Starting phenix.real_space_refine on Sun Dec 29 02:54:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btf_30178/12_2024/7btf_30178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btf_30178/12_2024/7btf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7btf_30178/12_2024/7btf_30178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btf_30178/12_2024/7btf_30178.map" model { file = "/net/cci-nas-00/data/ceres_data/7btf_30178/12_2024/7btf_30178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btf_30178/12_2024/7btf_30178.cif" } resolution = 2.95 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= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.84, per 1000 atoms: 0.60 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: 2.55 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.16 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: 3.65 Time building geometry restraints manager: 2.95 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: 1.710 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: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.360 ------------------------------------------------------------------------------- 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 : 0.009 0.061 9898 Z= 0.574 Angle : 0.726 12.674 13438 Z= 0.408 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 (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: -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 TRP 0.040 0.002 TRP B 182 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.002 PHE A 753 TYR 0.019 0.002 TYR A 80 ARG 0.005 0.001 ARG A 116 *********************** 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 : 1.157 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: 1.4329 time to fit residues: 219.2220 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 : 1.162 ------------------------------------------------------------------------------- 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 100 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 36 HIS B 118 ASN D 105 ASN D 157 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9898 Z= 0.175 Angle : 0.538 9.947 13438 Z= 0.285 Chirality : 0.043 0.274 1515 Planarity : 0.004 0.056 1718 Dihedral : 4.717 28.234 1325 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.61 % Allowed : 9.12 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1201 helix: -0.01 (0.22), residues: 534 sheet: -0.93 (0.43), residues: 131 loop : -2.09 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 182 HIS 0.007 0.001 HIS C 36 PHE 0.012 0.001 PHE A 753 TYR 0.012 0.001 TYR A 788 ARG 0.011 0.000 ARG C 21 *********************** 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 143 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.947 Fit side-chains REVERT: B 164 SER cc_start: 0.8974 (m) cc_final: 0.8742 (p) REVERT: D 96 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7413 (ttp-170) REVERT: D 161 ASP cc_start: 0.7370 (p0) cc_final: 0.6666 (t0) outliers start: 28 outliers final: 10 residues processed: 130 average time/residue: 1.2894 time to fit residues: 180.5933 Evaluate side-chains 113 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 883 LEU Chi-restraints excluded: chain A residue 924 MET 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 60 optimal weight: 0.2980 chunk 33 optimal weight: 0.0010 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9898 Z= 0.218 Angle : 0.538 11.643 13438 Z= 0.280 Chirality : 0.044 0.256 1515 Planarity : 0.003 0.056 1718 Dihedral : 4.541 27.735 1323 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.07 % Allowed : 11.08 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1201 helix: 0.36 (0.23), residues: 540 sheet: -0.68 (0.44), residues: 131 loop : -1.80 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.013 0.001 PHE A 741 TYR 0.013 0.001 TYR A 788 ARG 0.003 0.000 ARG A 555 *********************** 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 142 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 1.102 Fit side-chains REVERT: A 105 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7170 (ttp80) REVERT: A 160 LYS cc_start: 0.7707 (tppt) cc_final: 0.7377 (tttm) REVERT: A 252 THR cc_start: 0.8920 (t) cc_final: 0.8662 (m) REVERT: B 164 SER cc_start: 0.8951 (m) cc_final: 0.8715 (p) REVERT: D 96 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7444 (ttp-170) REVERT: D 161 ASP cc_start: 0.7227 (p0) cc_final: 0.6643 (t0) outliers start: 33 outliers final: 14 residues processed: 130 average time/residue: 1.3767 time to fit residues: 191.5878 Evaluate side-chains 117 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 462 THR 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 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 106 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9898 Z= 0.154 Angle : 0.510 10.853 13438 Z= 0.266 Chirality : 0.042 0.222 1515 Planarity : 0.003 0.053 1718 Dihedral : 4.337 26.242 1323 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.33 % Allowed : 13.31 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.67 (0.24), residues: 1201 helix: 0.62 (0.23), residues: 540 sheet: -0.47 (0.43), residues: 130 loop : -1.57 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 182 HIS 0.003 0.000 HIS C 36 PHE 0.011 0.001 PHE A 753 TYR 0.012 0.001 TYR A 788 ARG 0.014 0.000 ARG C 21 *********************** 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 130 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.106 Fit side-chains REVERT: A 160 LYS cc_start: 0.7698 (tppt) cc_final: 0.7392 (tttm) REVERT: A 252 THR cc_start: 0.8948 (t) cc_final: 0.8645 (m) REVERT: D 96 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7442 (ttp-170) REVERT: D 161 ASP cc_start: 0.7141 (p0) cc_final: 0.6678 (t0) outliers start: 25 outliers final: 11 residues processed: 120 average time/residue: 1.3643 time to fit residues: 175.1859 Evaluate side-chains 111 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 495 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS 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 170 SER 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 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.0670 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9898 Z= 0.188 Angle : 0.502 7.604 13438 Z= 0.264 Chirality : 0.043 0.221 1515 Planarity : 0.003 0.053 1718 Dihedral : 4.283 25.454 1323 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.98 % Allowed : 13.87 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1201 helix: 0.77 (0.23), residues: 538 sheet: -0.35 (0.43), residues: 130 loop : -1.43 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 182 HIS 0.004 0.001 HIS C 36 PHE 0.013 0.001 PHE A 741 TYR 0.013 0.001 TYR A 788 ARG 0.006 0.000 ARG C 21 *********************** 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 133 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 1.082 Fit side-chains REVERT: A 105 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7624 (tpp80) REVERT: A 160 LYS cc_start: 0.7749 (tppt) cc_final: 0.7450 (tttm) REVERT: A 252 THR cc_start: 0.8946 (t) cc_final: 0.8648 (m) REVERT: A 370 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7362 (pm20) REVERT: A 553 ARG cc_start: 0.8073 (ppt170) cc_final: 0.7848 (ppt-90) REVERT: A 894 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7310 (pp20) REVERT: D 96 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7425 (ttp-170) REVERT: D 161 ASP cc_start: 0.7123 (p0) cc_final: 0.6712 (t0) REVERT: D 174 MET cc_start: 0.2790 (mtm) cc_final: 0.2444 (ppp) outliers start: 32 outliers final: 12 residues processed: 121 average time/residue: 1.4562 time to fit residues: 188.2046 Evaluate side-chains 111 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 299 VAL Chi-restraints excluded: chain A residue 370 GLU 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 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 895 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 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9898 Z= 0.198 Angle : 0.508 9.566 13438 Z= 0.266 Chirality : 0.043 0.220 1515 Planarity : 0.004 0.070 1718 Dihedral : 4.274 25.118 1323 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.70 % Allowed : 14.62 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1201 helix: 0.80 (0.23), residues: 539 sheet: -0.30 (0.43), residues: 130 loop : -1.37 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 182 HIS 0.004 0.001 HIS C 36 PHE 0.013 0.001 PHE A 741 TYR 0.013 0.001 TYR A 788 ARG 0.016 0.000 ARG C 21 *********************** 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 128 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 1.112 Fit side-chains REVERT: A 105 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7542 (tpp80) REVERT: A 160 LYS cc_start: 0.7711 (tppt) cc_final: 0.7442 (tttm) REVERT: A 252 THR cc_start: 0.8958 (t) cc_final: 0.8651 (m) REVERT: A 370 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: A 553 ARG cc_start: 0.8145 (ppt170) cc_final: 0.7912 (ppt-90) REVERT: B 104 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8381 (t0) REVERT: D 96 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7442 (ttp-170) REVERT: D 161 ASP cc_start: 0.7116 (p0) cc_final: 0.6714 (t0) REVERT: D 174 MET cc_start: 0.2925 (mtm) cc_final: 0.2560 (ppp) outliers start: 29 outliers final: 14 residues processed: 119 average time/residue: 1.4183 time to fit residues: 180.2463 Evaluate side-chains 112 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 299 VAL Chi-restraints excluded: chain A residue 370 GLU 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 B residue 85 SER Chi-restraints excluded: chain B residue 104 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN A 791 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9898 Z= 0.221 Angle : 0.520 11.421 13438 Z= 0.271 Chirality : 0.043 0.223 1515 Planarity : 0.003 0.052 1718 Dihedral : 4.303 25.813 1323 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.07 % Allowed : 14.34 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1201 helix: 0.80 (0.23), residues: 537 sheet: -0.29 (0.43), residues: 130 loop : -1.35 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.013 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.005 0.000 ARG B 96 *********************** 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 132 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 1.086 Fit side-chains REVERT: A 105 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7645 (tpp80) REVERT: A 160 LYS cc_start: 0.7728 (tppt) cc_final: 0.7458 (tttm) REVERT: A 252 THR cc_start: 0.8966 (t) cc_final: 0.8652 (m) REVERT: A 370 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: A 553 ARG cc_start: 0.8132 (ppt170) cc_final: 0.7908 (ppt-90) REVERT: C 67 ASP cc_start: 0.6255 (OUTLIER) cc_final: 0.5989 (t0) REVERT: B 104 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8426 (t0) REVERT: D 96 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7413 (ttp-170) REVERT: D 161 ASP cc_start: 0.7124 (p0) cc_final: 0.6717 (t0) REVERT: D 174 MET cc_start: 0.2937 (mtm) cc_final: 0.2645 (ppp) outliers start: 33 outliers final: 15 residues processed: 121 average time/residue: 1.4172 time to fit residues: 183.3324 Evaluate side-chains 114 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 104 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9898 Z= 0.302 Angle : 0.554 11.379 13438 