Starting phenix.real_space_refine on Tue Jul 29 09:02:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6of3_20041/07_2025/6of3_20041.cif Found real_map, /net/cci-nas-00/data/ceres_data/6of3_20041/07_2025/6of3_20041.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6of3_20041/07_2025/6of3_20041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6of3_20041/07_2025/6of3_20041.map" model { file = "/net/cci-nas-00/data/ceres_data/6of3_20041/07_2025/6of3_20041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6of3_20041/07_2025/6of3_20041.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.657 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 7070 2.51 5 N 1938 2.21 5 O 2024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11096 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1471 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 4045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4045 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: E, D Time building chain proxies: 8.86, per 1000 atoms: 0.80 Number of scatterers: 11096 At special positions: 0 Unit cell: (150.12, 87.48, 88.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 6 15.00 Mg 2 11.99 O 2024 8.00 N 1938 7.00 C 7070 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: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 40.3% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 93 through 115 removed outlier: 3.612A pdb=" N ARG A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 134 through 146 removed outlier: 3.835A pdb=" N VAL A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.887A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.505A pdb=" N LEU B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.608A pdb=" N ASN B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 242 through 258 removed outlier: 3.704A pdb=" N ARG B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 367 through 387 Processing helix chain 'B' and resid 403 through 417 removed outlier: 3.758A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.621A pdb=" N SER B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 3.529A pdb=" N PHE B 483 " --> pdb=" O MET B 479 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS B 484 " --> pdb=" O GLN B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 544 removed outlier: 4.226A pdb=" N SER B 540 " --> pdb=" O PRO B 536 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 676 through 691 removed outlier: 4.188A pdb=" N TYR B 680 " --> pdb=" O PRO B 676 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 41 through 64 Processing helix chain 'D' and resid 67 through 84 Processing helix chain 'D' and resid 93 through 115 removed outlier: 3.613A pdb=" N ARG D 97 " --> pdb=" O GLY D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 134 through 146 removed outlier: 3.835A pdb=" N VAL D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 170 Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.887A pdb=" N GLY D 175 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 202 removed outlier: 3.504A pdb=" N LEU E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 211 removed outlier: 3.609A pdb=" N ASN E 207 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 242 through 258 removed outlier: 3.704A pdb=" N ARG E 258 " --> pdb=" O THR E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 367 through 387 Processing helix chain 'E' and resid 403 through 417 removed outlier: 3.759A pdb=" N ASP E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 443 removed outlier: 3.620A pdb=" N SER E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 484 removed outlier: 3.529A pdb=" N PHE E 483 " --> pdb=" O MET E 479 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS E 484 " --> pdb=" O GLN E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 544 removed outlier: 4.227A pdb=" N SER E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP E 541 " --> pdb=" O GLU E 537 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN E 544 " --> pdb=" O SER E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 625 No H-bonds generated for 'chain 'E' and resid 623 through 625' Processing helix chain 'E' and resid 654 through 660 Processing helix chain 'E' and resid 676 through 691 removed outlier: 4.189A pdb=" N TYR E 680 " --> pdb=" O PRO E 676 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL E 681 " --> pdb=" O THR E 677 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU E 684 " --> pdb=" O TYR E 680 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349 removed outlier: 7.347A pdb=" N GLU B 646 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL B 638 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS B 648 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU B 550 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU B 632 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET B 548 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 122 through 125 removed outlier: 3.920A pdb=" N GLU B 153 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP B 186 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN B 