Starting phenix.real_space_refine on Sun Jul 27 21:22:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d4f_30572/07_2025/7d4f_30572.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d4f_30572/07_2025/7d4f_30572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d4f_30572/07_2025/7d4f_30572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d4f_30572/07_2025/7d4f_30572.map" model { file = "/net/cci-nas-00/data/ceres_data/7d4f_30572/07_2025/7d4f_30572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d4f_30572/07_2025/7d4f_30572.cif" } resolution = 2.57 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= 0.000 sd= 0.007 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 76 5.16 5 C 6080 2.51 5 N 1589 2.21 5 O 1787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9534 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 882 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "C" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 485 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 Chain: "A" Number of atoms: 7261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7261 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 30, 'TRANS': 867} Chain breaks: 3 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {' ZN': 2, 'H3U': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4549 SG CYS A 301 40.622 64.140 49.126 1.00 43.57 S ATOM 4590 SG CYS A 306 40.066 63.364 45.411 1.00 41.16 S ATOM 4622 SG CYS A 310 43.866 63.104 46.921 1.00 37.28 S ATOM 6030 SG CYS A 487 23.435 59.649 59.210 1.00 46.10 S ATOM 7283 SG CYS A 645 22.049 59.178 55.510 1.00 50.36 S ATOM 7289 SG CYS A 646 25.497 61.610 56.659 1.00 49.35 S Time building chain proxies: 5.77, per 1000 atoms: 0.61 Number of scatterers: 9534 At special positions: 0 Unit cell: (99.417, 93.003, 133.625, 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 76 16.00 O 1787 8.00 N 1589 7.00 C 6080 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.3 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 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " Number of angles added : 3 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 51.3% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'B' and resid 79 through 98 Processing helix chain 'B' and resid 101 through 109 removed outlier: 3.651A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.701A pdb=" N ALA B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.777A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.597A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 60 removed outlier: 3.845A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.845A pdb=" N ASP G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 Processing helix chain 'G' and resid 134 through 141 Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 76 through 91 removed outlier: 4.207A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.578A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.668A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.504A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.600A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.027A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 removed outlier: 6.294A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (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: 3.611A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.671A 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: 4.520A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.576A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.539A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 481 removed outlier: 3.692A pdb=" N ASP A 481 " --> pdb=" O LYS A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.521A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.614A pdb=" N ASN A 507 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.059A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 580 removed outlier: 5.961A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.942A 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 removed outlier: 3.638A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.546A pdb=" N LEU A 663 " --> pdb=" O CYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.582A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.612A 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 