64 " ideal model delta sigma weight residual 120.54 127.91 -7.37 1.35e+00 5.49e-01 2.98e+01 angle pdb=" N LYS B 63 " pdb=" CA LYS B 63 " pdb=" C LYS B 63 " ideal model delta sigma weight residual 110.17 102.09 8.08 1.51e+00 4.39e-01 2.87e+01 angle pdb=" N LYS A 63 " pdb=" CA LYS A 63 " pdb=" C LYS A 63 " ideal model delta sigma weight residual 110.17 102.13 8.04 1.51e+00 4.39e-01 2.83e+01 angle pdb=" CA TYR A 511 " pdb=" CB TYR A 511 " pdb=" CG TYR A 511 " ideal model delta sigma weight residual 113.90 121.71 -7.81 1.80e+00 3.09e-01 1.88e+01 ... (remaining 19067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.81: 7895 29.81 - 59.61: 352 59.61 - 89.42: 15 89.42 - 119.22: 0 119.22 - 149.03: 2 Dihedral angle restraints: 8264 sinusoidal: 3890 harmonic: 4374 Sorted by residual: dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N ILE A 471 " pdb=" CA ILE A 471 " ideal model delta harmonic sigma weight residual -180.00 -143.69 -36.31 0 5.00e+00 4.00e-02 5.27e+01 dihedral pdb=" CA GLU B 470 " pdb=" C GLU B 470 " pdb=" N ILE B 471 " pdb=" CA ILE B 471 " ideal model delta harmonic sigma weight residual -180.00 -143.75 -36.25 0 5.00e+00 4.00e-02 5.26e+01 dihedral pdb=" CA ILE A 471 " pdb=" C ILE A 471 " pdb=" N GLU A 472 " pdb=" CA GLU A 472 " ideal model delta harmonic sigma weight residual -180.00 -148.14 -31.86 0 5.00e+00 4.00e-02 4.06e+01 ... (remaining 8261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1703 0.075 - 0.150: 351 0.150 - 0.225: 26 0.225 - 0.300: 4 0.300 - 0.375: 4 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CB ILE B 44 " pdb=" CA ILE B 44 " pdb=" CG1 ILE B 44 " pdb=" CG2 ILE B 44 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE A 44 " pdb=" CA ILE A 44 " pdb=" CG1 ILE A 44 " pdb=" CG2 ILE A 44 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB ILE A 596 " pdb=" CA ILE A 596 " pdb=" CG1 ILE A 596 " pdb=" CG2 ILE A 596 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2085 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 623 " -0.017 2.00e-02 2.50e+03 1.36e-02 4.60e+00 pdb=" CG TRP B 623 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 623 " 0.017 2.00e-02 2.50e+03 1.33e-02 4.42e+00 pdb=" CG TRP A 623 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 623 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 623 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 623 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 623 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 623 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 623 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 623 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 623 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 513 " -0.014 2.00e-02 2.50e+03 1.68e-02 4.24e+00 pdb=" CG HIS B 513 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS B 513 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS B 513 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS B 513 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 513 " -0.004 2.00e-02 2.50e+03 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 84 2.50 - 3.10: 9004 3.10 - 3.70: 21376 3.70 - 4.30: 32705 4.30 - 4.90: 52409 Nonbonded interactions: 115578 Sorted by model distance: nonbonded pdb=" OP2 DT D 1 " pdb="MN MN D 801 " model vdw 1.895 2.320 nonbonded pdb=" OP2 DT C 1 " pdb="MN MN C 801 " model vdw 1.895 2.320 nonbonded pdb=" OP1 DT D 1 " pdb="MN MN D 801 " model vdw 1.923 2.320 nonbonded pdb=" OP1 DT C 1 " pdb="MN MN C 801 " model vdw 1.923 2.320 nonbonded pdb=" NZ LYS B 54 " pdb=" CD1 LEU B 79 " model vdw 1.944 3.540 ... (remaining 115573 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.010 