Starting phenix.real_space_refine on Wed Mar 4 00:52:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btf_30178/03_2026/7btf_30178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btf_30178/03_2026/7btf_30178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7btf_30178/03_2026/7btf_30178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btf_30178/03_2026/7btf_30178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7btf_30178/03_2026/7btf_30178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btf_30178/03_2026/7btf_30178.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.082 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 72 5.16 5 C 6169 2.51 5 N 1623 2.21 5 O 1819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9685 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7376 Classifications: {'peptide': 915} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 884} Chain breaks: 1 Chain: "C" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 519 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "B" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 983 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 77.360 41.287 55.906 1.00 42.50 S ATOM 2487 SG CYS A 306 78.109 43.610 52.156 1.00 41.35 S ATOM 2519 SG CYS A 310 74.348 41.738 52.526 1.00 38.79 S ATOM 3927 SG CYS A 487 87.475 47.957 72.323 1.00 45.06 S ATOM 5180 SG CYS A 645 89.713 50.141 69.110 1.00 51.29 S ATOM 5186 SG CYS A 646 87.594 46.201 68.845 1.00 47.12 S Time building chain proxies: 2.31, per 1000 atoms: 0.24 Number of scatterers: 9685 At special positions: 0 Unit cell: (110.7, 103.32, 131.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 72 16.00 O 1819 8.00 N 1623 7.00 C 6169 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 415.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 48.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 4.091A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 198 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.159A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 removed outlier: 4.351A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.758A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.724A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.356A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.083A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.086A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 4.108A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.889A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.812A pdb=" N ASN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.730A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 852 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 896 removed outlier: 3.754A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.743A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.720A pdb=" N VAL C 6 " --> pdb=" O LYS C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 46 through 62 removed outlier: 3.841A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 95 Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.930A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 4.134A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.962A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.660A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 removed outlier: 4.046A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.926A pdb=" N ILE D 172 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 4.041A pdb=" N GLN A 57 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.097A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.479A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 116 removed outlier: 6.760A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR D 149 " --> pdb=" O ALA D 152 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1248 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: 1.71 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3131 1.34 - 1.46: 1963 1.46 - 1.57: 4695 1.57 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 9898 Sorted by residual: bond pdb=" CG LEU A 731 " pdb=" CD2 LEU A 731 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 bond pdb=" CB VAL A 605 " pdb=" CG2 VAL A 605 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.84e+00 bond pdb=" C LEU A 329 " pdb=" N VAL A 330 " ideal model delta sigma weight residual 1.329 1.297 0.032 2.08e-02 2.31e+03 2.43e+00 bond pdb=" CB ARG A 116 " pdb=" CG ARG A 116 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CA TYR A 606 " pdb=" C TYR A 606 " ideal model delta sigma weight residual 1.518 1.460 