845 through 851 removed outlier: 3.674A pdb=" N THR A 850 " --> pdb=" O ASP A 846 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 867 removed outlier: 3.621A pdb=" N MET A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 894 removed outlier: 4.081A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.203A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (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 sheet with id=AA1, first strand: chain 'B' and resid 114 through 116 removed outlier: 6.676A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 114 through 116 removed outlier: 9.371A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 146 through 148 removed outlier: 5.580A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS B 127 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU A 389 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET B 129 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG A 555 " --> pdb=" O LYS A 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 128 through 132 removed outlier: 6.699A pdb=" N ILE G 185 " --> pdb=" O VAL G 159 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL G 159 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR G 187 " --> pdb=" O GLN G 157 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR G 146 " --> pdb=" O ASP G 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 128 through 132 removed outlier: 6.699A pdb=" N ILE G 185 " --> pdb=" O VAL G 159 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL G 159 " --> pdb=" O ILE G 185 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR G 187 " --> pdb=" O GLN G 157 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL G 159 " --> pdb=" O VAL G 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.272A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 32 through 38 Processing sheet with id=AA8, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.106A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AB1, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB2, first strand: chain 'A' and resid 816 through 822 removed outlier: 4.056A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1284 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: 3.37 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1564 1.31 - 1.45: 2749 1.45 - 1.58: 5307 1.58 - 1.71: 19 1.71 - 1.85: 111 Bond restraints: 9750 Sorted by residual: bond pdb=" O24 H3U A1003 " pdb=" S17 H3U A1003 " ideal model delta sigma weight residual 1.468 1.674 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" O34 H3U A1003 " pdb=" S31 H3U A1003 " ideal model delta sigma weight residual 1.472 1.665 -0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" O29 H3U A1003 " pdb=" S21 H3U A1003 " ideal model delta sigma weight residual 1.474 1.665 -0.191 2.00e-02 2.50e+03 9.12e+01 bond pdb=" O30 H3U A1004 " pdb=" S21 H3U A1004 " ideal model delta sigma weight residual 1.471 1.660 -0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" O28 H3U A1004 " pdb=" S21 H3U A1004 " ideal model delta sigma weight residual 1.472 1.659 -0.187 2.00e-02 2.50e+03 8.75e+01 ... (remaining 9745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 12718 2.26 - 4.52: 482 4.52 - 6.78: 40 6.78 - 9.04: 8 9.04 - 11.30: 4 Bond angle restraints: 13252 Sorted by residual: angle pdb=" C VAL A 335 " pdb=" N ASP A 336 " pdb=" CA ASP A 336 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" CA ASP A 760 " pdb=" CB ASP A 760 " pdb=" CG ASP A 760 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" N MET A 242 " pdb=" CA MET A 242 " pdb=" C MET A 242 " ideal model delta sigma weight residual 113.45 118.87 -5.42 1.39e+00 5.18e-01 1.52e+01 angle pdb=" C2 H3U A1003 " pdb=" C5 H3U A1003 " pdb=" C8 H3U A1003 " ideal model delta sigma weight residual 123.83 112.53 11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CB ASP A 760 " pdb=" CG ASP A 760 " pdb=" OD1 ASP A 760 " ideal model delta sigma weight residual 118.40 126.86 -8.46 2.30e+00 1.89e-01 1.35e+01 ... (remaining 13247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5216 17.77 - 35.53: 471 35.53 - 53.30: 63 53.30 - 71.07: 13 71.07 - 88.84: 5 Dihedral angle restraints: 5768 sinusoidal: 2262 harmonic: 3506 Sorted by residual: dihedral pdb=" CA ASN A 611 " pdb=" C ASN A 611 " pdb=" N PRO A 612 " pdb=" CA