Starting phenix.real_space_refine on Fri Mar 14 06:33:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btf_30178/03_2025/7btf_30178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btf_30178/03_2025/7btf_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_30178/03_2025/7btf_30178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btf_30178/03_2025/7btf_30178.map" model { file = "/net/cci-nas-00/data/ceres_data/7btf_30178/03_2025/7btf_30178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btf_30178/03_2025/7btf_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-5624/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: 5.28, per 1000 atoms: 0.55 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: 2.14 Conformation dependent library (CDL) restraints added in 1.0 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: 1.08 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: 2.94 Time building geometry restraints manager: 2.57 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: 1.340 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.390 Find NCS groups from input model: 0.080 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:10.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.570 ------------------------------------------------------------------------------- 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 : 1.066 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: 1.4191 time to fit residues: 216.5826 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 : 1.143 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093695 restraints weight = 13643.891| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.65 r_work: 0.3018 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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 9.948 13438 Z= 0.285 Chirality : 0.043 0.274 1515 Planarity : 0.004 0.056 1718 Dihedral : 4.717 28.233 1325 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.59 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 : 1.016 Fit side-chains REVERT: A 50 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7430 (pttp) REVERT: A 365 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7477 (tpm170) REVERT: A 497 ASN cc_start: 0.8630 (t0) cc_final: 0.8423 (t0) REVERT: C 21 ARG cc_start: 0.8119 (mtm110) cc_final: 0.7713 (mtt90) REVERT: B 164 SER cc_start: 0.9052 (m) cc_final: 0.8792 (p) REVERT: D 96 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7484 (ttp-170) REVERT: D 161 ASP cc_start: 0.7386 (p0) cc_final: 0.6608 (t0) outliers start: 28 outliers final: 10 residues processed: 130 average time/residue: 1.2614 time to fit residues: 176.4743 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 : 1.074 ------------------------------------------------------------------------------- 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 21 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.092180 restraints weight = 13860.997| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.63 r_work: 0.2990 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9898 Z= 0.279 Angle : 0.563 12.252 13438 Z= 0.293 Chirality : 0.045 0.273 1515 Planarity : 0.004 0.056 1718 Dihedral : 4.669 28.433 1323 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.07 % Allowed : 11.36 % Favored : 85.57 % 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: -1.11 (0.24), residues: 1201 helix: 0.33 (0.23), residues: 532 sheet: -0.70 (0.44), residues: 131 loop : -1.84 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.014 0.002 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.004 0.000 ARG A 365 *********************** 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 141 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.959 Fit side-chains REVERT: A 105 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7364 (ttp80) REVERT: A 160 LYS cc_start: 0.7965 (tppt) cc_final: 0.7396 (tttm) REVERT: A 252 THR cc_start: 0.8971 (t) cc_final: 0.8709 (m) REVERT: C 60 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8453 (pt) REVERT: B 164 SER cc_start: 0.9036 (m) cc_final: 0.8776 (p) REVERT: D 96 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7522 (ttp-170) REVERT: D 161 ASP cc_start: 0.7352 (p0) cc_final: 0.6649 (t0) outliers start: 33 outliers final: 16 residues processed: 129 average time/residue: 1.3534 time to fit residues: 186.7985 Evaluate side-chains 119 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 223 ILE Chi-restraints excluded: chain A residue 235 ASP 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 60 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 42 optimal weight: 0.3980 chunk 60 optimal weight: 0.0270 chunk 83 optimal weight: 0.4980 chunk 26 optimal weight: 0.0040 chunk 115 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 HIS A 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.094510 restraints weight = 13716.653| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.79 r_work: 