0.058 4.01e-02 6.22e+02 2.08e+00 ... (remaining 9893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 13286 2.53 - 5.07: 137 5.07 - 7.60: 10 7.60 - 10.14: 4 10.14 - 12.67: 1 Bond angle restraints: 13438 Sorted by residual: angle pdb=" N TRP B 182 " pdb=" CA TRP B 182 " pdb=" C TRP B 182 " ideal model delta sigma weight residual 109.81 122.48 -12.67 2.21e+00 2.05e-01 3.29e+01 angle pdb=" CA TRP B 182 " pdb=" CB TRP B 182 " pdb=" CG TRP B 182 " ideal model delta sigma weight residual 113.60 105.63 7.97 1.90e+00 2.77e-01 1.76e+01 angle pdb=" N THR A 20 " pdb=" CA THR A 20 " pdb=" C THR A 20 " ideal model delta sigma weight residual 109.83 104.89 4.94 1.27e+00 6.20e-01 1.51e+01 angle pdb=" N VAL A 588 " pdb=" CA VAL A 588 " pdb=" C VAL A 588 " ideal model delta sigma weight residual 106.21 110.19 -3.98 1.07e+00 8.73e-01 1.38e+01 angle pdb=" N TRP D 182 " pdb=" CA TRP D 182 " pdb=" C TRP D 182 " ideal model delta sigma weight residual 109.81 117.79 -7.98 2.21e+00 2.05e-01 1.31e+01 ... (remaining 13433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5430 17.75 - 35.50: 399 35.50 - 53.25: 58 53.25 - 71.00: 8 71.00 - 88.75: 9 Dihedral angle restraints: 5904 sinusoidal: 2305 harmonic: 3599 Sorted by residual: dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual -180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ALA B 181 " pdb=" C ALA B 181 " pdb=" N TRP B 182 " pdb=" CA TRP B 182 " ideal model delta harmonic sigma weight residual -180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ALA D 181 " pdb=" C ALA D 181 " pdb=" N TRP D 182 " pdb=" CA TRP D 182 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 5901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1387 0.087 - 0.175: 125 0.175 - 0.262: 2 0.262 - 0.349: 0 0.349 - 0.436: 1 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA TRP B 182 " pdb=" N TRP B 182 " pdb=" C TRP B 182 " pdb=" CB TRP B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA TRP D 182 " pdb=" N TRP D 182 " pdb=" C TRP D 182 " pdb=" CB TRP D 182 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL A 588 " pdb=" CA VAL A 588 " pdb=" CG1 VAL A 588 " pdb=" CG2 VAL A 588 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 1512 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.77e+00 pdb=" N PRO D 183 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 182 " 0.021 2.00e-02 2.50e+03 1.48e-02 5.45e+00 pdb=" CG TRP B 182 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 182 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 182 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 182 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 182 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 182 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 182 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 182 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 182 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 302 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C LEU A 302 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU A 302 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 303 " -0.013 2.00e-02 2.50e+03 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2466 2.79 - 3.32: 8758 3.32 - 3.84: 15542 3.84 - 4.37: 19069 4.37 - 4.90: 33014 Nonbonded interactions: 78849 Sorted by model distance: nonbonded pdb=" OD1 ASP A 194 " pdb=" OH TYR A 289 " model vdw 2.262 3.040 nonbonded pdb=" O ASP A 235 " pdb=" OG SER A 239 " model vdw 2.290 3.040 nonbonded pdb=" O SER B 76 " pdb=" N LYS B 79 " model vdw 2.296 3.120 nonbonded pdb=" OD1 ASP A 164 " pdb=" N PHE A 165 " model vdw 2.317 3.120 nonbonded pdb=" OG SER A 343 " pdb=" OD1 ASP A 377 " model vdw 2.349 3.040 ... (remaining 78844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.260 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.830 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.015 0.475 9906 Z= 0.560 Angle : 0.760 21.784 13444 Z= 0.412 Chirality : 0.052 0.436 1515 Planarity : 0.004 0.060 1718 Dihedral : 12.871 88.750 3576 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.20), residues: 1201 helix: -1.20 (0.19), residues: 526 sheet: -1.53 (0.40), residues: 134 loop : -2.77 (0.22), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.019 0.002 TYR A 80 PHE 0.016 0.002 PHE A 753 TRP 0.040 0.002 TRP B 182 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00894 ( 9898) covalent geometry : angle 0.72555 (13438) hydrogen bonds : bond 0.07462 ( 453) hydrogen bonds : angle 5.07754 ( 1248) metal coordination : bond 0.44446 ( 8) metal coordination : angle 10.71301 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 