Starting phenix.real_space_refine on Fri Feb 14 02:21:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7btf_30178/02_2025/7btf_30178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7btf_30178/02_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_30178/02_2025/7btf_30178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7btf_30178/02_2025/7btf_30178.map" model { file = "/net/cci-nas-00/data/ceres_data/7btf_30178/02_2025/7btf_30178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7btf_30178/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.07, per 1000 atoms: 0.63 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: 2.45 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: 1.08 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: 3.24 Time building geometry restraints manager: 2.82 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: 1.130 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.870 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.090 ------------------------------------------------------------------------------- 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 : 1.204 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: 1.4117 time to fit residues: 215.2236 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 : 1.027 ------------------------------------------------------------------------------- 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 = 0.114629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093689 restraints weight = 13643.700| |-----------------------------------------------------------------------------| 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 9.947 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 : 1.051 Fit side-chains REVERT: A 50 LYS cc_start: 0.7666 (ttpp) cc_final: 0.7430 (pttp) REVERT: A 365 ARG cc_start: 0.7928 (mtp85) cc_final: 0.7478 (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: 0.7483 (ttp-170) REVERT: D 161 ASP cc_start: 0.7382 (p0) cc_final: 0.6604 (t0) outliers start: 28 outliers final: 10 residues processed: 130 average time/residue: 1.3166 time to fit residues: 183.6787 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 : 1.148 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.9990 chunk 99 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.112026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.089118 restraints weight = 13890.282| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.83 r_work: 0.2949 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9898 Z= 0.289 Angle : 0.567 12.181 13438 Z= 0.295 Chirality : 0.045 0.275 1515 Planarity : 0.004 0.056 1718 Dihedral : 4.681 28.398 1323 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.17 % Allowed : 11.36 % Favored : 85.47 % 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: -0.69 (0.44), residues: 131 loop : -1.85 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.002 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.006 0.000 ARG C 21 *********************** 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: 34 poor density : 108 time to evaluate : 1.045 Fit side-chains REVERT: A 105 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7370 (ttp80) REVERT: A 160 LYS cc_start: 0.7956 (tppt) cc_final: 0.7382 (tttm) REVERT: A 252 THR cc_start: 0.8979 (t) cc_final: 0.8720 (m) REVERT: C 60 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8488 (pt) REVERT: B 164 SER cc_start: 0.9047 (m) cc_final: 0.8793 (p) REVERT: D 96 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7565 (ttp-170) REVERT: D 161 ASP cc_start: 0.7393 (p0) cc_final: 0.6678 (t0) outliers start: 34 outliers final: 16 residues processed: 129 average time/residue: 1.4035 time to fit residues: 193.1335 Evaluate side-chains 118 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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: 0.9980 chunk 60 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 chunk 115 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 88 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.093631 restraints weight = 13698.991| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.82 r_work: 0.3015 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1713 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= 0.140 Angle : 0.508 10.193 13438 Z= 0.266 Chirality : 0.042 0.217 1515 Planarity : 0.003 0.055 1718 Dihedral : 4.366 26.329 1323 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % 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: -0.68 (0.24), residues: 1201 helix: 0.64 (0.23), residues: 539 sheet: -0.48 (0.43), residues: 130 loop : -1.59 (0.25), 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 753 TYR 0.012 0.001 TYR A 831 ARG 0.012 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 136 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 1.038 Fit side-chains REVERT: A 160 LYS cc_start: 0.7994 (tppt) cc_final: 0.7434 (tttm) REVERT: A 252 THR cc_start: 0.8988 (t) cc_final: 0.8675 (m) REVERT: A 365 ARG cc_start: 0.7977 (mtm110) cc_final: 0.7775 (mmm-85) REVERT: A 553 ARG cc_start: 0.8289 (ppt170) cc_final: 0.7977 (ppt-90) REVERT: C 21 ARG cc_start: 0.8158 (mtm110) cc_final: 0.7725 (mtt90) REVERT: B 164 SER cc_start: 0.9005 (m) cc_final: 0.8711 (p) REVERT: D 96 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7445 (ttp-170) REVERT: D 161 ASP cc_start: 0.7054 (p0) cc_final: 0.6499 (t0) outliers start: 27 outliers final: 8 residues processed: 123 average time/residue: 1.3531 time to fit residues: 177.9846 Evaluate side-chains 109 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 104 optimal weight: 0.1980 chunk 116 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.115489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.092870 restraints weight = 13761.036| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.82 r_work: 0.3003 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9898 Z= 0.179 Angle : 0.507 11.064 13438 Z= 0.265 Chirality : 0.043 0.220 1515 Planarity : 0.003 0.051 1718 Dihedral : 4.278 25.229 1323 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.07 % Allowed : 13.22 % Favored : 83.71 % 