0.3030 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9898 Z= 0.125 Angle : 0.500 10.055 13438 Z= 0.262 Chirality : 0.042 0.209 1515 Planarity : 0.003 0.052 1718 Dihedral : 4.297 25.782 1323 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.51 % Allowed : 13.13 % 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: -0.63 (0.24), residues: 1201 helix: 0.67 (0.23), residues: 539 sheet: -0.46 (0.43), residues: 130 loop : -1.56 (0.26), residues: 532 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 0.010 0.001 PHE A 741 TYR 0.011 0.001 TYR A 149 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 138 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.030 Fit side-chains REVERT: A 160 LYS cc_start: 0.7954 (tppt) cc_final: 0.7400 (tttm) REVERT: A 252 THR cc_start: 0.8965 (t) cc_final: 0.8652 (m) REVERT: A 365 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7766 (mmm-85) REVERT: A 553 ARG cc_start: 0.8307 (ppt170) cc_final: 0.7995 (ppt-90) REVERT: C 21 ARG cc_start: 0.8193 (mtm110) cc_final: 0.7800 (mtt90) REVERT: D 96 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7451 (ttp-170) REVERT: D 161 ASP cc_start: 0.7034 (p0) cc_final: 0.6551 (t0) outliers start: 27 outliers final: 9 residues processed: 124 average time/residue: 1.3574 time to fit residues: 180.5427 Evaluate side-chains 109 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 105 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 0.0010 chunk 14 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.094207 restraints weight = 13740.955| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.82 r_work: 0.3026 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9898 Z= 0.148 Angle : 0.492 10.819 13438 Z= 0.257 Chirality : 0.042 0.208 1515 Planarity : 0.003 0.051 1718 Dihedral : 4.151 24.361 1323 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.61 % Allowed : 14.06 % Favored : 83.33 % 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: -0.36 (0.24), residues: 1201 helix: 0.87 (0.24), residues: 540 sheet: -0.35 (0.43), residues: 130 loop : -1.37 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 182 HIS 0.004 0.000 HIS C 36 PHE 0.012 0.001 PHE A 741 TYR 0.012 0.001 TYR A 788 ARG 0.011 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 131 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.006 Fit side-chains REVERT: A 105 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7807 (tpp80) REVERT: A 160 LYS cc_start: 0.8000 (tppt) cc_final: 0.7471 (tttm) REVERT: A 370 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7857 (pm20) REVERT: A 553 ARG cc_start: 0.8346 (ppt170) cc_final: 0.8070 (ppt-90) REVERT: A 555 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.8163 (mmm-85) REVERT: A 894 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7168 (pp20) REVERT: C 21 ARG cc_start: 0.8209 (mtm110) cc_final: 0.7864 (mtt90) REVERT: D 96 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7435 (ttp-170) REVERT: D 161 ASP cc_start: 0.6986 (p0) cc_final: 0.6587 (t0) REVERT: D 174 MET cc_start: 0.2960 (mtm) cc_final: 0.2466 (ppp) outliers start: 28 outliers final: 8 residues processed: 123 average time/residue: 1.3547 time to fit residues: 178.6148 Evaluate side-chains 110 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 551 LYS 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 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 1 optimal weight: 0.3980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.092008 restraints weight = 13849.549| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.82 r_work: 0.2990 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9898 Z= 0.222 Angle : 0.520 11.118 13438 Z= 0.271 Chirality : 0.043 0.223 1515 Planarity : 0.003 0.051 1718 Dihedral : 4.275 25.200 1323 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.89 % Allowed : 14.34 % Favored : 82.77 % 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: -0.33 (0.24), residues: 1201 helix: 0.87 (0.23), residues: 539 sheet: -0.29 (0.43), residues: 130 loop : -1.33 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.014 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.004 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 132 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 1.103 Fit side-chains REVERT: A 105 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7783 (tpp80) REVERT: A 160 LYS cc_start: 0.8013 (tppt) cc_final: 0.7503 (tttm) REVERT: A 252 THR cc_start: 0.8983 (t) cc_final: 0.8704 (m) REVERT: A 370 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: A 553 ARG cc_start: 0.8362 (ppt170) cc_final: 0.8103 (ppt-90) REVERT: A 780 LYS cc_start: 0.8289 (pttt) cc_final: 0.7891 (pttp) REVERT: A 894 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7180 (pp20) REVERT: B 104 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8386 (t0) REVERT: D 96 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7488 (ttp-170) REVERT: D 161 ASP cc_start: 0.7020 (p0) cc_final: 