PRO A 612 " ideal model delta harmonic sigma weight residual 180.00 -156.51 -23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA THR A 806 " pdb=" C THR A 806 " pdb=" N LYS A 807 " pdb=" CA LYS A 807 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ALA A 762 " pdb=" C ALA A 762 " pdb=" N VAL A 763 " pdb=" CA VAL A 763 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 5765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1080 0.065 - 0.130: 340 0.130 - 0.196: 48 0.196 - 0.261: 6 0.261 - 0.326: 3 Chirality restraints: 1477 Sorted by residual: chirality pdb=" CA TYR A 606 " pdb=" N TYR A 606 " pdb=" C TYR A 606 " pdb=" CB TYR A 606 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA ASP A 760 " pdb=" N ASP A 760 " pdb=" C ASP A 760 " pdb=" CB ASP A 760 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA PHE G 92 " pdb=" N PHE G 92 " pdb=" C PHE G 92 " pdb=" CB PHE G 92 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1474 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 177 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO G 178 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO G 178 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 178 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO B 178 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 H3U A1003 " 0.016 2.00e-02 2.50e+03 2.36e-02 6.98e+00 pdb=" C3 H3U A1003 " -0.028 2.00e-02 2.50e+03 pdb=" C5 H3U A1003 " -0.023 2.00e-02 2.50e+03 pdb=" N1 H3U A1003 " 0.034 2.00e-02 2.50e+03 pdb=" O4 H3U A1003 " 0.001 2.00e-02 2.50e+03 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 1486 2.76 - 3.47: 12497 3.47 - 4.19: 23763 4.19 - 4.90: 41811 Nonbonded interactions: 79558 Sorted by model distance: nonbonded pdb=" CG1 VAL A 14 " pdb=" OD2 ASP A 100 " model vdw 1.326 3.460 nonbonded pdb=" N1 H3U A1003 " pdb=" O25 H3U A1003 " model vdw 2.076 3.120 nonbonded pdb=" OG1 THR A 540 " pdb=" OE1 GLU A 665 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP B 112 " pdb=" OH TYR A 273 " model vdw 2.283 3.040 nonbonded pdb=" OG SER G 173 " pdb=" OD1 ASP G 175 " model vdw 2.292 3.040 ... (remaining 79553 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 84 through 179 or resid 182 through 191)) selection = chain 'G' } 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: 1.090 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.310 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 41.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.794 9758 Z= 1.020 Angle : 0.952 11.298 13255 Z= 0.563 Chirality : 0.064 0.326 1477 Planarity : 0.006 0.067 1682 Dihedral : 13.567 88.836 3498 Min Nonbonded Distance : 1.326 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.76 % Allowed : 5.15 % Favored : 94.08 % 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: -2.50 (0.21), residues: 1165 helix: -1.81 (0.18), residues: 522 sheet: -1.47 (0.37), residues: 153 loop : -1.31 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 182 HIS 0.010 0.002 HIS A 613 PHE 0.026 0.003 PHE A 741 TYR 0.020 0.003 TYR A 867 ARG 0.005 0.001 ARG A 132 Details of bonding type rmsd hydrogen bonds : bond 0.20430 ( 454) hydrogen bonds : angle 6.91787 ( 1284) metal coordination : bond 0.12645 ( 7) metal coordination : angle 5.47465 ( 3) covalent geometry : bond 0.01249 ( 9750) covalent geometry : angle 0.94815 (13252) Misc. bond : bond 0.79446 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 1.123 Fit side-chains REVERT: B 80 ARG cc_start: 0.8156 (ttt90) cc_final: 0.7873 (ttt180) REVERT: B 88 GLN cc_start: 0.8467 (tt0) cc_final: 0.8216 (tt0) REVERT: B 127 LYS cc_start: 0.8817 (mttt) cc_final: 0.8336 (mtmt) REVERT: C 34 GLN cc_start: 0.8292 (tp40) cc_final: 0.7650 (tm-30) REVERT: C 44 ASP cc_start: 0.8175 (p0) cc_final: 0.7970 (p0) REVERT: G 106 ILE cc_start: 0.8094 (mt) cc_final: 0.7778 (mp) REVERT: G 111 ARG cc_start: 0.6329 (ttt180) cc_final: 0.6021 (tpp-160) REVERT: A 66 ILE cc_start: 0.7487 (tp) cc_final: 0.7237 (OUTLIER) REVERT: A 91 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8164 (ptmt) REVERT: A 104 PHE cc_start: 0.8104 (t80) cc_final: 0.7807 (t80) REVERT: A 110 MET cc_start: 0.6345 (mmm) cc_final: 0.5890 (mmp) REVERT: A 452 ASP cc_start: 0.8529 (t70) cc_final: 0.8016 (t0) REVERT: A 497 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8073 (p0) REVERT: A 520 SER cc_start: 