151 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL B 188 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL B 149 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLU B 190 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B 147 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 192 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR B 145 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY B 143 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 161 removed outlier: 3.572A pdb=" N LEU B 142 " --> pdb=" O GLN B 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 358 removed outlier: 7.010A pdb=" N LEU B 320 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N MET B 356 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 318 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET B 301 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASN B 396 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B 303 " --> pdb=" O ASN B 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 349 removed outlier: 7.347A pdb=" N GLU E 646 " --> pdb=" O VAL E 638 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL E 638 " --> pdb=" O GLU E 646 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS E 648 " --> pdb=" O ARG E 636 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU E 550 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU E 632 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET E 548 " --> pdb=" O LEU E 632 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.920A pdb=" N GLU E 153 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP E 186 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN E 151 " --> pdb=" O ASP E 186 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL E 188 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL E 149 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU E 190 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL E 147 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU E 192 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR E 145 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY E 143 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 159 through 161 removed outlier: 3.573A pdb=" N LEU E 142 " --> pdb=" O GLN E 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 351 through 358 removed outlier: 7.010A pdb=" N LEU E 320 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET E 356 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL E 318 " --> pdb=" O MET E 356 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET E 301 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ASN E 396 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU E 303 " --> pdb=" O ASN E 396 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 3761 1.37 - 1.51: 3752 1.51 - 1.65: 3795 1.65 - 1.80: 60 1.80 - 1.94: 30 Bond restraints: 11398 Sorted by residual: bond pdb=" C GLN E 115 " pdb=" N PRO E 116 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.14e+00 bond pdb=" C GLN B 115 " pdb=" N PRO B 116 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.06e+00 bond pdb=" O3G AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.558 1.503 0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" O3G AGS B 801 " pdb=" PG AGS B 801 " ideal model delta sigma weight residual 1.558 1.504 0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" O2G AGS B 801 " pdb=" PG AGS B 801 " ideal model delta sigma weight residual 1.557 1.503 0.054 2.00e-02 2.50e+03 7.31e+00 ... (remaining 11393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 14802 3.30 - 6.61: 652 6.61 - 9.91: 86 9.91 - 13.21: 24 13.21 - 16.52: 6 Bond angle restraints: 15570 Sorted by residual: angle pdb=" C THR B 641 " pdb=" N ALA B 642 " pdb=" CA ALA B 642 " ideal model delta sigma weight residual 121.54 138.06 -16.52 1.91e+00 2.74e-01 7.48e+01 angle pdb=" C THR E 641 " pdb=" N ALA E 642 " pdb=" CA ALA E 642 " ideal model delta sigma weight residual 121.54 138.00 -16.46 1.91e+00 2.74e-01 7.42e+01 angle pdb=" C ALA E 184 " pdb=" N ASN E 185 " pdb=" CA ASN E 185 " ideal model delta sigma weight residual 121.54 137.98 -16.44 1.91e+00 2.74e-01 7.41e+01 angle pdb=" C ALA B 184 " pdb=" N ASN B 185 " pdb=" CA ASN B 185 " ideal model delta sigma weight residual 121.54 137.97 -16.43 1.91e+00 2.74e-01 7.40e+01 angle pdb=" C LYS B 293 " pdb=" N SER B 294 " pdb=" CA SER B 294 " ideal model delta sigma weight residual 121.54 137.35 -15.81 1.91e+00 2.74e-01 6.86e+01 ... (remaining 15565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 6621 33.07 - 66.13: 181 66.13 - 99.20: 2 99.20 - 132.26: 0 132.26 - 165.33: 2 Dihedral angle restraints: 6806 sinusoidal: 2688 harmonic: 4118 Sorted by residual: dihedral pdb=" CA ALA E 184 " pdb=" C ALA E 184 " pdb=" N ASN E 185 " pdb=" CA ASN E 185 " ideal model delta harmonic sigma weight residual -180.00 -136.55 -43.45 0 5.00e+00 4.00e-02 7.55e+01 dihedral pdb=" CA ALA B 184 " pdb=" C ALA B 184 " pdb=" N ASN B 185 " pdb=" CA ASN B 185 " ideal model delta harmonic sigma weight residual -180.00 -136.58 -43.42 0 5.00e+00 4.00e-02 7.54e+01 dihedral pdb=" CA TYR E 225 " pdb=" C TYR E 