780 LYS cc_start: 0.8202 (pttt) cc_final: 0.7852 (pttp) REVERT: B 164 SER cc_start: 0.9011 (m) cc_final: 0.8733 (p) REVERT: D 90 MET cc_start: 0.7881 (ttm) cc_final: 0.7664 (ttp) REVERT: D 96 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7381 (ttp-170) REVERT: D 161 ASP cc_start: 0.7537 (p0) cc_final: 0.6686 (t0) outliers start: 0 outliers final: 1 residues processed: 143 average time/residue: 0.6295 time to fit residues: 95.6826 Evaluate side-chains 106 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.1980 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 117 GLN A 312 ASN A 356 ASN A 414 ASN A 573 GLN A 611 ASN A 613 HIS A 713 ASN A 773 GLN A 790 ASN C 31 GLN C 36 HIS B 118 ASN D 105 ASN D 157 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.093767 restraints weight = 13726.959| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.62 r_work: 0.3020 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9906 Z= 0.115 Angle : 0.540 10.019 13444 Z= 0.285 Chirality : 0.043 0.278 1515 Planarity : 0.004 0.054 1718 Dihedral : 4.727 28.492 1325 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.51 % Allowed : 9.12 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.23), residues: 1201 helix: -0.03 (0.22), residues: 534 sheet: -1.00 (0.41), residues: 144 loop : -2.14 (0.24), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 21 TYR 0.012 0.001 TYR A 788 PHE 0.011 0.001 PHE A 753 TRP 0.029 0.001 TRP B 182 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9898) covalent geometry : angle 0.53772 (13438) hydrogen bonds : bond 0.03570 ( 453) hydrogen bonds : angle 4.46170 ( 1248) metal coordination : bond 0.01531 ( 8) metal coordination : angle 2.56674 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.316 Fit side-chains REVERT: A 50 LYS cc_start: 0.7653 (ttpp) cc_final: 0.7427 (pttp) REVERT: A 365 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7489 (tpm170) REVERT: A 497 ASN cc_start: 0.8626 (t0) cc_final: 0.8422 (t0) REVERT: C 21 ARG cc_start: 0.8135 (mtm110) cc_final: 0.7736 (mtt90) REVERT: B 164 SER cc_start: 0.9052 (m) cc_final: 0.8810 (p) REVERT: D 96 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7533 (ttp-170) REVERT: D 161 ASP cc_start: 0.7467 (p0) cc_final: 0.6679 (t0) outliers start: 27 outliers final: 10 residues processed: 128 average time/residue: 0.5861 time to fit residues: 80.1803 Evaluate side-chains 114 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain B residue 170 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 4.9990 chunk 98 optimal weight: 0.0170 chunk 114 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 790 ASN C 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.089286 restraints weight = 13879.387| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.63 r_work: 0.2949 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 9906 Z= 0.303 Angle : 0.645 10.213 13444 Z= 0.337 Chirality : 0.049 0.317 1515 Planarity : 0.004 0.056 1718 Dihedral : 5.024 30.314 1323 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.26 % Allowed : 10.80 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.23), residues: 1201 helix: 0.13 (0.22), residues: 529 sheet: -0.79 (0.44), residues: 131 loop : -2.00 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 365 TYR 0.019 0.002 TYR D 135 PHE 0.016 0.002 PHE A 741 TRP 0.023 0.002 TRP B 182 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00736 ( 9898) covalent geometry : angle 0.64304 (13438) hydrogen bonds : bond 0.05094 ( 453) hydrogen bonds : angle 4.68669 ( 1248) metal coordination : bond 0.01145 ( 8) metal coordination : angle 2.59573 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.373 Fit side-chains REVERT: A 50 LYS cc_start: 0.7687 (ttpp) cc_final: 0.7434 (pttm) REVERT: A 105 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7390 (ttp80) REVERT: A 160 LYS cc_start: 0.7987 (tppt) cc_final: 0.7367 (tttm) REVERT: A 497 ASN cc_start: 0.8689 (t0) cc_final: 0.8418 (t0) REVERT: A 726 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7367 (mtp85) REVERT: A 780 LYS cc_start: 0.8401 (pttt) cc_final: 0.7967 (pttp) REVERT: B 164 SER cc_start: 0.9056 (m) cc_final: 0.8794 (p) REVERT: D 96 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7561 (ttp-170) REVERT: D 161 ASP cc_start: 0.7396 (p0) cc_final: 0.6633 (t0) outliers start: 35 outliers final: 15 residues processed: 123 average time/residue: 0.6697 time to fit residues: 87.4200 Evaluate side-chains 115 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 9 optimal weight: 0.0060 chunk 56 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095004 