0.6594 (t0) REVERT: D 174 MET cc_start: 0.3138 (mtm) cc_final: 0.2584 (ppp) outliers start: 31 outliers final: 17 residues processed: 122 average time/residue: 1.3942 time to fit residues: 181.5562 Evaluate side-chains 118 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 235 ASP 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 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET 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 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 72 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 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 = 0.3423 r_free = 0.3423 target = 0.113797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.091198 restraints weight = 13875.187| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.82 r_work: 0.2976 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9898 Z= 0.256 Angle : 0.537 11.153 13438 Z= 0.279 Chirality : 0.044 0.231 1515 Planarity : 0.004 0.079 1718 Dihedral : 4.389 26.292 1323 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.26 % Allowed : 14.25 % Favored : 82.50 % 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: 543 sheet: -0.30 (0.43), residues: 131 loop : -1.35 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.014 0.001 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.015 0.000 ARG C 21 *********************** 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 133 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 1.003 Fit side-chains REVERT: A 105 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7849 (tpp80) REVERT: A 160 LYS cc_start: 0.8063 (tppt) cc_final: 0.7543 (tttm) REVERT: A 252 THR cc_start: 0.8979 (t) cc_final: 0.8693 (m) REVERT: A 370 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: A 553 ARG cc_start: 0.8374 (ppt170) cc_final: 0.8126 (ppt-90) REVERT: A 780 LYS cc_start: 0.8305 (pttt) cc_final: 0.7898 (pttp) REVERT: A 894 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7228 (pp20) REVERT: B 104 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8393 (t0) REVERT: D 96 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7440 (ttp-170) REVERT: D 161 ASP cc_start: 0.7068 (p0) cc_final: 0.6605 (t0) REVERT: D 174 MET cc_start: 0.3188 (mtm) cc_final: 0.2669 (ppp) outliers start: 35 outliers final: 17 residues processed: 122 average time/residue: 1.3426 time to fit residues: 175.1942 Evaluate side-chains 118 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 235 ASP 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 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain C residue 57 SER 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 102 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN D 105 ASN D 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.093545 restraints weight = 13887.130| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.81 r_work: 0.3016 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9898 Z= 0.155 Angle : 0.489 8.437 13438 Z= 0.257 Chirality : 0.042 0.201 1515 Planarity : 0.004 0.067 1718 Dihedral : 4.182 24.283 1323 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.23 % Allowed : 15.74 % 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: -0.19 (0.24), residues: 1201 helix: 0.95 (0.23), residues: 539 sheet: -0.20 (0.43), residues: 130 loop : -1.22 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 182 HIS 0.004 0.000 HIS C 36 PHE 0.011 0.001 PHE A 741 TYR 0.013 0.001 TYR A 831 ARG 0.015 0.000 ARG C 21 *********************** 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 125 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.990 Fit side-chains REVERT: A 105 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7830 (tpp80) REVERT: A 160 LYS cc_start: 0.8003 (tppt) cc_final: 0.7532 (tttm) REVERT: A 252 THR cc_start: 0.8975 (t) cc_final: 0.8691 (m) REVERT: A 370 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: A 553 ARG cc_start: 0.8390 (ppt170) cc_final: 0.8156 (ppt-90) REVERT: A 894 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7276 (pp20) REVERT: C 21 ARG cc_start: 0.8182 (mtm110) cc_final: 0.7906 (mtt90) REVERT: B 104 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8345 (t0) REVERT: D 96 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7490 (ttp-170) REVERT: D 161 ASP cc_start: 0.7049 (p0) cc_final: 0.6617 (t0) REVERT: D 174 MET cc_start: 0.3049 (mtm) cc_final: 0.2603 (ppp) outliers start: 24 outliers final: 14 residues processed: 117 average time/residue: 1.4136 time to fit residues: 176.7099 Evaluate side-chains 113 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 495 VAL 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 858 ARG Chi-restraints excluded: chain A residue 883 LEU 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 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 chunk 42 optimal weight: 0.0040 chunk 79 optimal weight: 0.3980 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.095757 