225 " pdb=" N THR E 226 " pdb=" CA THR E 226 " ideal model delta harmonic sigma weight residual -180.00 -145.87 -34.13 0 5.00e+00 4.00e-02 4.66e+01 ... (remaining 6803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1201 0.066 - 0.132: 370 0.132 - 0.198: 133 0.198 - 0.264: 35 0.264 - 0.330: 5 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CB ILE B 391 " pdb=" CA ILE B 391 " pdb=" CG1 ILE B 391 " pdb=" CG2 ILE B 391 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE E 391 " pdb=" CA ILE E 391 " pdb=" CG1 ILE E 391 " pdb=" CG2 ILE E 391 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL B 667 " pdb=" CA VAL B 667 " pdb=" CG1 VAL B 667 " pdb=" CG2 VAL B 667 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1741 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 644 " 0.018 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C ASN E 644 " -0.060 2.00e-02 2.50e+03 pdb=" O ASN E 644 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO E 645 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 644 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ASN B 644 " 0.059 2.00e-02 2.50e+03 pdb=" O ASN B 644 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO B 645 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 259 " -0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO E 260 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 260 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 260 " -0.045 5.00e-02 4.00e+02 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 106 2.63 - 3.20: 9297 3.20 - 3.76: 15729 3.76 - 4.33: 19753 4.33 - 4.90: 34995 Nonbonded interactions: 79880 Sorted by model distance: nonbonded pdb=" O2B AGS B 801 " pdb="MG MG B 802 " model vdw 2.058 2.170 nonbonded pdb=" O2B AGS E 801 " pdb="MG MG E 802 " model vdw 2.059 2.170 nonbonded pdb=" O3G AGS E 801 " pdb="MG MG E 802 " model vdw 2.131 2.170 nonbonded pdb=" O3G AGS B 801 " pdb="MG MG B 802 " model vdw 2.131 2.170 nonbonded pdb=" OG SER B 275 " pdb="MG MG B 802 " model vdw 2.188 2.170 ... (remaining 79875 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: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.460 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 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 : 0.008 0.069 11398 Z= 0.376 Angle : 1.590 16.517 15570 Z= 0.886 Chirality : 0.076 0.330 1744 Planarity : 0.011 0.080 1990 Dihedral : 14.843 165.331 4138 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 2.01 % Allowed : 16.07 % Favored : 81.92 % Rotamer: Outliers : 0.85 % Allowed : 4.67 % Favored : 94.48 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.18), residues: 1394 helix: -2.16 (0.17), residues: 446 sheet: -1.48 (0.32), residues: 234 loop : -4.03 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 297 HIS 0.007 0.002 HIS B 334 PHE 0.029 0.004 PHE D 104 TYR 0.036 0.004 TYR E 685 ARG 0.009 0.001 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.19908 ( 490) hydrogen bonds : angle 6.07747 ( 1398) covalent geometry : bond 0.00810 (11398) covalent geometry : angle 1.59035 (15570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 366 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.7568 (mm) cc_final: 0.7278 (mm) REVERT: A 23 TYR cc_start: 0.7407 (m-80) cc_final: 0.7143 (m-80) REVERT: A 107 PHE cc_start: 0.6231 (t80) cc_final: 0.6028 (t80) REVERT: B 364 PRO cc_start: 0.5826 (Cg_exo) cc_final: 0.5620 (Cg_endo) REVERT: D 5 ILE cc_start: 0.7433 (mm) cc_final: 0.7118 (mm) REVERT: E 222 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7209 (pp30) REVERT: E 349 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7355 (mp0) REVERT: E 432 THR cc_start: 0.8161 (t) cc_final: 0.7928 (m) outliers start: 10 outliers final: 4 residues processed: 372 average time/residue: 0.9361 time to fit residues: 382.7189 Evaluate side-chains 227 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 222 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 143 GLN B 144 ASN B 171 HIS B 198 GLN B 357 HIS B 644 ASN B 689 ASN D 26 HIS D 143 GLN E 117 ASN E 144 ASN E 174 HIS E 185 ASN E 222 GLN E 357 HIS E 644 ASN E 689 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.116625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.095495 restraints weight = 18540.914| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.43 r_work: 0.3193 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 11398 Z= 0.293 Angle : 1.071 14.830 15570 Z= 0.533 Chirality : 0.053 0.176 1744 Planarity : 0.009 0.092 1990 Dihedral : 10.247 158.748 1588 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.33 % Favored : 89.02 % Rotamer: Outliers : 6.54 % Allowed : 15.45 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.22), residues: 1394 helix: 1.48 (0.22), residues: 472 sheet: -1.07 (0.36), residues: 194 loop : -3.05 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 722 HIS 0.014 0.003 HIS E 532 PHE 0.046 0.004 PHE B 265 TYR 0.024 0.003 TYR D 4 ARG 0.011 0.001 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.06180 ( 490) hydrogen bonds : angle 5.09019 ( 1398) covalent geometry : bond 0.00669 (11398) covalent geometry : angle 1.07056 (15570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 276 time to evaluate : 1.099 Fit side-chains REVERT: A 5 ILE cc_start: 0.8868 (mm) cc_final: 0.8587 (pp) REVERT: B 141 ILE cc_start: 0.9168 (mt) cc_final: 0.8741 (mp) REVERT: B 147 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8443 (t) REVERT: B 149 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8368 (t) REVERT: B 367 ASP cc_start: 0.7311 (t0) cc_final: 0.7066 (m-30) REVERT: B 672 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8293 (mmtp) REVERT: B 720 VAL cc_start: 0.8404 (t) cc_final: 0.8037 (p) REVERT: D 153 THR cc_start: 0.8312 (m) cc_final: 0.8007 (p) REVERT: D 172 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7390 (ttpt) REVERT: E 121 PHE cc_start: 0.6586 (OUTLIER) cc_final: 0.6290 (t80) REVERT: E 312 PHE cc_start: 0.8278 (m-80) cc_final: 0.8053 (m-80) REVERT: E 364 PRO cc_start: 0.6161 (Cg_exo) cc_final: 0.5947 (Cg_endo) REVERT: E 500 TRP cc_start: 0.8820 (m-90) cc_final: 0.8558 (m-90) REVERT: E 537 GLU cc_start: 0.8311 (mp0) cc_final: 0.8062 (mp0) REVERT: E 559 LEU cc_start: 0.8545 (mt) cc_final: 0.8331 (tp) REVERT: E 672 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8373 (mmmt) outliers start: 77 outliers final: 20 residues processed: 329 average time/residue: 1.1124 time to fit residues: 403.5216 Evaluate side-chains 241 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 639 SER Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 639 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 41 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 0.0870 chunk 19 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 26 HIS B 283 ASN D 21 GLN D 26 HIS D 68 HIS ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN E 171 HIS E 283 ASN E 533 GLN E 644 ASN E 689 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097724 restraints weight = 18257.156| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.43 r_work: 0.3221 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11398 Z= 0.162 Angle : 0.863 11.547 15570 Z= 0.418 Chirality : 0.046 0.186 1744 Planarity : 0.006 0.067 1990 Dihedral : 9.353 155.491 1581 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.54 % Favored : 91.10 % Rotamer: Outliers : 6.11 % Allowed : 21.39 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1394 helix: 2.61 (0.23), residues: 466 sheet: -1.00 (0.34), residues: 196 loop : -2.54 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 347 HIS 0.013 0.001 HIS D 68 PHE 0.029 0.002 PHE A 107 TYR 0.019 0.002 TYR E 225 ARG 0.004 0.001 ARG B 205 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 490) hydrogen bonds : angle 4.60892 ( 1398) covalent geometry : bond 0.00359 (11398) covalent geometry : angle 0.86284 (15570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 226 time to evaluate : 1.269 Fit side-chains REVERT: A 5 ILE cc_start: 0.8885 (mm) cc_final: 0.8465 (pp) REVERT: A 23 TYR cc_start: 0.8030 (m-80) cc_final: 0.7541 (m-80) REVERT: A 156 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6946 (ttp80) REVERT: B 141 ILE cc_start: 0.9108 (mt) cc_final: 0.8815 (mp) REVERT: B 420 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7354 (mm-30) REVERT: B 672 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8292 (mmmt) REVERT: D 68 HIS cc_start: 0.8548 (t70) cc_final: 0.8260 (t-170) REVERT: D 72 SER cc_start: 0.8120 (t) cc_final: 0.7796 (p) REVERT: D 94 TYR cc_start: 0.6586 (OUTLIER) cc_final: 0.6262 (t80) REVERT: D 153 THR cc_start: 0.8286 (m) cc_final: 0.8029 (p) REVERT: D 172 LYS cc_start: 0.7859 (tppt) cc_final: 0.7334 (ttmt) REVERT: E 121 PHE cc_start: 0.6566 (m-80) cc_final: 0.5872 (m-80) REVERT: E 213 LEU cc_start: 0.8087 (mt) cc_final: 0.7861 (mt) REVERT: E 364 PRO cc_start: 0.6150 (Cg_exo) cc_final: 0.5943 (Cg_endo) REVERT: E 420 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7351 (mm-30) REVERT: E 567 ASP cc_start: 0.6122 (OUTLIER) cc_final: 0.5369 (t0) REVERT: E 630 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7616 (m) REVERT: E 664 ASP cc_start: 0.6073 (t0) cc_final: 0.5683 (m-30) outliers start: 72 outliers final: 31 residues processed: 271 average time/residue: 0.8174 time to fit residues: 248.7019 Evaluate side-chains 237 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 333 CYS Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 567 ASP Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 720 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 26 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN B 357 HIS D 21 GLN D 26 HIS ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 HIS E 648 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093433 restraints weight = 18353.408| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.52 r_work: 0.3155 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.8223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11398 Z= 0.249 Angle : 0.887 14.347 15570 Z= 0.432 Chirality : 0.049 0.176 1744 Planarity : 0.007 0.052 1990 Dihedral : 9.141 150.154 1579 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.11 % Favored : 90.60 % Rotamer: Outliers : 6.62 % Allowed : 21.56 