restraints weight = 13796.692| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.67 r_work: 0.3033 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9906 Z= 0.102 Angle : 0.515 11.157 13444 Z= 0.269 Chirality : 0.042 0.214 1515 Planarity : 0.003 0.052 1718 Dihedral : 4.460 26.664 1323 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.89 % Allowed : 13.13 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.24), residues: 1201 helix: 0.52 (0.23), residues: 544 sheet: -0.50 (0.43), residues: 131 loop : -1.66 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.011 0.001 TYR A 788 PHE 0.010 0.001 PHE A 753 TRP 0.017 0.001 TRP B 182 HIS 0.003 0.000 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9898) covalent geometry : angle 0.51320 (13438) hydrogen bonds : bond 0.03092 ( 453) hydrogen bonds : angle 4.29602 ( 1248) metal coordination : bond 0.00338 ( 8) metal coordination : angle 1.86039 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.352 Fit side-chains REVERT: A 105 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7413 (ttp80) REVERT: A 160 LYS cc_start: 0.7925 (tppt) cc_final: 0.7419 (tttm) REVERT: A 553 ARG cc_start: 0.8326 (ppt170) cc_final: 0.8049 (ppt-90) REVERT: B 164 SER cc_start: 0.9018 (m) cc_final: 0.8779 (p) REVERT: D 96 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7549 (ttp-170) REVERT: D 161 ASP cc_start: 0.7316 (p0) cc_final: 0.6698 (t0) outliers start: 31 outliers final: 11 residues processed: 131 average time/residue: 0.6101 time to fit residues: 85.2424 Evaluate side-chains 116 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 34 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 10 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.092524 restraints weight = 13904.163| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.83 r_work: 0.2998 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9906 Z= 0.118 Angle : 0.521 11.129 13444 Z= 0.270 Chirality : 0.043 0.217 1515 Planarity : 0.004 0.063 1718 Dihedral : 4.355 26.328 1323 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.07 % Allowed : 13.87 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.24), residues: 1201 helix: 0.66 (0.23), residues: 545 sheet: -0.43 (0.43), residues: 131 loop : -1.51 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 21 TYR 0.013 0.001 TYR A 788 PHE 0.013 0.001 PHE A 741 TRP 0.017 0.001 TRP B 182 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9898) covalent geometry : angle 0.51954 (13438) hydrogen bonds : bond 0.03286 ( 453) hydrogen bonds : angle 4.23009 ( 1248) metal coordination : bond 0.00477 ( 8) metal coordination : angle 1.71148 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8017 (tppt) cc_final: 0.7499 (tttm) REVERT: A 252 THR cc_start: 0.8993 (t) cc_final: 0.8711 (m) REVERT: A 370 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: A 553 ARG cc_start: 0.8378 (ppt170) cc_final: 0.8127 (ppt-90) REVERT: A 894 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7236 (pp20) REVERT: C 21 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7797 (mtt90) REVERT: B 67 MET cc_start: 0.3081 (ptp) cc_final: 0.2628 (ttm) REVERT: D 96 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7519 (ttp-170) REVERT: D 161 ASP cc_start: 0.7162 (p0) cc_final: 0.6594 (t0) REVERT: D 174 MET cc_start: 0.3100 (mtm) cc_final: 0.2520 (ppp) outliers start: 33 outliers final: 15 residues processed: 125 average time/residue: 0.6183 time to fit residues: 82.1946 Evaluate side-chains 118 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN C 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.088894 restraints weight = 14004.262| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.83 r_work: 0.2940 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9906 Z= 0.234 Angle : 0.587 11.591 13444 Z= 0.305 Chirality : 0.047 0.262 1515 Planarity : 0.004 0.056 1718 Dihedral : 4.677 27.970 1323 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.45 % Allowed : 14.25 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.24), residues: 1201 helix: 0.58 (0.23), residues: 542 sheet: -0.45 (0.43), residues: 131 loop : -1.56 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 21 TYR 0.016 0.002 TYR A 788 PHE 0.016 0.002 PHE A 741 TRP 0.014 0.001 TRP B 182 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 9898) covalent geometry : angle 0.58556 (13438) hydrogen bonds : bond 0.04395 ( 453) hydrogen bonds : angle 4.45760 ( 1248) metal coordination : bond 0.00799 ( 8) metal coordination : angle 1.96139 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.356 Fit side-chains REVERT: A 