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: -0.46 (0.24), residues: 1201 helix: 0.77 (0.23), residues: 540 sheet: -0.37 (0.43), residues: 130 loop : -1.41 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 0.007 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 138 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.875 Fit side-chains REVERT: A 105 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7766 (tpp80) REVERT: A 160 LYS cc_start: 0.8025 (tppt) cc_final: 0.7493 (tttm) REVERT: A 252 THR cc_start: 0.8997 (t) cc_final: 0.8688 (m) REVERT: A 370 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: A 553 ARG cc_start: 0.8363 (ppt170) cc_final: 0.8106 (ppt-90) REVERT: A 894 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7222 (pp20) REVERT: C 21 ARG cc_start: 0.8194 (mtm110) cc_final: 0.7748 (mtt90) REVERT: D 96 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7474 (ttp-170) REVERT: D 161 ASP cc_start: 0.7039 (p0) cc_final: 0.6573 (t0) REVERT: D 174 MET cc_start: 0.3026 (mtm) cc_final: 0.2459 (ppp) outliers start: 33 outliers final: 11 residues processed: 127 average time/residue: 1.3970 time to fit residues: 189.9609 Evaluate side-chains 112 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.113404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.090786 restraints weight = 13872.939| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.83 r_work: 0.2966 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9898 Z= 0.272 Angle : 0.542 11.318 13438 Z= 0.283 Chirality : 0.045 0.240 1515 Planarity : 0.004 0.051 1718 Dihedral : 4.441 26.249 1323 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.26 % Allowed : 13.97 % 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: -0.50 (0.24), residues: 1201 helix: 0.73 (0.23), residues: 537 sheet: -0.32 (0.43), residues: 130 loop : -1.45 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 PHE 0.015 0.001 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.006 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 135 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 1.185 Fit side-chains REVERT: A 105 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7276 (ttp80) REVERT: A 160 LYS cc_start: 0.8035 (tppt) cc_final: 0.7564 (tttm) REVERT: A 252 THR cc_start: 0.8995 (t) cc_final: 0.8688 (m) REVERT: A 370 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: A 553 ARG cc_start: 0.8459 (ppt170) cc_final: 0.8212 (ppt-90) REVERT: A 726 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7429 (mtp85) REVERT: A 780 LYS cc_start: 0.8350 (pttt) cc_final: 0.7981 (pttp) REVERT: A 894 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7240 (pp20) REVERT: B 104 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8430 (t0) REVERT: D 96 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7570 (ttp-170) REVERT: D 161 ASP cc_start: 0.7247 (p0) cc_final: 0.6698 (t0) REVERT: D 174 MET cc_start: 0.3281 (mtm) cc_final: 0.2670 (ppp) outliers start: 35 outliers final: 17 residues processed: 123 average time/residue: 1.4702 time to fit residues: 192.4996 Evaluate side-chains 121 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 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 726 ARG 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 72 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN C 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.090582 restraints weight = 13897.668| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.79 r_work: 0.2968 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9898 Z= 0.286 Angle : 0.550 11.293 13438 Z= 0.287 Chirality : 0.045 0.242 1515 Planarity : 0.004 0.082 1718 Dihedral : 4.511 26.977 1323 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.26 % Allowed : 14.62 % Favored : 82.12 % 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: -0.49 (0.24), residues: 1201 helix: 0.78 (0.23), residues: 531 sheet: -0.32 (0.44), residues: 130 loop : -1.45 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.001 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.017 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 136 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.865 Fit side-chains REVERT: A 105 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7324 (ttp80) REVERT: A 160 LYS cc_start: 0.8037 (tppt) cc_final: 0.7561 (tttm) REVERT: A 370 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: A 500 LYS cc_start: 0.8454 (mtmt) cc_final: 0.8207 (mtmt) REVERT: A 553 ARG cc_start: 0.8428 (ppt170) cc_final: 0.8171 (ppt-90) REVERT: A 726 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7416 (mtp85) REVERT: A 780 LYS cc_start: 0.8338 (pttt) cc_final: 0.7955 (pttp) REVERT: A 894 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7224 (pp20) REVERT: C 67 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6571 (t0) REVERT: B 104 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8433 (t0) REVERT: D 96 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7555 (ttp-170) REVERT: D 161 ASP cc_start: 0.7230 (p0) cc_final: 0.6651 (t0) outliers start: 35 outliers final: 17 residues processed: 125 average time/residue: 1.4015 time to fit residues: 187.2134 Evaluate side-chains 122 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 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 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 726 ARG 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 C residue 57 SER 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 102 optimal weight: 3.9990 chunk 41 optimal weight: 0.0570 chunk 110 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.116989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.094372 restraints weight = 13889.276| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.83 r_work: 0.3028 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9898 Z= 0.134 Angle : 0.481 8.548 13438 Z= 0.253 Chirality : 0.042 0.196 1515 Planarity : 0.004 0.064 1718 Dihedral : 4.147 24.063 1323 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.14 % Allowed : 15.83 % 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: -0.21 (0.24), residues: 1201 helix: 