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1394 helix: 2.42 (0.23), residues: 482 sheet: -0.50 (0.38), residues: 166 loop : -2.65 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 347 HIS 0.006 0.002 HIS B 150 PHE 0.041 0.002 PHE D 107 TYR 0.018 0.002 TYR B 382 ARG 0.006 0.001 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.06006 ( 490) hydrogen bonds : angle 4.59272 ( 1398) covalent geometry : bond 0.00586 (11398) covalent geometry : angle 0.88714 (15570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 227 time to evaluate : 1.108 Fit side-chains REVERT: A 156 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7048 (ttp80) REVERT: B 141 ILE cc_start: 0.9161 (mt) cc_final: 0.8875 (mp) REVERT: B 367 ASP cc_start: 0.7890 (t0) cc_final: 0.7556 (m-30) REVERT: B 420 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7357 (mm-30) REVERT: B 527 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7822 (mp) REVERT: B 567 ASP cc_start: 0.6044 (OUTLIER) cc_final: 0.5578 (t70) REVERT: B 618 THR cc_start: 0.9168 (m) cc_final: 0.8925 (t) REVERT: B 662 ARG cc_start: 0.8614 (tpp80) cc_final: 0.7779 (ttp80) REVERT: B 664 ASP cc_start: 0.6070 (t0) cc_final: 0.5741 (m-30) REVERT: D 23 TYR cc_start: 0.8432 (m-80) cc_final: 0.7639 (m-80) REVERT: D 72 SER cc_start: 0.8474 (t) cc_final: 0.8244 (p) REVERT: D 107 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7296 (t80) REVERT: D 153 THR cc_start: 0.8515 (m) cc_final: 0.8202 (p) REVERT: D 172 LYS cc_start: 0.8557 (tppt) cc_final: 0.8134 (ttmt) REVERT: E 333 CYS cc_start: 0.8266 (t) cc_final: 0.8064 (m) REVERT: E 420 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7424 (mm-30) REVERT: E 424 MET cc_start: 0.8494 (mmm) cc_final: 0.6926 (mtm) REVERT: E 527 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7768 (mp) REVERT: E 618 THR cc_start: 0.9193 (m) cc_final: 0.8958 (t) REVERT: E 625 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: E 630 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7812 (p) REVERT: E 662 ARG cc_start: 0.8528 (tpp80) cc_final: 0.7748 (ttp-110) REVERT: E 664 ASP cc_start: 0.6371 (t0) cc_final: 0.5988 (m-30) outliers start: 78 outliers final: 41 residues processed: 277 average time/residue: 0.8121 time to fit residues: 251.8605 Evaluate side-chains 232 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 249 ILE Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 567 ASP Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 630 VAL Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 720 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 144 ASN B 644 ASN B 648 HIS D 21 GLN D 26 HIS E 144 ASN E 174 HIS ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN E 644 ASN E 689 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.116401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094552 restraints weight = 18284.870| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.50 r_work: 0.3167 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.8671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11398 Z= 0.154 Angle : 0.802 14.809 15570 Z= 0.381 Chirality : 0.045 0.236 1744 Planarity : 0.006 0.048 1990 Dihedral : 9.000 149.552 1579 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.25 % Favored : 91.61 % Rotamer: Outliers : 5.69 % Allowed : 24.02 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.23), residues: 1394 helix: 2.67 (0.23), residues: 474 sheet: -0.72 (0.33), residues: 218 loop : -2.50 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 347 HIS 0.011 0.001 HIS E 174 PHE 0.034 0.002 PHE D 107 TYR 0.013 0.001 TYR B 382 ARG 0.006 0.000 ARG E 237 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 490) hydrogen bonds : angle 4.28220 ( 1398) covalent geometry : bond 0.00348 (11398) covalent geometry : angle 0.80249 (15570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 212 time to evaluate : 1.511 Fit side-chains REVERT: A 94 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7690 (t80) REVERT: A 156 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7028 (ttp80) REVERT: B 141 ILE cc_start: 0.9113 (mt) cc_final: 0.8870 (mp) REVERT: B 420 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7369 (mm-30) REVERT: B 618 THR cc_start: 0.9198 (m) cc_final: 0.8990 (t) REVERT: B 662 ARG cc_start: 0.8592 (tpp80) cc_final: 0.7887 (ttt-90) REVERT: B 664 ASP cc_start: 0.6105 (t0) cc_final: 0.5555 (m-30) REVERT: D 23 TYR cc_start: 0.8307 (m-80) cc_final: 0.7893 (m-80) REVERT: D 94 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7404 (t80) REVERT: D 153 THR cc_start: 0.8389 (m) cc_final: 0.8135 (p) REVERT: D 172 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8160 (ttmt) REVERT: E 333 CYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7980 (m) REVERT: E 420 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7382 (mm-30) REVERT: E 424 MET cc_start: 0.8504 (mmm) cc_final: 0.7012 (mtm) REVERT: E 618 THR cc_start: 0.9192 (m) cc_final: 0.8990 (t) REVERT: E 662 ARG cc_start: 0.8696 (tpp80) cc_final: 0.7806 (ttp80) REVERT: E 664 ASP cc_start: 0.6356 (t0) cc_final: 0.5911 (m-30) outliers start: 67 outliers final: 37 residues processed: 258 