Normalize map: mean=0, sd=1: 2.520 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.680 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.093 13926 Z= 0.396 Angle : 0.963 9.336 19072 Z= 0.533 Chirality : 0.060 0.375 2088 Planarity : 0.006 0.043 2180 Dihedral : 14.778 149.028 5476 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.15 % Allowed : 1.95 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.18), residues: 1486 helix: -2.44 (0.18), residues: 444 sheet: -2.15 (0.24), residues: 342 loop : -1.52 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 721 TYR 0.027 0.003 TYR A 511 PHE 0.025 0.004 PHE B 591 TRP 0.033 0.006 TRP B 623 HIS 0.020 0.004 HIS B 513 Details of bonding type rmsd covalent geometry : bond 0.00965 (13926) covalent geometry : angle 0.96315 (19072) hydrogen bonds : bond 0.20092 ( 492) hydrogen bonds : angle 9.18993 ( 1336) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 202 average time/residue: 0.6313 time to fit residues: 139.5923 Evaluate side-chains 89 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain B residue 432 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS A 298 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 298 GLN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.095531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.073030 restraints weight = 34127.626| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.73 r_work: 0.3143 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13926 Z= 0.156 Angle : 0.633 8.222 19072 Z= 0.345 Chirality : 0.045 0.267 2088 Planarity : 0.004 0.031 2180 Dihedral : 17.587 152.623 2402 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.10 % Allowed : 8.53 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.20), residues: 1486 helix: -0.42 (0.23), residues: 436 sheet: -1.79 (0.25), residues: 332 loop : -0.83 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 158 TYR 0.019 0.001 TYR A 306 PHE 0.020 0.001 PHE A 250 TRP 0.015 0.002 TRP B 623 HIS 0.007 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00350 (13926) covalent geometry : angle 0.63302 (19072) hydrogen bonds : bond 0.04100 ( 492) hydrogen bonds : angle 5.77654 ( 1336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.8144 (p90) cc_final: 0.7768 (p90) REVERT: A 132 GLU cc_start: 0.7898 (pm20) cc_final: 0.7666 (pm20) REVERT: A 142 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 217 GLU cc_start: 0.8923 (tp30) cc_final: 0.8443 (mp0) REVERT: A 415 TYR cc_start: 0.8777 (m-80) cc_final: 0.8526 (m-10) REVERT: B 81 PHE cc_start: 0.8076 (p90) cc_final: 0.7727 (p90) REVERT: B 132 GLU cc_start: 0.7919 (pm20) cc_final: 0.7687 (pm20) REVERT: B 142 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 217 GLU cc_start: 0.8908 (tp30) cc_final: 0.8404 (mp0) REVERT: B 399 ILE cc_start: 0.9474 (mt) cc_final: 0.9238 (pp) REVERT: B 415 TYR cc_start: 0.8772 (m-80) cc_final: 0.8564 (m-10) outliers start: 28 outliers final: 10 residues processed: 139 average time/residue: 0.5158 time to fit residues: 80.3616 Evaluate side-chains 98 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 547 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 274 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.091688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070259 restraints weight = 34485.415| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.47 r_work: 0.3075 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13926 Z= 0.249 Angle : 0.643 6.680 19072 Z= 0.345 Chirality : 0.046 0.185 2088 Planarity : 0.003 0.025 2180 Dihedral : 17.235 150.189 2402 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.54 % Allowed : 9.88 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.21), residues: 1486 helix: 0.16 (0.24), residues: 450 sheet: -1.55 (0.26), residues: 326 loop : -0.56 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 721 TYR 0.019 0.002 TYR B 306 PHE 0.019 0.002 PHE A 250 TRP 0.009 0.001 TRP B 623 HIS 0.006 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00568 (13926) covalent geometry : angle 0.64335 (19072) hydrogen bonds : bond 0.04018 ( 492) hydrogen bonds : angle 5.43724 ( 1336) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.8462 (p90) cc_final: 0.7986 (p90) REVERT: A 132 GLU cc_start: 0.7893 (pm20) cc_final: 0.7582 (pm20) REVERT: A 142 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8154 (tm-30) REVERT: A 217 GLU cc_start: 0.8952 (tp30) cc_final: 0.8433 (mp0) REVERT: A 415 TYR cc_start: 0.8805 (m-80) cc_final: 0.8506 (m-10) REVERT: A 601 GLU cc_start: 0.8495 (mp0) cc_final: 0.8137 (mp0) REVERT: B 81 PHE cc_start: 0.8453 (p90) cc_final: 0.7975 (p90) REVERT: B 132 GLU cc_start: 0.7865 (pm20) cc_final: 0.7550 (pm20) REVERT: B 142 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 217 GLU cc_start: 0.8941 (tp30) cc_final: 0.8406 (mp0) REVERT: B 415 TYR cc_start: 0.8812 (m-80) cc_final: 0.8543 (m-10) REVERT: B 601 GLU cc_start: 0.8501 (mp0) cc_final: 0.8152 (mp0) outliers start: 34 outliers final: 12 residues processed: 116 average time/residue: 0.5269 time to fit residues: 68.6605 Evaluate side-chains 95 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 ASN B 274 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.092408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070891 restraints weight = 34378.242| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.50 r_work: 0.3118 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13926 Z= 0.186 Angle : 0.595 6.888 19072 Z= 0.320 Chirality : 0.045 0.190 2088 Planarity : 0.003 0.025 2180 Dihedral : 17.066 151.063 2400 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.84 % Allowed : 10.78 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.21), residues: 1486 helix: 0.58 (0.24), residues: 448 sheet: -1.47 (0.27), residues: 322 loop : -0.40 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 721 TYR 0.016 0.001 TYR B 510 PHE 0.015 0.002 PHE B 250 TRP 0.005 0.001 TRP A 623 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00425 (13926) covalent geometry : angle 0.59533 (19072) hydrogen bonds : bond 0.03559 ( 492) hydrogen bonds : angle 5.09896 ( 1336) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8644 (mmtp) REVERT: A 81 PHE cc_start: 0.8614 (p90) cc_final: 0.8138 (p90) REVERT: A 132 GLU cc_start: 0.7927 (pm20) cc_final: 0.7601 (pm20) REVERT: A 142 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 146 GLU cc_start: 0.7495 (mp0) cc_final: 0.7211 (mp0) REVERT: A 217 GLU cc_start: 0.8921 (tp30) cc_final: 0.8421 (mp0) REVERT: A 259 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8335 (mp) REVERT: A 332 LYS cc_start: 0.7824 (mttt) cc_final: 0.7544 (pptt) REVERT: A 365 ILE cc_start: 0.8747 (tp) cc_final: 0.8535 (tp) REVERT: A 415 TYR cc_start: 0.8736 (m-80) cc_final: 0.8429 (m-10) REVERT: A 557 CYS cc_start: 0.9329 (m) cc_final: 0.8985 (p) REVERT: A 601 GLU cc_start: 0.8641 (mp0) cc_final: 0.8239 (mp0) REVERT: A 744 VAL cc_start: 0.8990 (t) cc_final: 0.8780 (p) REVERT: B 81 PHE cc_start: 0.8601 (p90) cc_final: 0.8124 (p90) REVERT: B 132 GLU cc_start: 0.7929 (pm20) cc_final: 0.7601 (pm20) REVERT: B 142 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 146 GLU cc_start: 0.7493 (mp0) cc_final: 0.7201 (mp0) REVERT: B 217 GLU cc_start: 0.8913 (tp30) cc_final: 0.8364 (mp0) REVERT: B 332 LYS cc_start: 0.7846 (mttt) cc_final: 0.7552 (pptt) REVERT: B 365 ILE cc_start: 0.8750 (tp) cc_final: 0.8538 (tp) REVERT: B 415 TYR cc_start: 0.8726 (m-80) cc_final: 0.8397 (m-10) REVERT: B 557 CYS cc_start: 0.9344 (m) cc_final: 0.9001 (p) REVERT: B 592 ASP cc_start: 0.8383 (m-30) cc_final: 0.8103 (m-30) REVERT: B 601 GLU cc_start: 0.8645 (mp0) cc_final: 0.8242 (mp0) REVERT: B 744 VAL cc_start: 0.8974 (t) cc_final: 0.8759 (p) outliers start: 38 outliers final: 10 residues processed: 137 average time/residue: 0.5029 time to fit residues: 77.6261 Evaluate side-chains 99 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 144 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.092194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070876 restraints weight = 34510.766| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.47 r_work: 0.3107 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13926 Z= 0.177 Angle : 0.589 6.541 19072 Z= 0.319 Chirality : 0.044 0.165 2088 Planarity : 0.003 0.025 2180 Dihedral : 16.909 150.647 2398 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.99 % Allowed : 11.00 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.22), residues: 1486 helix: 0.97 (0.25), residues: 436 sheet: -1.35 (0.27), residues: 326 loop : -0.20 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 721 TYR 0.017 0.001 TYR B 510 PHE 0.031 0.002 PHE A 250 TRP 0.003 0.001 TRP A 623 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00404 (13926) covalent geometry : angle 0.58927 (19072) hydrogen bonds : bond 0.03408 ( 492) hydrogen bonds : angle 4.95143 ( 1336) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.8102 (pmm) cc_final: 0.7682 (ptp) REVERT: A 58 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8644 (mmtp) REVERT: A 81 PHE cc_start: 0.8746 (p90) cc_final: 0.8323 (p90) REVERT: A 132 GLU cc_start: 0.7945 (pm20) cc_final: 0.7603 (pm20) REVERT: A 142 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8065 (tm-30) REVERT: A 146 GLU cc_start: 0.7530 (mp0) cc_final: 0.7292 (mp0) REVERT: A 217 GLU cc_start: 0.8920 (tp30) cc_final: 0.8428 (mp0) REVERT: A 259 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 304 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8755 (mmm) REVERT: A 332 LYS cc_start: 0.7813 (mttt) cc_final: 0.7546 (pptt) REVERT: A 353 MET cc_start: 0.8149 (mmt) cc_final: 0.7707 (mmm) REVERT: A 365 ILE cc_start: 0.8748 (tp) cc_final: 0.8548 (tp) REVERT: A 415 TYR cc_start: 0.8672 (m-80) cc_final: 0.8364 (m-10) REVERT: A 592 ASP cc_start: 0.8409 (m-30) cc_final: 0.8121 (m-30) REVERT: A 601 GLU cc_start: 0.8625 (mp0) cc_final: 0.8291 (mp0) REVERT: B 24 MET cc_start: 0.7972 (pmm) cc_final: 0.7626 (ptp) REVERT: B 81 PHE cc_start: 0.8719 (p90) cc_final: 0.8297 (p90) REVERT: B 132 GLU cc_start: 0.7956 (pm20) cc_final: 0.7613 (pm20) REVERT: B 142 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 146 GLU cc_start: 0.7526 (mp0) cc_final: 0.7277 (mp0) REVERT: B 217 GLU cc_start: 0.8915 (tp30) cc_final: 0.8421 (mp0) REVERT: B 259 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8335 (mp) REVERT: B 304 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8745 (mmm) REVERT: B 332 LYS cc_start: 0.7826 (mttt) cc_final: 0.7558 (pptt) REVERT: B 353 MET cc_start: 0.8129 (mmt) cc_final: 0.7691 (mmm) REVERT: B 365 ILE cc_start: 0.8771 (tp) cc_final: 0.8571 (tp) REVERT: B 415 TYR cc_start: 0.8666 (m-80) cc_final: 0.8381 (m-10) REVERT: B 592 ASP cc_start: 0.8411 (m-30) cc_final: 0.8123 (m-30) REVERT: B 601 GLU cc_start: 0.8641 (mp0) cc_final: 0.8308 (mp0) outliers start: 40 outliers final: 18 residues processed: 129 average