Z= 0.288 Chirality : 0.045 0.246 1515 Planarity : 0.004 0.052 1718 Dihedral : 4.483 26.912 1323 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.79 % Allowed : 15.18 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1201 helix: 0.78 (0.23), residues: 529 sheet: -0.24 (0.44), residues: 130 loop : -1.41 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 PHE 0.015 0.002 PHE A 741 TYR 0.015 0.001 TYR A 831 ARG 0.005 0.000 ARG B 96 *********************** 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 126 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 1.227 Fit side-chains REVERT: A 105 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7721 (tpp80) REVERT: A 116 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7289 (mtt180) REVERT: A 160 LYS cc_start: 0.7786 (tppt) cc_final: 0.7522 (tttm) REVERT: A 370 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: A 780 LYS cc_start: 0.8069 (pttt) cc_final: 0.7769 (pttp) REVERT: B 104 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8411 (t0) REVERT: D 96 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7420 (ttp-170) REVERT: D 97 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7833 (pttt) REVERT: D 161 ASP cc_start: 0.7154 (p0) cc_final: 0.6664 (t0) REVERT: D 174 MET cc_start: 0.2910 (mtm) cc_final: 0.2664 (ppp) outliers start: 30 outliers final: 14 residues processed: 117 average time/residue: 1.4359 time to fit residues: 179.4256 Evaluate side-chains 114 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 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 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 104 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.0570 chunk 109 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9898 Z= 0.160 Angle : 0.502 10.995 13438 Z= 0.261 Chirality : 0.042 0.203 1515 Planarity : 0.003 0.052 1718 Dihedral : 4.192 24.419 1323 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.23 % Allowed : 16.20 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1201 helix: 0.87 (0.23), residues: 539 sheet: -0.21 (0.43), residues: 130 loop : -1.23 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 182 HIS 0.003 0.000 HIS C 36 PHE 0.011 0.001 PHE A 753 TYR 0.013 0.001 TYR A 831 ARG 0.004 0.000 ARG A 555 *********************** 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 124 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.134 Fit side-chains REVERT: A 105 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7643 (tpp80) REVERT: A 160 LYS cc_start: 0.7692 (tppt) cc_final: 0.7450 (tttm) REVERT: A 370 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: A 553 ARG cc_start: 0.8125 (ppt170) cc_final: 0.7910 (ppt-90) REVERT: B 104 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8342 (t0) REVERT: D 96 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7409 (ttp-170) REVERT: D 161 ASP cc_start: 0.7065 (p0) cc_final: 0.6661 (t0) outliers start: 24 outliers final: 14 residues processed: 118 average time/residue: 1.3780 time to fit residues: 174.4289 Evaluate side-chains 114 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 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 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 104 ASN 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 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 790 ASN C 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9898 Z= 0.420 Angle : 0.618 11.881 13438 Z= 0.320 Chirality : 0.047 0.261 1515 Planarity : 0.004 0.050 1718 Dihedral : 4.628 28.286 1323 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.14 % Allowed : 16.67 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.24), residues: 1201 helix: 0.67 (0.23), residues: 530 sheet: -0.28 (0.44), residues: 131 loop : -1.38 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 290 HIS 0.008 0.001 HIS C 36 PHE 0.017 0.002 PHE A 56 TYR 0.017 0.002 TYR A 788 ARG 0.005 0.000 ARG A 555 ********************** 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 118 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.184 Fit side-chains REVERT: A 105 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7746 (tpp80) REVERT: A 370 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: A 780 LYS cc_start: 0.8091 (pttt) cc_final: 0.7797 (pttp) REVERT: D 96 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7413 (ttp-170) REVERT: D 135 TYR cc_start: 0.7544 (p90) cc_final: 0.6225 (t80) REVERT: D 161 ASP cc_start: 0.7193 (p0) cc_final: 0.6638 (t0) outliers start: 23 outliers final: 13 residues processed: 111 average time/residue: 1.4577 time to fit residues: 172.7295 Evaluate side-chains 109 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 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 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 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 68 optimal weight: 4.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.091431 restraints weight = 13693.427| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.82 r_work: 0.2996 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9898 Z= 0.184 Angle : 0.531 11.571 13438 Z= 0.275 Chirality : 0.043 0.211 1515 Planarity : 0.003 0.052 1718 Dihedral : 4.321 24.961 1323 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.86 % Allowed : 16.76 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1201 helix: 0.83 (0.23), residues: 538 sheet: -0.17 (0.44), residues: 130 loop : -1.24 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 182 HIS 0.004 0.001 HIS C 36 PHE 0.012 0.001 PHE A 753 TYR 0.015 0.001 TYR A 831 ARG 0.006 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3540.50 seconds wall clock time: 64 minutes 13.20 seconds (3853.20 seconds total)