restraints weight = 13764.308| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.84 r_work: 0.3051 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9898 Z= 0.124 Angle : 0.473 9.409 13438 Z= 0.249 Chirality : 0.041 0.184 1515 Planarity : 0.004 0.058 1718 Dihedral : 3.965 23.158 1323 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.05 % Allowed : 16.29 % 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 (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: 0.00 (0.25), residues: 1201 helix: 1.18 (0.24), residues: 538 sheet: -0.14 (0.44), residues: 130 loop : -1.19 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 182 HIS 0.003 0.000 HIS C 36 PHE 0.011 0.001 PHE A 741 TYR 0.012 0.001 TYR A 831 ARG 0.015 0.000 ARG C 21 *********************** 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: 22 poor density : 107 time to evaluate : 0.983 Fit side-chains REVERT: A 105 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7688 (tpp80) REVERT: A 160 LYS cc_start: 0.7987 (tppt) cc_final: 0.7479 (tttm) REVERT: A 252 THR cc_start: 0.8986 (t) cc_final: 0.8690 (m) REVERT: A 370 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: A 553 ARG cc_start: 0.8369 (ppt170) cc_final: 0.8128 (ppt-90) REVERT: A 894 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7294 (pp20) REVERT: C 21 ARG cc_start: 0.8154 (mtm110) cc_final: 0.7895 (mtt90) REVERT: B 104 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8296 (t0) REVERT: D 96 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7450 (ttp-170) REVERT: D 97 LYS cc_start: 0.8111 (tmmt) cc_final: 0.7774 (pttt) REVERT: D 161 ASP cc_start: 0.6909 (p0) cc_final: 0.6599 (t0) REVERT: D 174 MET cc_start: 0.2918 (mtm) cc_final: 0.2504 (ppp) outliers start: 22 outliers final: 13 residues processed: 123 average time/residue: 1.3045 time to fit residues: 172.7536 Evaluate side-chains 115 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 495 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU 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 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 0.3980 chunk 114 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.092583 restraints weight = 13835.533| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.83 r_work: 0.2997 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9898 Z= 0.233 Angle : 0.533 10.376 13438 Z= 0.278 Chirality : 0.043 0.218 1515 Planarity : 0.004 0.063 1718 Dihedral : 4.145 24.513 1323 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.86 % Allowed : 16.95 % 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: -0.09 (0.25), residues: 1201 helix: 1.07 (0.24), residues: 538 sheet: -0.13 (0.44), residues: 130 loop : -1.21 (0.26), residues: 533 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 0.014 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.014 0.000 ARG C 21 ********************** 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 122 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 1.152 Fit side-chains REVERT: A 105 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7798 (tpp80) REVERT: A 160 LYS cc_start: 0.8030 (tppt) cc_final: 0.7484 (tttm) REVERT: A 252 THR cc_start: 0.8989 (t) cc_final: 0.8693 (m) REVERT: A 370 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: A 553 ARG cc_start: 0.8360 (ppt170) cc_final: 0.8100 (ppt-90) REVERT: A 780 LYS cc_start: 0.8310 (pttt) cc_final: 0.7900 (pttp) REVERT: A 894 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7301 (pp20) REVERT: C 21 ARG cc_start: 0.8208 (mtm110) cc_final: 0.7925 (mtt90) REVERT: D 96 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7441 (ttp-170) REVERT: D 97 LYS cc_start: 0.8121 (tmmt) cc_final: 0.7769 (pttt) REVERT: D 161 ASP cc_start: 0.6947 (p0) cc_final: 0.6556 (t0) REVERT: D 174 MET cc_start: 0.2953 (mtm) cc_final: 0.2524 (ppp) outliers start: 20 outliers final: 14 residues processed: 116 average time/residue: 1.3447 time to fit residues: 166.7671 Evaluate side-chains 117 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 495 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 615 MET 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 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.094579 restraints weight = 13756.049| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.84 r_work: 0.3030 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9898 Z= 0.150 Angle : 0.508 11.484 13438 Z= 0.264 Chirality : 0.042 0.198 1515 Planarity : 0.004 0.057 1718 Dihedral : 4.045 23.621 1323 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.77 % Allowed : 17.04 % 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: 0.01 (0.25), residues: 1201 helix: 1.18 (0.24), residues: 539 sheet: -0.17 (0.44), residues: 131 loop : -1.17 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.013 0.000 ARG C 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7030.68 seconds wall clock time: 121 minutes 34.91 seconds (7294.91 seconds total)