0.8341 (m) cc_final: 0.8114 (p) REVERT: A 555 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.7960 (mmm160) REVERT: A 601 MET cc_start: 0.8967 (mtp) cc_final: 0.8733 (mtm) outliers start: 8 outliers final: 5 residues processed: 179 average time/residue: 1.1559 time to fit residues: 222.4122 Evaluate side-chains 148 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 497 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN C 18 GLN C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN A 81 GLN A 113 HIS A 117 GLN A 138 ASN A 158 ASN A 191 GLN A 357 GLN A 408 GLN A 497 ASN A 642 HIS A 790 ASN A 791 ASN A 822 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.089879 restraints weight = 11953.732| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.98 r_work: 0.2938 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9758 Z= 0.118 Angle : 0.564 12.193 13255 Z= 0.287 Chirality : 0.042 0.166 1477 Planarity : 0.006 0.197 1682 Dihedral : 6.108 67.439 1310 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.48 % Allowed : 10.78 % Favored : 86.74 % 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: -0.81 (0.23), residues: 1165 helix: -0.18 (0.21), residues: 548 sheet: -0.73 (0.38), residues: 149 loop : -0.72 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 182 HIS 0.009 0.001 HIS C 36 PHE 0.019 0.001 PHE A 652 TYR 0.020 0.001 TYR G 138 ARG 0.034 0.001 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 454) hydrogen bonds : angle 4.55721 ( 1284) metal coordination : bond 0.00439 ( 7) metal coordination : angle 1.03390 ( 3) covalent geometry : bond 0.00254 ( 9750) covalent geometry : angle 0.56414 (13252) Misc. bond : bond 0.00503 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.119 Fit side-chains REVERT: B 88 GLN cc_start: 0.8430 (tt0) cc_final: 0.8070 (tt0) REVERT: B 105 ASN cc_start: 0.7818 (t0) cc_final: 0.7526 (t0) REVERT: C 26 SER cc_start: 0.8036 (OUTLIER) cc_final: 0.7643 (p) REVERT: C 34 GLN cc_start: 0.8587 (tp40) cc_final: 0.7949 (tm-30) REVERT: C 38 ASP cc_start: 0.8175 (m-30) cc_final: 0.7716 (m-30) REVERT: C 44 ASP cc_start: 0.8143 (p0) cc_final: 0.7868 (p0) REVERT: C 50 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7157 (mp0) REVERT: G 111 ARG cc_start: 0.6447 (ttt180) cc_final: 0.5990 (tpp-160) REVERT: G 129 MET cc_start: 0.8488 (mtm) cc_final: 0.8246 (mtm) REVERT: A 66 ILE cc_start: 0.7083 (tp) cc_final: 0.6749 (pt) REVERT: A 91 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8026 (ptmt) REVERT: A 104 PHE cc_start: 0.7467 (t80) cc_final: 0.6930 (t80) REVERT: A 110 MET cc_start: 0.6122 (mmm) cc_final: 0.5586 (mmp) REVERT: A 161 ASP cc_start: 0.7543 (m-30) cc_final: 0.7242 (p0) REVERT: A 568 ASN cc_start: 0.8526 (m-40) cc_final: 0.8216 (m-40) outliers start: 26 outliers final: 10 residues processed: 173 average time/residue: 1.2160 time to fit residues: 226.7098 Evaluate side-chains 154 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 717 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 115 optimal weight: 0.0770 chunk 4 optimal weight: 0.0010 overall best weight: 0.7346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN G 108 ASN A 81 GLN A 705 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.095564 restraints weight = 12448.255| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.87 r_work: 0.3043 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9758 Z= 0.103 Angle : 0.502 7.407 13255 Z= 0.258 Chirality : 0.041 0.159 1477 Planarity : 0.005 0.140 1682 Dihedral : 5.460 67.799 1304 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.39 % Allowed : 12.88 % Favored : 84.73 % 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: -0.03 (0.24), residues: 1165 helix: 0.57 (0.22), residues: 554 sheet: -0.47 (0.38), residues: 149 loop : -0.43 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 182 HIS 0.009 0.001 HIS C 36 PHE 0.015 0.001 PHE A 652 TYR 0.013 0.001 TYR A 788 ARG 0.015 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 454) hydrogen bonds : angle 4.16888 ( 1284) metal coordination : bond 0.00512 ( 7) metal coordination : angle 1.04307 ( 3) covalent geometry : bond 0.00226 ( 9750) covalent geometry : angle 0.50148 (13252) Misc. bond : bond 0.00332 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: B 88 GLN cc_start: 0.8482 (tt0) cc_final: 0.8058 (mt0) REVERT: B 