average time/residue: 1.0885 time to fit residues: 313.2079 Evaluate side-chains 233 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 644 ASN Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 333 CYS Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 639 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN D 21 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS E 644 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.109708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087442 restraints weight = 18694.340| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.39 r_work: 0.3060 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.9837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 11398 Z= 0.291 Angle : 0.876 15.001 15570 Z= 0.428 Chirality : 0.049 0.204 1744 Planarity : 0.007 0.052 1990 Dihedral : 8.903 146.370 1579 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.54 % Favored : 90.24 % Rotamer: Outliers : 8.23 % Allowed : 22.75 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1394 helix: 2.31 (0.23), residues: 484 sheet: -0.94 (0.32), residues: 236 loop : -2.50 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.009 0.002 HIS E 174 PHE 0.041 0.003 PHE D 107 TYR 0.021 0.002 TYR B 382 ARG 0.005 0.001 ARG B 522 Details of bonding type rmsd hydrogen bonds : bond 0.06767 ( 490) hydrogen bonds : angle 4.56669 ( 1398) covalent geometry : bond 0.00695 (11398) covalent geometry : angle 0.87588 (15570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 211 time to evaluate : 2.494 Fit side-chains TARDY: cannot create tardy model for: "THR B 568 " (corrupted residue). Skipping it. REVERT: A 75 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7962 (mt) REVERT: A 156 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7035 (ttp80) REVERT: A 362 ILE cc_start: 0.9299 (tt) cc_final: 0.8890 (pt) REVERT: B 141 ILE cc_start: 0.9201 (mt) cc_final: 0.8902 (mp) REVERT: B 237 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7881 (mtm-85) REVERT: B 367 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: B 499 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: B 506 THR cc_start: 0.9075 (m) cc_final: 0.8753 (p) REVERT: B 614 ILE cc_start: 0.8695 (mt) cc_final: 0.8428 (mp) REVERT: B 646 GLU cc_start: 0.8166 (pt0) cc_final: 0.7936 (pp20) REVERT: B 662 ARG cc_start: 0.8673 (tpp80) cc_final: 0.7872 (ttp80) REVERT: B 664 ASP cc_start: 0.6431 (t0) cc_final: 0.6073 (m-30) REVERT: D 84 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7325 (tm-30) REVERT: D 94 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.8169 (t80) REVERT: D 172 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8561 (ttmt) REVERT: E 223 ILE cc_start: 0.7720 (mm) cc_final: 0.7474 (mm) REVERT: E 266 ILE cc_start: 0.8211 (pt) cc_final: 0.8011 (pp) REVERT: E 377 ASP cc_start: 0.8460 (t70) cc_final: 0.8112 (t0) REVERT: E 420 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7644 (mm-30) REVERT: E 503 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7986 (t) REVERT: E 506 THR cc_start: 0.9096 (m) cc_final: 0.8806 (p) REVERT: E 625 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: E 646 GLU cc_start: 0.8260 (pt0) cc_final: 0.7876 (pp20) REVERT: E 662 ARG cc_start: 0.8674 (tpp80) cc_final: 0.7883 (ttp80) REVERT: E 664 ASP cc_start: 0.6881 (t0) cc_final: 0.6557 (t0) outliers start: 97 outliers final: 51 residues processed: 284 average time/residue: 1.4510 time to fit residues: 458.0779 Evaluate side-chains 245 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 625 GLN Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 651 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN D 21 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 174 HIS E 242 HIS E 309 GLN E 533 GLN E 644 ASN E 689 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090663 restraints weight = 18552.579| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.40 r_work: 0.3115 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 1.0076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11398 Z= 0.149 Angle : 0.804 15.482 15570 Z= 0.383 Chirality : 0.045 0.251 1744 Planarity : 0.006 0.049 1990 Dihedral : 8.866 145.935 1579 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.11 % Favored : 91.75 % Rotamer: Outliers : 5.01 % Allowed : 27.59 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.23), residues: 1394 helix: 2.43 (0.23), residues: 492 sheet: -1.01 (0.31), residues: 242 loop : -2.31 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.011 0.001 HIS E 174 PHE 0.031 0.002 PHE D 107 TYR 0.012 0.002 TYR E 382 ARG 0.007 0.000 ARG E 279 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 490) hydrogen bonds : angle 4.28985 ( 1398) covalent geometry : bond 0.00346 (11398) covalent geometry : angle 0.80400 (15570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7462 (mt) REVERT: A 362 ILE cc_start: 0.9290 (tt) cc_final: 0.8899 (pt) REVERT: B 141 ILE cc_start: 0.9202 (mt) cc_final: 0.8972 (mp) REVERT: B 321 THR cc_start: 0.8730 (m) cc_final: 0.8529 (p) REVERT: B 367 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: B 377 ASP cc_start: 0.8399 (t70) cc_final: 0.8163 (t70) REVERT: B 382 TYR cc_start: 0.8295 (t80) cc_final: 0.7833 (t80) REVERT: B 662 ARG cc_start: 0.8598 (tpp80) cc_final: 0.7939 (ttp80) REVERT: B 664 ASP cc_start: 0.6400 (t0) cc_final: 0.6004 (m-30) REVERT: D 84 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7227 (tm-30) REVERT: D 172 LYS cc_start: 0.8786 (tppt) cc_final: 0.8416 (ttmt) REVERT: E 222 GLN cc_start: 0.8328 (pt0) cc_final: 0.7981 (pp30) REVERT: E 420 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7612 (mm-30) REVERT: E 424 MET cc_start: 0.8598 (mmm) cc_final: 0.7442 (mtm) REVERT: E 506 THR cc_start: 0.8976 (m) cc_final: 0.8692 (p) REVERT: E 662 ARG cc_start: 0.8647 (tpp80) cc_final: 0.7922 (ttp80) REVERT: E 664 ASP cc_start: 0.6810 (t0) cc_final: 0.6261 (m-30) outliers start: 59 outliers final: 29 residues processed: 243 average time/residue: 0.8322 time to fit residues: 226.7342 Evaluate side-chains 209 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 644 ASN Chi-restraints excluded: chain E residue 650 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 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 21 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 62 GLN ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS E 533 GLN E 644 ASN E 689 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.113618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091237 restraints weight = 18371.554| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.36 r_work: 0.3124 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 1.0256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11398 Z= 0.149 Angle : 0.787 14.592 15570 Z= 0.374 Chirality : 0.045 0.206 1744 Planarity : 0.006 0.048 1990 Dihedral : 8.705 145.465 1579 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.90 % Favored : 90.96 % Rotamer: Outliers : 4.41 % Allowed : 29.03 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1394 helix: 2.61 (0.23), residues: 480 sheet: -0.98 (0.31), residues: 242 loop : -2.10 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.011 0.001 HIS E 174 PHE 0.033 0.002 PHE D 107 TYR 0.021 0.001 TYR E 382 ARG 0.006 0.000 ARG E 279 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 490) hydrogen bonds : angle 4.22513 ( 1398) covalent geometry : bond 0.00350 (11398) covalent geometry : angle 0.78732 (15570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 362 ILE cc_start: 0.9289 (tt) cc_final: 0.8930 (pt) REVERT: B 141 ILE cc_start: 0.9177 (mt) cc_final: 0.8951 (mp) REVERT: B 219 ASP cc_start: 0.7798 (t0) cc_final: 0.7562 (t0) REVERT: B 321 THR cc_start: 0.8717 (m) cc_final: 0.8493 (p) REVERT: B 367 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: B 382 TYR cc_start: 0.8251 (t80) cc_final: 0.7606 (t80) REVERT: B 420 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7382 (mm-30) REVERT: B 662 ARG cc_start: 0.8564 (tpp80) cc_final: 0.7973 (ttp80) REVERT: B 664 ASP cc_start: 0.6446 (t0) cc_final: 0.6066 (m-30) REVERT: D 84 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7176 (tm-30) REVERT: D 172 LYS cc_start: 0.8780 (tppt) cc_final: 0.8415 (ttmt) REVERT: E 121 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6867 (t80) REVERT: E 377 ASP cc_start: 0.8342 (t70) cc_final: 0.7947 (t0) REVERT: E 420 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7566 (mm-30) REVERT: E 424 MET cc_start: 0.8548 (mmm) cc_final: 0.7369 (mtm) REVERT: E 662 ARG cc_start: 0.8688 (tpp80) cc_final: 0.7960 (ttp80) REVERT: E 664 ASP cc_start: 0.6791 (t0) cc_final: 0.6270 (m-30) outliers start: 52 outliers final: 30 residues processed: 233 average time/residue: 0.7702 time to fit residues: 201.5406 Evaluate side-chains 208 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 640 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 62 GLN ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS E 644 ASN E 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090570 restraints weight = 18319.874| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.33 r_work: 0.3111 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 1.0535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11398 Z= 0.164 Angle : 0.796 14.689 15570 Z= 0.381 Chirality : 0.045 0.223 1744 Planarity : 0.006 0.048 1990 Dihedral : 8.637 145.380 1579 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.18 % Favored : 91.68 % Rotamer: Outliers : 4.50 % Allowed : 29.20 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1394 helix: 2.43 (0.23), residues: 494 sheet: -1.05 (0.31), residues: 244 loop : -2.01 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 168 HIS 0.012 0.001 HIS A 68 PHE 0.033 0.002 PHE D 107 TYR 0.043 0.002 TYR E 382 ARG 0.006 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 490) hydrogen bonds : angle 4.22847 ( 1398) covalent geometry : bond 0.00385 (11398) covalent geometry : angle 0.79617 (15570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 1.244 Fit side-chains REVERT: A 362 ILE cc_start: 0.9285 (tt) cc_final: 0.8955 (pt) REVERT: B 141 ILE cc_start: 0.9177 (mt) cc_final: 0.8953 (mp) REVERT: B 219 ASP cc_start: 0.7961 (t0) cc_final: 0.7680 (t0) REVERT: B 251 