time/residue: 0.5284 time to fit residues: 76.6757 Evaluate side-chains 111 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 85 ASN ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.086942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064415 restraints weight = 35085.596| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.57 r_work: 0.2952 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.089 13926 Z= 0.432 Angle : 0.771 11.844 19072 Z= 0.405 Chirality : 0.052 0.250 2088 Planarity : 0.004 0.033 2180 Dihedral : 17.262 149.026 2398 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.82 % Allowed : 11.90 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.22), residues: 1486 helix: 0.40 (0.24), residues: 436 sheet: -1.56 (0.27), residues: 328 loop : -0.34 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 721 TYR 0.020 0.002 TYR B 101 PHE 0.044 0.003 PHE B 250 TRP 0.008 0.002 TRP A 482 HIS 0.004 0.002 HIS B 513 Details of bonding type rmsd covalent geometry : bond 0.00993 (13926) covalent geometry : angle 0.77060 (19072) hydrogen bonds : bond 0.04403 ( 492) hydrogen bonds : angle 5.46932 ( 1336) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 85 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8367 (pmm) cc_final: 0.8013 (ptp) REVERT: A 81 PHE cc_start: 0.8865 (p90) cc_final: 0.8458 (p90) REVERT: A 132 GLU cc_start: 0.7871 (pm20) cc_final: 0.7488 (pm20) REVERT: A 142 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8194 (tm-30) REVERT: A 146 GLU cc_start: 0.7584 (mp0) cc_final: 0.7356 (mp0) REVERT: A 217 GLU cc_start: 0.8933 (tp30) cc_final: 0.8371 (mp0) REVERT: A 304 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8791 (mmm) REVERT: A 337 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8667 (t) REVERT: A 353 MET cc_start: 0.8089 (mmt) cc_final: 0.7790 (mmm) REVERT: A 415 TYR cc_start: 0.8632 (m-80) cc_final: 0.8354 (m-10) REVERT: A 601 GLU cc_start: 0.8600 (mp0) cc_final: 0.8313 (mp0) REVERT: B 81 PHE cc_start: 0.8860 (p90) cc_final: 0.8453 (p90) REVERT: B 132 GLU cc_start: 0.7874 (pm20) cc_final: 0.7487 (pm20) REVERT: B 142 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 146 GLU cc_start: 0.7561 (mp0) cc_final: 0.7329 (mp0) REVERT: B 217 GLU cc_start: 0.8957 (tp30) cc_final: 0.8399 (mp0) REVERT: B 304 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8790 (mmm) REVERT: B 337 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8675 (t) REVERT: B 353 MET cc_start: 0.8093 (mmt) cc_final: 0.7790 (mmm) REVERT: B 415 TYR cc_start: 0.8633 (m-80) cc_final: 0.8384 (m-10) REVERT: B 592 ASP cc_start: 0.8435 (m-30) cc_final: 0.8093 (m-30) REVERT: B 601 GLU cc_start: 0.8608 (mp0) cc_final: 0.8324 (mp0) outliers start: 51 outliers final: 24 residues processed: 119 average time/residue: 0.5336 time to fit residues: 71.1116 Evaluate side-chains 105 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.092290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071352 restraints weight = 33981.162| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.36 r_work: 0.3140 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13926 Z= 0.138 Angle : 0.600 8.834 19072 Z= 0.321 Chirality : 0.044 0.251 2088 Planarity : 0.003 0.027 2180 Dihedral : 17.053 152.861 2398 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.62 % Allowed : 13.62 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.22), residues: 1486 helix: 1.05 (0.25), residues: 438 sheet: -1.28 (0.28), residues: 326 loop : -0.11 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 743 TYR 0.016 0.001 TYR B 510 PHE 0.026 0.002 PHE B 250 TRP 0.009 0.001 TRP B 482 