127 LYS cc_start: 0.9192 (ttpt) cc_final: 0.8973 (ttpt) REVERT: C 34 GLN cc_start: 0.8701 (tp40) cc_final: 0.8057 (tm-30) REVERT: G 111 ARG cc_start: 0.6325 (ttt180) cc_final: 0.5955 (tpp-160) REVERT: A 66 ILE cc_start: 0.7289 (tp) cc_final: 0.7047 (OUTLIER) REVERT: A 104 PHE cc_start: 0.7773 (t80) cc_final: 0.7269 (t80) REVERT: A 110 MET cc_start: 0.6003 (mmm) cc_final: 0.5444 (mmp) REVERT: A 136 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: A 523 ASP cc_start: 0.8640 (m-30) cc_final: 0.8411 (m-30) REVERT: A 568 ASN cc_start: 0.8431 (m-40) cc_final: 0.8173 (m-40) outliers start: 25 outliers final: 12 residues processed: 158 average time/residue: 1.2001 time to fit residues: 203.7402 Evaluate side-chains 152 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 110 optimal weight: 0.0670 chunk 31 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 176 ASN C 19 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN A 81 GLN A 113 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.096157 restraints weight = 12518.006| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.89 r_work: 0.3081 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9758 Z= 0.094 Angle : 0.457 5.405 13255 Z= 0.242 Chirality : 0.041 0.156 1477 Planarity : 0.004 0.107 1682 Dihedral : 5.270 69.677 1299 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.29 % Allowed : 14.03 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1165 helix: 0.98 (0.23), residues: 555 sheet: -0.24 (0.39), residues: 139 loop : -0.23 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 154 HIS 0.008 0.001 HIS C 36 PHE 0.013 0.001 PHE A 652 TYR 0.019 0.001 TYR G 138 ARG 0.018 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 454) hydrogen bonds : angle 3.99217 ( 1284) metal coordination : bond 0.00385 ( 7) metal coordination : angle 1.12769 ( 3) covalent geometry : bond 0.00204 ( 9750) covalent geometry : angle 0.45699 (13252) Misc. bond : bond 0.00324 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.997 Fit side-chains REVERT: B 88 GLN cc_start: 0.8489 (tt0) cc_final: 0.8072 (mt0) REVERT: C 24 SER cc_start: 0.8644 (m) cc_final: 0.8317 (t) REVERT: C 34 GLN cc_start: 0.8672 (tp40) cc_final: 0.7935 (tm-30) REVERT: C 38 ASP cc_start: 0.8168 (m-30) cc_final: 0.7706 (m-30) REVERT: G 111 ARG cc_start: 0.6297 (ttt180) cc_final: 0.5952 (tpp-160) REVERT: G 184 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6691 (pp) REVERT: A 66 ILE cc_start: 0.7321 (tp) cc_final: 0.7006 (pt) REVERT: A 100 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8196 (t0) REVERT: A 104 PHE cc_start: 0.7774 (t80) cc_final: 0.7237 (t80) REVERT: A 110 MET cc_start: 0.5967 (mmm) cc_final: 0.5519 (mmp) REVERT: A 568 ASN cc_start: 0.8314 (m-40) cc_final: 0.8060 (m-40) outliers start: 24 outliers final: 5 residues processed: 158 average time/residue: 1.1864 time to fit residues: 201.5096 Evaluate side-chains 149 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 717 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 109 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.093920 restraints weight = 12409.727| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.88 r_work: 0.3015 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9758 Z= 0.145 Angle : 0.497 5.544 13255 Z= 0.266 Chirality : 0.043 0.163 1477 Planarity : 0.003 0.034 1682 Dihedral : 4.891 69.014 1297 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.19 % Allowed : 14.98 % Favored : 82.82 % 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: 0.48 (0.25), residues: 1165 helix: 1.04 (0.23), residues: 554 sheet: -0.21 (0.38), residues: 155 loop : -0.25 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 182 HIS 0.007 0.001 HIS C 36 PHE 0.018 0.002 PHE A 652 TYR 0.016 0.001 TYR A 788 ARG 0.004 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 454) hydrogen bonds : angle 4.05384 ( 1284) metal coordination : bond 0.00897 ( 7) metal coordination : angle 1.30421 ( 3) covalent geometry : bond 0.00338 ( 9750) covalent geometry : angle 0.49715 (13252) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.971 Fit side-chains REVERT: B 88 GLN cc_start: 0.8543 (tt0) cc_final: 0.8127 (mt0) REVERT: C 24 SER cc_start: 0.8659 (m) cc_final: 0.8329 (t) REVERT: C 34 GLN cc_start: 0.8692 (tp40) cc_final: 0.8005 (tm-30) REVERT: C 38 ASP cc_start: 0.8142 (m-30) cc_final: 0.7730 (m-30) REVERT: C 50 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: G 111 ARG cc_start: 0.6378 (ttt180) cc_final: 0.5981 (tpp-160) REVERT: G 184 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6710 (pp) REVERT: A 100 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8226 (t0) REVERT: A 104 PHE cc_start: 0.7825 (t80) cc_final: 0.7286 (t80) REVERT: A 110 MET cc_start: 0.6009 (mmm) cc_final: 0.5562 (mmp) REVERT: A 568 ASN cc_start: 0.8395 (m-40) cc_final: 0.8162 (m-40) outliers start: 23 outliers final: 12 residues processed: 148 average time/residue: 1.1967 time to fit residues: 190.2373 Evaluate side-chains 151 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 844 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 26 optimal weight: 8.9990 chunk 74 optimal weight: 0.0270 chunk 85 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 109 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.096181 restraints weight = 12423.670| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.91 r_work: 0.3057 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9758 Z= 0.094 Angle : 0.449 5.501 13255 Z= 0.240 Chirality : 0.041 0.155 1477 Planarity : 0.003 0.036 1682 Dihedral : 4.648 68.943 1297 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.91 % Allowed : 15.27 % Favored : 82.82 % 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: 0.71 (0.25), residues: 1165 helix: 1.20 (0.23), residues: 549 sheet: -0.05 (0.39), residues: 140 loop : -0.10 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 154 HIS 0.008 0.001 HIS C 36 PHE 0.013 0.001 PHE A 652 TYR 0.012 0.001 TYR A 788 ARG 0.004 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 454) hydrogen bonds : angle 3.88397 ( 1284) metal coordination : bond 0.00389 ( 7) metal coordination : angle 1.12140 ( 3) covalent geometry : bond 0.00205 ( 9750) covalent geometry : angle 0.44828 (13252) Misc. bond : bond 0.00067 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.183 Fit side-chains REVERT: B 88 GLN cc_start: 0.8512 (tt0) cc_final: 0.8046 (mt0) REVERT: C 24 SER cc_start: 0.8631 (m) cc_final: 0.8372 (t) REVERT: C 34 GLN cc_start: 0.8719 (tp40) cc_final: 0.7982 (tm-30) REVERT: C 38 ASP cc_start: 0.8201 (m-30) cc_final: 0.7741 (m-30) REVERT: C 50 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: G 111 ARG cc_start: 0.6347 (ttt180) cc_final: 0.5949 (tpp-160) REVERT: G 184 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6680 (pp) REVERT: A 100 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8227 (t0) REVERT: A 104 PHE cc_start: 0.7767 (t80) cc_final: 0.7195 (t80) REVERT: A 110 MET cc_start: 0.6024 (mmm) cc_final: 0.5541 (mmp) REVERT: A 568 ASN cc_start: 0.8356 (m-40) cc_final: 0.8080 (m-40) outliers start: 20 outliers final: 11 residues processed: 147 average time/residue: 1.3276 time to fit residues: 210.2627 Evaluate side-chains 150 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 844 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 109 ASN C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN G 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.128490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094354 restraints weight = 12461.317| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.89 r_work: 0.3022 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9758 Z= 0.126 Angle : 0.484 9.248 13255 Z= 0.257 Chirality : 0.043 0.160 1477 Planarity : 0.003 0.035 1682 Dihedral : 4.708 67.753 1297 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.00 % Allowed : 15.17 % Favored : 82.82 % 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 (0.25), residues: 1165 helix: 1.19 (0.23), residues: 550 sheet: -0.08 (0.39), residues: 150 loop : -0.12 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 182 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.001 PHE A 652 TYR 0.016 0.001 TYR G 138 ARG 0.003 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 454) hydrogen bonds : angle 3.93857 ( 1284) metal coordination : bond 0.00766 ( 7) metal coordination : angle 1.25459 ( 3) covalent geometry : bond 0.00289 ( 9750) covalent geometry : angle 0.48391 (13252) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: B 88 GLN cc_start: 0.8527 (tt0) cc_final: 0.8123 (mt0) REVERT: C 24 SER cc_start: 0.8615 (m) cc_final: 0.8346 (t) REVERT: C 34 