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7583 (tp30) REVERT: B 320 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6939 (pt) REVERT: B 321 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8521 (p) REVERT: B 367 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: B 377 ASP cc_start: 0.8373 (t70) cc_final: 0.8120 (t70) REVERT: B 662 ARG cc_start: 0.8573 (tpp80) cc_final: 0.7998 (ttp80) REVERT: D 84 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7216 (tm-30) REVERT: D 172 LYS cc_start: 0.8818 (tppt) cc_final: 0.8472 (tmmt) REVERT: D 362 ILE cc_start: 0.9312 (tt) cc_final: 0.8948 (pt) REVERT: E 121 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6515 (t80) REVERT: E 166 ASP cc_start: 0.8679 (m-30) cc_final: 0.8064 (m-30) REVERT: E 239 LEU cc_start: 0.8482 (tp) cc_final: 0.8243 (tt) REVERT: E 320 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6960 (pt) REVERT: E 377 ASP cc_start: 0.8351 (t70) cc_final: 0.8117 (t70) REVERT: E 424 MET cc_start: 0.8659 (mmm) cc_final: 0.7549 (mtm) REVERT: E 662 ARG cc_start: 0.8661 (tpp80) cc_final: 0.7980 (ttp80) REVERT: E 664 ASP cc_start: 0.7082 (t0) cc_final: 0.6513 (m-30) outliers start: 53 outliers final: 33 residues processed: 237 average time/residue: 0.8215 time to fit residues: 217.6787 Evaluate side-chains 216 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 644 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 110 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 95 optimal weight: 0.1980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS E 533 GLN E 644 ASN E 689 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.114801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.092558 restraints weight = 18221.657| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.32 r_work: 0.3148 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 1.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11398 Z= 0.133 Angle : 0.787 14.783 15570 Z= 0.373 Chirality : 0.044 0.204 1744 Planarity : 0.005 0.046 1990 Dihedral : 8.536 144.811 1579 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.82 % Favored : 91.03 % Rotamer: Outliers : 3.57 % Allowed : 30.81 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1394 helix: 2.32 (0.23), residues: 508 sheet: -0.95 (0.31), residues: 238 loop : -1.93 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 214 HIS 0.013 0.001 HIS A 68 PHE 0.030 0.002 PHE D 107 TYR 0.030 0.002 TYR E 382 ARG 0.006 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 490) hydrogen bonds : angle 4.16729 ( 1398) covalent geometry : bond 0.00307 (11398) covalent geometry : angle 0.78735 (15570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 362 ILE cc_start: 0.9278 (tt) cc_final: 0.8963 (pt) REVERT: B 141 ILE cc_start: 0.9157 (mt) cc_final: 0.8956 (mp) REVERT: B 219 ASP cc_start: 0.7954 (t0) cc_final: 0.7656 (t0) REVERT: B 367 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7766 (OUTLIER) REVERT: B 424 MET cc_start: 0.8687 (mmm) cc_final: 0.7513 (mtm) REVERT: B 662 ARG cc_start: 0.8561 (tpp80) cc_final: 0.7947 (ttp80) REVERT: D 172 LYS cc_start: 0.8758 (tppt) cc_final: 0.8369 (tmmt) REVERT: D 362 ILE cc_start: 0.9313 (tt) cc_final: 0.8958 (pt) REVERT: E 121 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6438 (t80) REVERT: E 222 GLN cc_start: 0.8316 (pt0) cc_final: 0.7991 (pp30) REVERT: E 239 LEU cc_start: 0.8466 (tp) cc_final: 0.8227 (tt) REVERT: E 424 MET cc_start: 0.8638 (mmm) cc_final: 0.7495 (mtm) REVERT: E 662 ARG cc_start: 0.8574 (tpp80) cc_final: 0.7929 (ttp80) REVERT: E 664 ASP cc_start: 0.7050 (t0) cc_final: 0.6510 (m-30) outliers start: 42 outliers final: 28 residues processed: 222 average time/residue: 0.8327 time to fit residues: 206.5104 Evaluate side-chains 216 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 640 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 75 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 62 GLN ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN E 174 HIS E 644 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086802 restraints weight = 18529.380| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.34 r_work: 0.3055 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 1.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11398 Z= 0.244 Angle : 0.858 12.592 15570 Z= 0.416 Chirality : 0.048 0.206 1744 Planarity : 0.006 0.053 1990 Dihedral : 8.601 145.507 1579 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.47 % Favored : 90.39 % Rotamer: Outliers : 3.48 % Allowed : 31.15 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1394 helix: 2.15 (0.23), residues: 508 sheet: -1.08 (0.31), residues: 238 loop : -2.01 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 469 HIS 0.014 0.002 HIS A 68 PHE 0.032 0.003 PHE D 107 TYR 0.047 0.003 TYR E 382 ARG 0.006 0.001 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.06202 ( 490) hydrogen bonds : angle 4.44838 ( 1398) covalent geometry : bond 0.00584 (11398) covalent geometry : angle 0.85800 (15570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7372.58 seconds wall clock time: 131 minutes 35.46 seconds (7895.46 seconds total)