160 LYS cc_start: 0.8024 (tppt) cc_final: 0.7479 (tttm) REVERT: A 252 THR cc_start: 0.8994 (t) cc_final: 0.8718 (m) REVERT: A 370 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: A 726 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7411 (mtp85) REVERT: A 780 LYS cc_start: 0.8345 (pttt) cc_final: 0.7935 (pttp) REVERT: A 894 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7160 (pp20) REVERT: B 67 MET cc_start: 0.2676 (ptp) cc_final: 0.2422 (ttm) REVERT: D 96 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7476 (ttp-170) REVERT: D 161 ASP cc_start: 0.7184 (p0) cc_final: 0.6554 (t0) outliers start: 37 outliers final: 15 residues processed: 124 average time/residue: 0.5947 time to fit residues: 78.7595 Evaluate side-chains 116 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.091789 restraints weight = 13931.823| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.83 r_work: 0.2985 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9906 Z= 0.130 Angle : 0.521 11.099 13444 Z= 0.271 Chirality : 0.043 0.224 1515 Planarity : 0.003 0.049 1718 Dihedral : 4.437 26.150 1323 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.51 % Allowed : 15.08 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.24), residues: 1201 helix: 0.73 (0.23), residues: 543 sheet: -0.39 (0.43), residues: 131 loop : -1.41 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 21 TYR 0.014 0.001 TYR A 831 PHE 0.012 0.001 PHE A 741 TRP 0.015 0.001 TRP B 182 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9898) covalent geometry : angle 0.51945 (13438) hydrogen bonds : bond 0.03416 ( 453) hydrogen bonds : angle 4.29264 ( 1248) metal coordination : bond 0.00511 ( 8) metal coordination : angle 1.74226 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8007 (tppt) cc_final: 0.7490 (tttm) REVERT: A 252 THR cc_start: 0.8998 (t) cc_final: 0.8708 (m) REVERT: A 370 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: A 553 ARG cc_start: 0.8396 (ppt170) cc_final: 0.8136 (ppt-90) REVERT: A 894 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7190 (pp20) REVERT: C 21 ARG cc_start: 0.8212 (mtm110) cc_final: 0.7864 (mtt90) REVERT: B 67 MET cc_start: 0.2527 (ptp) cc_final: 0.2292 (ttm) REVERT: D 96 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7465 (ttp-170) REVERT: D 161 ASP cc_start: 0.7083 (p0) cc_final: 0.6522 (t0) outliers start: 27 outliers final: 18 residues processed: 120 average time/residue: 0.6306 time to fit residues: 80.6418 Evaluate side-chains 115 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 36 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 ASN D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.092761 restraints weight = 13873.002| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.83 r_work: 0.2999 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9906 Z= 0.115 Angle : 0.502 8.536 13444 Z= 0.263 Chirality : 0.043 0.212 1515 Planarity : 0.003 0.051 1718 Dihedral : 4.287 25.365 1323 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.70 % Allowed : 15.64 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1201 helix: 0.86 (0.23), residues: 539 sheet: -0.31 (0.43), residues: 130 loop : -1.30 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 21 TYR 0.014 0.001 TYR A 831 PHE 0.012 0.001 PHE A 741 TRP 0.017 0.001 TRP B 182 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9898) covalent geometry : angle 0.50103 (13438) hydrogen bonds : bond 0.03199 ( 453) hydrogen bonds : angle 4.20374 ( 1248) metal coordination : bond 0.00451 ( 8) metal coordination : angle 1.60869 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8022 (tppt) cc_final: 0.7501 (tttm) REVERT: A 252 THR cc_start: 0.8995 (t) cc_final: 0.8699 (m) REVERT: A 370 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: A 553 ARG cc_start: 0.8394 (ppt170) cc_final: 0.8134 (ppt-90) REVERT: A 894 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7232 (pp20) REVERT: C 21 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7866 (mtt90) REVERT: D 96 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7452 (ttp-170) REVERT: D 161 ASP cc_start: 0.7019 (p0) cc_final: 0.6479 (t0) REVERT: D 174 MET cc_start: 0.3084 (mtm) cc_final: 0.2614 (ppp) outliers start: 29 outliers final: 18 residues processed: 120 average time/residue: 0.6252 time to fit residues: 80.0165 Evaluate side-chains 117 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.092031 restraints weight = 13811.030| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.89 r_work: 0.2996 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9906 Z= 0.128 Angle : 0.522 10.332 13444 