GLN cc_start: 0.8808 (tp40) cc_final: 0.8562 (tp-100) REVERT: C 50 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: G 111 ARG cc_start: 0.6371 (ttt180) cc_final: 0.5968 (tpp-160) REVERT: G 184 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6679 (pp) REVERT: A 100 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8195 (t0) REVERT: A 104 PHE cc_start: 0.7764 (t80) cc_final: 0.7175 (t80) REVERT: A 110 MET cc_start: 0.6063 (mmm) cc_final: 0.5578 (mmp) REVERT: A 568 ASN cc_start: 0.8411 (m-40) cc_final: 0.8168 (m-40) REVERT: A 668 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8674 (ttm) outliers start: 21 outliers final: 11 residues processed: 145 average time/residue: 1.2208 time to fit residues: 190.8398 Evaluate side-chains 149 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 844 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 0.0970 chunk 97 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 109 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.097044 restraints weight = 12538.905| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.89 r_work: 0.3086 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9758 Z= 0.089 Angle : 0.444 8.009 13255 Z= 0.236 Chirality : 0.041 0.154 1477 Planarity : 0.003 0.033 1682 Dihedral : 4.527 67.985 1297 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.62 % Allowed : 15.17 % Favored : 83.21 % 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: 0.85 (0.25), residues: 1165 helix: 1.33 (0.23), residues: 554 sheet: 0.04 (0.40), residues: 140 loop : -0.06 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 154 HIS 0.007 0.001 HIS C 36 PHE 0.013 0.001 PHE A 652 TYR 0.013 0.001 TYR A 788 ARG 0.003 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.02977 ( 454) hydrogen bonds : angle 3.84328 ( 1284) metal coordination : bond 0.00337 ( 7) metal coordination : angle 1.12502 ( 3) covalent geometry : bond 0.00194 ( 9750) covalent geometry : angle 0.44353 (13252) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: B 88 GLN cc_start: 0.8477 (tt0) cc_final: 0.8056 (mt0) REVERT: B 96 ARG cc_start: 0.6616 (mtt180) cc_final: 0.6415 (mtt-85) REVERT: C 24 SER cc_start: 0.8636 (m) cc_final: 0.8385 (t) REVERT: C 34 GLN cc_start: 0.8721 (tp40) cc_final: 0.8018 (tm-30) REVERT: C 38 ASP cc_start: 0.8140 (m-30) cc_final: 0.7713 (m-30) REVERT: C 50 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: G 111 ARG cc_start: 0.6306 (ttt180) cc_final: 0.5900 (tpp-160) REVERT: G 184 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6413 (pp) REVERT: A 100 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8207 (t0) REVERT: A 104 PHE cc_start: 0.7612 (t80) cc_final: 0.7206 (t80) REVERT: A 568 ASN cc_start: 0.8329 (m-40) cc_final: 0.8045 (m-40) REVERT: A 668 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8680 (ttm) outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 1.2791 time to fit residues: 207.1180 Evaluate side-chains 150 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 93 optimal weight: 0.0040 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN C 19 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094383 restraints weight = 12408.322| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.87 r_work: 0.3041 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9758 Z= 0.133 Angle : 0.491 8.156 13255 Z= 0.261 Chirality : 0.043 0.160 1477 Planarity : 0.003 0.034 1682 Dihedral : 4.680 67.048 1297 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.91 % Allowed : 15.84 % Favored : 82.25 % 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: 0.75 (0.25), residues: 1165 helix: 1.22 (0.23), residues: 550 sheet: -0.00 (0.40), residues: 150 loop : -0.07 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 182 HIS 0.007 0.001 HIS C 36 PHE 0.017 0.002 PHE A 652 TYR 0.015 0.001 TYR A 788 ARG 0.003 0.000 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 454) hydrogen bonds : angle 3.93576 ( 1284) metal coordination : bond 0.00825 ( 7) metal coordination : angle 1.29620 ( 3) covalent geometry : bond 0.00307 ( 9750) covalent geometry : angle 0.49035 (13252) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.118 Fit side-chains REVERT: B 88 GLN cc_start: 0.8504 (tt0) cc_final: 0.8123 (mt0) REVERT: B 96 ARG cc_start: 0.6664 (mtt180) cc_final: 0.6359 (mtt-85) REVERT: C 24 SER