0.95 (0.23), residues: 539 sheet: -0.26 (0.44), residues: 130 loop : -1.24 (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 0.011 0.001 PHE A 753 TYR 0.014 0.001 TYR A 831 ARG 0.014 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 130 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.110 Fit side-chains REVERT: A 160 LYS cc_start: 0.7994 (tppt) cc_final: 0.7475 (tttm) REVERT: A 370 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: A 553 ARG cc_start: 0.8400 (ppt170) cc_final: 0.8139 (ppt-90) REVERT: A 894 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7187 (pp20) REVERT: C 21 ARG cc_start: 0.8171 (mtm110) cc_final: 0.7891 (mtt90) REVERT: B 104 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8329 (t0) REVERT: D 96 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7452 (ttp-170) REVERT: D 161 ASP cc_start: 0.6962 (p0) cc_final: 0.6517 (t0) REVERT: D 174 MET cc_start: 0.3044 (mtm) cc_final: 0.2595 (ppp) outliers start: 23 outliers final: 14 residues processed: 126 average time/residue: 1.3650 time to fit residues: 183.8296 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 : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU 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 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 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: 2.9990 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 42 optimal weight: 0.0040 chunk 79 optimal weight: 2.9990 overall best weight: 1.9398 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.113076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.090449 restraints weight = 13872.347| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.83 r_work: 0.2985 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9898 Z= 0.304 Angle : 0.555 9.880 13438 Z= 0.291 Chirality : 0.045 0.235 1515 Planarity : 0.004 0.069 1718 Dihedral : 4.421 27.069 1323 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.42 % Allowed : 16.39 % 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: -0.37 (0.24), residues: 1201 helix: 0.82 (0.23), residues: 541 sheet: -0.26 (0.44), residues: 131 loop : -1.36 (0.26), residues: 529 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 0.016 0.001 TYR A 831 ARG 0.014 0.001 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: 26 poor density : 103 time to evaluate : 1.013 Fit side-chains REVERT: A 105 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7341 (ttp80) REVERT: A 160 LYS cc_start: 0.8072 (tppt) cc_final: 0.7526 (tttm) REVERT: A 252 THR cc_start: 0.8969 (t) cc_final: 0.8688 (m) REVERT: A 370 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: A 780 LYS cc_start: 0.8309 (pttt) cc_final: 0.7887 (pttp) REVERT: A 894 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7271 (pp20) REVERT: D 96 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7441 (ttp-170) REVERT: D 161 ASP cc_start: 0.7054 (p0) cc_final: 0.6489 (t0) REVERT: D 174 MET cc_start: 0.3045 (mtm) cc_final: 0.2537 (ppp) outliers start: 26 outliers final: 14 residues processed: 119 average time/residue: 1.4792 time to fit residues: 187.8212 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 : 1.074 ------------------------------------------------------------------------------- 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 495 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 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: 0.8980 chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.113748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.091022 restraints weight = 13865.576| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.84 r_work: 0.2974 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9898 Z= 0.258 Angle : 0.544 10.314 13438 Z= 0.284 Chirality : 0.044 0.236 1515 Planarity : 0.004 0.064 1718 Dihedral : 4.399 26.033 1323 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.96 % Allowed : 16.76 % Favored : 81.28 % 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: -0.35 (0.24), residues: 1201 helix: 0.83 (0.23), residues: 536 sheet: -0.23 (0.45), residues: 130 loop : -1.33 (0.26), residues: 535 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 0.016 0.001 TYR A 831 ARG 0.013 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 120 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.896 Fit side-chains REVERT: A 105 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7846 (tpp80) REVERT: A 110 MET cc_start: 0.8318 (mmm) cc_final: 0.8101 (mmm) REVERT: A 160 LYS cc_start: 0.8030 (tppt) cc_final: 0.7493 (tttm) REVERT: A 252 THR cc_start: 0.8972 (t) cc_final: 0.8689 (m) REVERT: A 370 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: A 894 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7298 (pp20) REVERT: D 96 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7456 (ttp-170) REVERT: D 161 ASP cc_start: 0.7055 (p0) cc_final: 0.6507 (t0) REVERT: D 174 MET cc_start: 0.3014 (mtm) cc_final: 0.2541 (ppp) outliers start: 21 outliers final: 15 residues processed: 113 average time/residue: 1.4436 time to fit residues: 174.0965 Evaluate side-chains 116 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU 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 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 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.114225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.091478 restraints weight = 13797.022| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.84 r_work: 0.2980 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9898 Z= 0.234 Angle : 0.540 10.614 13438 Z= 0.281 Chirality : 0.044 0.225 1515 Planarity : 0.004 0.061 1718 Dihedral : 4.373 26.804 1323 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.33 % Allowed : 16.39 % Favored : 81.28 % 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: -0.32 (0.24), residues: 1201 helix: 0.85 (0.23), residues: 537 sheet: -0.24 (0.44), residues: 130 loop : -1.30 (0.26), 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 0.016 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: 6597.04 seconds wall clock time: 117 minutes 4.37 seconds (7024.37 seconds total)