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00310 (13926) covalent geometry : angle 0.60029 (19072) hydrogen bonds : bond 0.03354 ( 492) hydrogen bonds : angle 4.82511 ( 1336) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.8827 (p90) cc_final: 0.8397 (p90) REVERT: A 132 GLU cc_start: 0.8002 (pm20) cc_final: 0.7651 (pm20) REVERT: A 142 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8047 (tm-30) REVERT: A 146 GLU cc_start: 0.7612 (mp0) cc_final: 0.7357 (mp0) REVERT: A 259 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8327 (mp) REVERT: A 304 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8619 (mmm) REVERT: A 332 LYS cc_start: 0.7833 (mttt) cc_final: 0.7612 (pptt) REVERT: A 353 MET cc_start: 0.7982 (mmt) cc_final: 0.7705 (mmm) REVERT: A 365 ILE cc_start: 0.8742 (tp) cc_final: 0.8519 (tp) REVERT: A 592 ASP cc_start: 0.8411 (m-30) cc_final: 0.8109 (m-30) REVERT: A 601 GLU cc_start: 0.8698 (mp0) cc_final: 0.8334 (mp0) REVERT: A 624 TYR cc_start: 0.8321 (m-80) cc_final: 0.8024 (m-10) REVERT: B 81 PHE cc_start: 0.8824 (p90) cc_final: 0.8432 (p90) REVERT: B 132 GLU cc_start: 0.8007 (pm20) cc_final: 0.7656 (pm20) REVERT: B 142 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 146 GLU cc_start: 0.7617 (mp0) cc_final: 0.7352 (mp0) REVERT: B 304 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8620 (mmm) REVERT: B 332 LYS cc_start: 0.7826 (mttt) cc_final: 0.7622 (pptt) REVERT: B 353 MET cc_start: 0.7952 (mmt) cc_final: 0.7677 (mmm) REVERT: B 365 ILE cc_start: 0.8742 (tp) cc_final: 0.8519 (tp) REVERT: B 592 ASP cc_start: 0.8423 (m-30) cc_final: 0.8123 (m-30) REVERT: B 601 GLU cc_start: 0.8707 (mp0) cc_final: 0.8348 (mp0) REVERT: B 624 TYR cc_start: 0.8324 (m-80) cc_final: 0.8038 (m-10) outliers start: 35 outliers final: 11 residues processed: 124 average time/residue: 0.5050 time to fit residues: 70.8471 Evaluate side-chains 105 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.087791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.065514 restraints weight = 34616.427| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.53 r_work: 0.2982 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 13926 Z= 0.368 Angle : 0.744 9.538 19072 Z= 0.388 Chirality : 0.050 0.228 2088 Planarity : 0.004 0.038 2180 Dihedral : 17.142 148.985 2398 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.54 % Allowed : 14.30 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.22), residues: 1486 helix: 0.60 (0.24), residues: 438 sheet: -1.50 (0.28), residues: 328 loop : -0.15 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 743 TYR 0.018 0.002 TYR A 284 PHE 0.026 0.002 PHE B 250 TRP 0.007 0.002 TRP B 482 HIS 0.006 0.002 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00849 (13926) covalent geometry : angle 0.74394 (19072) hydrogen bonds : bond 0.04112 ( 492) hydrogen bonds : angle 5.27959 ( 1336) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 81 PHE cc_start: 0.8876 (p90) cc_final: 0.8472 (p90) REVERT: A 132 GLU cc_start: 0.7917 (pm20) cc_final: 0.7546 (pm20) REVERT: A 142 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 217 GLU cc_start: 0.8946 (tp30) cc_final: 0.8376 (mp0) REVERT: A 259 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8309 (mp) REVERT: A 304 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8769 (mmm) REVERT: A 332 LYS cc_start: 0.7823 (mttt) cc_final: 0.7472 (pptt) REVERT: A 337 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8763 (t) REVERT: A 353 MET cc_start: 0.7932 (mmt) cc_final: 0.7669 (mmm) REVERT: A 592 ASP cc_start: 0.8435 (m-30) cc_final: 0.8106 (m-30) REVERT: A 601 GLU cc_start: 0.8628 (mp0) cc_final: 0.8320 (mp0) REVERT: B 58 