cc_start: 0.8648 (m) cc_final: 0.8385 (t) REVERT: C 34 GLN cc_start: 0.8759 (tp40) cc_final: 0.8542 (tp-100) REVERT: C 50 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: G 111 ARG cc_start: 0.6342 (ttt180) cc_final: 0.5934 (tpp-160) REVERT: G 184 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6462 (pp) REVERT: A 100 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8199 (t0) REVERT: A 104 PHE cc_start: 0.7614 (t80) cc_final: 0.7099 (t80) REVERT: A 568 ASN cc_start: 0.8410 (m-40) cc_final: 0.8172 (m-40) REVERT: A 668 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8705 (ttm) outliers start: 20 outliers final: 10 residues processed: 149 average time/residue: 1.1603 time to fit residues: 186.2046 Evaluate side-chains 153 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 844 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 32 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 75 optimal weight: 0.0060 chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN C 19 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.130937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097081 restraints weight = 12556.239| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.89 r_work: 0.3086 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9758 Z= 0.094 Angle : 0.477 7.697 13255 Z= 0.249 Chirality : 0.041 0.160 1477 Planarity : 0.011 0.441 1682 Dihedral : 5.238 101.579 1297 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.34 % Allowed : 16.32 % Favored : 82.35 % 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: 0.87 (0.25), residues: 1165 helix: 1.30 (0.23), residues: 550 sheet: 0.17 (0.41), residues: 140 loop : -0.03 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 154 HIS 0.007 0.001 HIS C 36 PHE 0.013 0.001 PHE A 652 TYR 0.012 0.001 TYR B 135 ARG 0.023 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 454) hydrogen bonds : angle 3.86038 ( 1284) metal coordination : bond 0.00415 ( 7) metal coordination : angle 1.20968 ( 3) covalent geometry : bond 0.00201 ( 9750) covalent geometry : angle 0.47677 (13252) Misc. bond : bond 0.00309 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 3.360 Fit side-chains REVERT: B 88 GLN cc_start: 0.8482 (tt0) cc_final: 0.8140 (mt0) REVERT: B 96 ARG cc_start: 0.6673 (mtt180) cc_final: 0.6440 (mtt-85) REVERT: C 24 SER cc_start: 0.8635 (m) cc_final: 0.8384 (t) REVERT: C 34 GLN cc_start: 0.8727 (tp40) cc_final: 0.8522 (tp-100) REVERT: C 50 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: G 111 ARG cc_start: 0.6410 (ttt180) cc_final: 0.5988 (tpp-160) REVERT: G 184 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6419 (pp) REVERT: A 100 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8201 (t0) REVERT: A 568 ASN cc_start: 0.8322 (m-40) cc_final: 0.8064 (m-40) REVERT: A 668 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8652 (ttm) REVERT: A 857 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8320 (mt-10) outliers start: 14 outliers final: 9 residues processed: 147 average time/residue: 1.3279 time to fit residues: 210.0074 Evaluate side-chains 150 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 8 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096244 restraints weight = 12477.457| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.88 r_work: 0.3052 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9758 Z= 0.109 Angle : 0.483 7.729 13255 Z= 0.254 Chirality : 0.042 0.158 1477 Planarity : 0.011 0.423 1682 Dihedral : 4.964 75.507 1297 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.24 % Allowed : 16.60 % Favored : 82.16 % 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: 0.88 (0.25), residues: 1165 helix: 1.31 (0.23), residues: 549 sheet: 0.18 (0.40), residues: 140 loop : -0.04 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 182 HIS 0.007 0.001 HIS C 36 PHE 0.014 0.001 PHE A 652 TYR 0.014 0.001 TYR A 788 ARG 0.026 0.001 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 454) hydrogen bonds : angle 3.87280 ( 1284) metal coordination : bond 0.00594 ( 7) metal coordination : angle 1.19660 ( 3) covalent geometry : bond 0.00245 ( 9750) covalent geometry : angle 0.48261 (13252) Misc. bond : bond 0.00538 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8465.07 seconds wall clock time: 147 minutes 36.28 seconds (8856.28 seconds total)