Z= 0.271 Chirality : 0.043 0.216 1515 Planarity : 0.004 0.053 1718 Dihedral : 4.278 25.394 1323 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.61 % Allowed : 16.29 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.24), residues: 1201 helix: 0.89 (0.23), residues: 539 sheet: -0.23 (0.44), residues: 130 loop : -1.28 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 21 TYR 0.015 0.001 TYR A 831 PHE 0.013 0.001 PHE A 741 TRP 0.016 0.001 TRP B 182 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9898) covalent geometry : angle 0.52053 (13438) hydrogen bonds : bond 0.03306 ( 453) hydrogen bonds : angle 4.21627 ( 1248) metal coordination : bond 0.00498 ( 8) metal coordination : angle 1.62188 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7407 (ttp80) REVERT: A 160 LYS cc_start: 0.7982 (tppt) cc_final: 0.7481 (tttm) REVERT: A 252 THR cc_start: 0.9004 (t) cc_final: 0.8702 (m) REVERT: A 370 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: A 553 ARG cc_start: 0.8386 (ppt170) cc_final: 0.8131 (ppt-90) REVERT: A 894 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7271 (pp20) REVERT: C 21 ARG cc_start: 0.8242 (mtm110) cc_final: 0.7935 (mtt90) REVERT: D 96 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7498 (ttp-170) REVERT: D 161 ASP cc_start: 0.7042 (p0) cc_final: 0.6520 (t0) REVERT: D 174 MET cc_start: 0.3061 (mtm) cc_final: 0.2588 (ppp) outliers start: 28 outliers final: 22 residues processed: 121 average time/residue: 0.6590 time to fit residues: 84.8235 Evaluate side-chains 122 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 35 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 101 optimal weight: 0.0670 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.094631 restraints weight = 13569.358| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.83 r_work: 0.3032 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9906 Z= 0.094 Angle : 0.501 11.281 13444 Z= 0.259 Chirality : 0.042 0.191 1515 Planarity : 0.003 0.058 1718 Dihedral : 4.116 23.966 1323 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.14 % Allowed : 16.85 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1201 helix: 0.99 (0.23), residues: 544 sheet: -0.25 (0.44), residues: 131 loop : -1.21 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 21 TYR 0.012 0.001 TYR A 831 PHE 0.010 0.001 PHE A 741 TRP 0.020 0.001 TRP B 182 HIS 0.003 0.000 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 9898) covalent geometry : angle 0.50015 (13438) hydrogen bonds : bond 0.02819 ( 453) hydrogen bonds : angle 4.13853 ( 1248) metal coordination : bond 0.00327 ( 8) metal coordination : angle 1.47501 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7294 (ttp80) REVERT: A 160 LYS cc_start: 0.7992 (tppt) cc_final: 0.7461 (tttm) REVERT: A 252 THR cc_start: 0.8983 (t) cc_final: 0.8675 (m) REVERT: A 370 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: A 553 ARG cc_start: 0.8390 (ppt170) cc_final: 0.8139 (ppt-90) REVERT: A 894 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7305 (pp20) REVERT: C 21 ARG cc_start: 0.8194 (mtm110) cc_final: 0.7912 (mtt90) REVERT: D 96 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7485 (ttp-170) REVERT: D 161 ASP cc_start: 0.6929 (p0) cc_final: 0.6510 (t0) REVERT: D 174 MET cc_start: 0.2955 (mtm) cc_final: 0.2514 (ppp) outliers start: 23 outliers final: 14 residues processed: 118 average time/residue: 0.6591 time to fit residues: 82.7590 Evaluate side-chains 114 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 62 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.093077 restraints weight = 13597.039| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.83 r_work: 0.3010 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9906 Z= 0.118 Angle : 0.517 11.273 13444 Z= 0.267 Chirality : 0.043 0.205 1515 Planarity : 0.004 0.057 1718 Dihedral : 4.157 24.836 1323 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.77 % Allowed : 17.60 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.24), residues: 1201 helix: 1.01 (0.23), residues: 544 sheet: -0.22 (0.44), residues: 131 loop : -1.20 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.016 0.001 TYR A 831 PHE 0.012 0.001 PHE A 741 TRP 0.017 0.001 TRP B 182 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9898) covalent geometry : angle 0.51621 (13438) hydrogen bonds : bond 0.03149 ( 453) hydrogen bonds : angle 4.15793 ( 1248) metal coordination : bond 0.00441 ( 8) metal coordination : angle 1.48248 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.79 seconds wall clock time: 57 minutes 45.36 seconds (3465.36 seconds total)