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8752 (mmtp) REVERT: B 81 PHE cc_start: 0.8900 (p90) cc_final: 0.8522 (p90) REVERT: B 132 GLU cc_start: 0.7906 (pm20) cc_final: 0.7534 (pm20) REVERT: B 142 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8148 (tm-30) REVERT: B 259 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8324 (mp) REVERT: B 332 LYS cc_start: 0.7821 (mttt) cc_final: 0.7469 (pptt) REVERT: B 337 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8769 (t) REVERT: B 353 MET cc_start: 0.7946 (mmt) cc_final: 0.7679 (mmm) REVERT: B 491 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8195 (mtm) REVERT: B 592 ASP cc_start: 0.8435 (m-30) cc_final: 0.8104 (m-30) REVERT: B 601 GLU cc_start: 0.8632 (mp0) cc_final: 0.8326 (mp0) outliers start: 34 outliers final: 12 residues processed: 105 average time/residue: 0.5325 time to fit residues: 62.5611 Evaluate side-chains 90 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.091252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.070579 restraints weight = 34148.574| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.36 r_work: 0.3138 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13926 Z= 0.153 Angle : 0.634 11.745 19072 Z= 0.335 Chirality : 0.045 0.237 2088 Planarity : 0.003 0.026 2180 Dihedral : 16.985 152.499 2398 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.80 % Allowed : 15.19 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.23), residues: 1486 helix: 1.03 (0.25), residues: 438 sheet: -1.27 (0.29), residues: 326 loop : 0.01 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 158 TYR 0.016 0.001 TYR A 511 PHE 0.048 0.002 PHE B 250 TRP 0.008 0.001 TRP B 482 HIS 0.005 0.001 HIS B 513 Details of bonding type rmsd covalent geometry : bond 0.00347 (13926) covalent geometry : angle 0.63431 (19072) hydrogen bonds : bond 0.03308 ( 492) hydrogen bonds : angle 4.84973 ( 1336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.8886 (p90) cc_final: 0.8502 (p90) REVERT: A 132 GLU cc_start: 0.7990 (pm20) cc_final: 0.7639 (pm20) REVERT: A 142 GLU cc_start: 0.8642 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 217 GLU cc_start: 0.8940 (tp30) cc_final: 0.8424 (mp0) REVERT: A 259 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8300 (mp) REVERT: A 304 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8633 (mmm) REVERT: A 332 LYS cc_start: 0.7863 (mttt) cc_final: 0.7657 (pptt) REVERT: A 353 MET cc_start: 0.7916 (mmt) cc_final: 0.7697 (mmm) REVERT: A 365 ILE cc_start: 0.8709 (tp) cc_final: 0.8497 (tp) REVERT: A 592 ASP cc_start: 0.8416 (m-30) cc_final: 0.8099 (m-30) REVERT: A 601 GLU cc_start: 0.8679 (mp0) cc_final: 0.8393 (mp0) REVERT: A 624 TYR cc_start: 0.8364 (m-80) cc_final: 0.8061 (m-10) REVERT: B 81 PHE cc_start: 0.8862 (p90) cc_final: 0.8471 (p90) REVERT: B 132 GLU cc_start: 0.7995 (pm20) cc_final: 0.7649 (pm20) REVERT: B 142 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8008 (tm-30) REVERT: B 259 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 332 LYS cc_start: 0.7859 (mttt) cc_final: 0.7653 (pptt) REVERT: B 353 MET cc_start: 0.7920 (mmt) cc_final: 0.7700 (mmm) REVERT: B 365 ILE cc_start: 0.8719 (tp) cc_final: 0.8507 (tp) REVERT: B 592 ASP cc_start: 0.8440 (m-30) cc_final: 0.8123 (m-30) REVERT: B 601 GLU cc_start: 0.8687 (mp0) cc_final: 0.8401 (mp0) REVERT: B 624 TYR cc_start: 0.8331 (m-80) cc_final: 0.8036 (m-10) outliers start: 24 outliers final: 12 residues processed: 109 average time/residue: 0.5114 time to fit residues: 62.5170 Evaluate side-chains 102 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.091620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.071012 restraints weight = 33899.629| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.33 r_work: 0.3136 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13926 Z= 0.153 Angle : 0.642 11.684 19072 Z= 0.339 Chirality : 0.045 0.235 2088 Planarity : 0.003 0.027 2180 Dihedral : 16.734 149.913 2398 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.57 % Allowed : 15.72 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.23), residues: 1486 helix: 1.14 (0.25), residues: 438 sheet: -1.21 (0.29), residues: 320 loop : 0.00 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 721 TYR 0.016 0.001 TYR A 511 PHE 0.049 0.002 PHE A 250 TRP 0.007 0.001 TRP A 482 HIS 0.006 0.001 HIS B 513 Details of bonding type rmsd covalent geometry : bond 0.00349 (13926) covalent geometry : angle 0.64199 (19072) hydrogen bonds : bond 0.03240 ( 492) hydrogen bonds : angle 4.79146 ( 1336) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 81 PHE cc_start: 0.8854 (p90) cc_final: 0.8497 (p90) REVERT: A 132 GLU cc_start: 0.7987 (pm20) cc_final: 0.7640 (pm20) REVERT: A 142 GLU cc_start: 0.8608 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 259 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8327 (mp) REVERT: A 304 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8732 (mmm) REVERT: A 353 MET cc_start: 0.7882 (mmt) cc_final: 0.7673 (mmm) REVERT: A 365 ILE cc_start: 0.8703 (tp) cc_final: 0.8478 (tp) REVERT: A 415 TYR cc_start: 0.8486 (m-80) cc_final: 0.8240 (m-10) REVERT: A 491 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8108 (mtm) REVERT: A 592 ASP cc_start: 0.8375 (m-30) cc_final: 0.8040 (m-30) REVERT: A 601 GLU cc_start: 0.8668 (mp0) cc_final: 0.8378 (mp0) REVERT: B 16 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 81 PHE cc_start: 0.8828 (p90) cc_final: 0.8464 (p90) REVERT: B 132 GLU cc_start: 0.8012 (pm20) cc_final: 0.7663 (pm20) REVERT: B 142 GLU cc_start: 0.8632 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 191 MET cc_start: 0.7438 (mmp) cc_final: 0.7209 (mmp) REVERT: B 353 MET cc_start: 0.7893 (mmt) cc_final: 0.7684 (mmm) REVERT: B 365 ILE cc_start: 0.8715 (tp) cc_final: 0.8508 (tp) REVERT: B 491 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8096 (mtm) REVERT: B 592 ASP cc_start: 0.8409 (m-30) cc_final: 0.8090 (m-30) REVERT: B 601 GLU cc_start: 0.8670 (mp0) cc_final: 0.8376 (mp0) outliers start: 21 outliers final: 14 residues processed: 106 average time/residue: 0.5663 time to fit residues: 66.7713 Evaluate side-chains 103 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.092604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.072074 restraints weight = 34140.665| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.35 r_work: 0.3163 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13926 Z= 0.141 Angle : 0.638 11.237 19072 Z= 0.337 Chirality : 0.045 0.232 2088 Planarity : 0.003 0.046 2180 Dihedral : 16.620 149.772 2398 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.80 % Allowed : 16.02 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.23), residues: 1486 helix: 1.24 (0.25), residues: 438 sheet: -0.99 (0.29), residues: 342 loop : 0.06 (0.26), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 743 TYR 0.016 0.001 TYR A 511 PHE 0.038 0.001 PHE A 250 TRP 0.008 0.001 TRP A 482 HIS 0.004 0.001 HIS B 513 Details of bonding type rmsd covalent geometry : bond 0.00321 (13926) covalent geometry : angle 0.63772 (19072) hydrogen bonds : bond 0.03147 ( 492) hydrogen bonds : angle 4.69507 ( 1336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3643.23 seconds wall clock time: 63 minutes 34.56 seconds (3814.56 seconds total)