Starting phenix.real_space_refine on Tue Jun 17 20:46:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxm_47291/06_2025/9dxm_47291_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxm_47291/06_2025/9dxm_47291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dxm_47291/06_2025/9dxm_47291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxm_47291/06_2025/9dxm_47291.map" model { file = "/net/cci-nas-00/data/ceres_data/9dxm_47291/06_2025/9dxm_47291_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxm_47291/06_2025/9dxm_47291_trim.cif" } resolution = 3.2 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= 0.015 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: 7 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 6512 2.51 5 N 1646 2.21 5 O 1842 1.98 5 H 10147 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20203 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 17368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 17368 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 40, 'TRANS': 1012} Chain breaks: 5 Chain: "B" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2802 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.07, per 1000 atoms: 0.45 Number of scatterers: 20203 At special positions: 0 Unit cell: (85.078, 99.946, 130.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 52 16.00 P 3 15.00 Mg 1 11.99 O 1842 8.00 N 1646 7.00 C 6512 6.00 H 10147 1.00 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: 5.19 Conformation dependent library (CDL) restraints added in 1.4 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2362 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 1 sheets defined 78.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 removed outlier: 3.899A pdb=" N ILE A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 39 Processing helix chain 'A' and resid 41 through 53 Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 79 through 96 Processing helix chain 'A' and resid 102 through 121 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.749A pdb=" N LYS A 126 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 141 through 153 removed outlier: 3.580A pdb=" N ASN A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 173 Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.558A pdb=" N LYS A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.546A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.173A pdb=" N THR A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 220 through 235 Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 236 through 248 Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.805A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.562A pdb=" N SER A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 293 Processing helix chain 'A' and resid 297 through 311 removed outlier: 3.642A pdb=" N TYR A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 334 through 347 removed outlier: 3.647A pdb=" N CYS A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 355 Proline residue: A 353 - end of helix Processing helix chain 'A' and resid 360 through 374 Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.801A pdb=" N THR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.605A pdb=" N GLN A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 428 through 436 removed outlier: 4.398A pdb=" N ILE A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 464 Processing helix chain 'A' and resid 464 through 480 Processing helix chain 'A' and resid 482 through 490 Processing helix chain 'A' and resid 498 through 525 removed outlier: 3.689A pdb=" N LYS A 522 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 551 Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.644A pdb=" N LYS A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 591 removed outlier: 3.704A pdb=" N PHE A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 627 Processing helix chain 'A' and resid 627 through 633 removed outlier: 3.539A pdb=" N LEU A 631 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 646 Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 668 removed outlier: 4.098A pdb=" N SER A 656 " --> pdb=" O HIS A 652 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.765A pdb=" N ARG A 676 " --> pdb=" O MET A 672 " (cutoff:3.500A) Proline residue: A 683 - end of helix Processing helix chain 'A' and resid 687 through 689 No H-bonds generated for 'chain 'A' and resid 687 through 689' Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 733 through 751 removed outlier: 3.607A pdb=" N SER A 749 " --> pdb=" O LYS A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 769 through 785 Proline residue: A 782 - end of helix Processing helix chain 'A' and resid 787 through 802 removed outlier: 4.176A pdb=" N HIS A 802 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 810 removed outlier: 3.575A pdb=" N GLY A 809 " --> pdb=" O ASN A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 849 through 877 removed outlier: 3.583A pdb=" N SER A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 887 through 897 removed outlier: 3.567A pdb=" N ILE A 896 " --> pdb=" O LEU A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 922 Processing helix chain 'A' and resid 922 through 929 Processing helix chain 'A' and resid 934 through 960 Proline residue: A 940 - end of helix Proline residue: A 944 - end of helix removed outlier: 3.864A pdb=" N SER A 960 " --> pdb=" O GLN A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1003 Processing helix chain 'A' and resid 1017 through 1030 removed outlier: 3.615A pdb=" N LYS A1025 " --> pdb=" O MET A1021 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A1026 " --> pdb=" O GLU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1047 Proline residue: A1036 - end of helix Processing helix chain 'A' and resid 1049 through 1068 removed outlier: 5.504A pdb=" N THR A1065 " --> pdb=" O LYS A1061 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER A1066 " --> pdb=" O CYS A1062 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A1068 " --> pdb=" O LEU A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1086 Processing helix chain 'A' and resid 1102 through 1115 Processing helix chain 'B' and resid 24 through 34 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 96 through 102 removed outlier: 3.877A pdb=" N TYR B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.411A pdb=" N ASN B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 172 Processing sheet with id=AA1, first strand: chain 'B' and resid 147 through 150 removed outlier: 3.807A pdb=" N GLN B 147 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 88 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N CYS B 122 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 90 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN B 124 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE B 92 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N CYS B 87 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS B 14 " --> pdb=" O CYS B 87 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE B 89 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 16 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N MET B 91 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 18 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ASP B 93 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE B 13 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TRP B 66 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 15 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR B 68 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 17 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B 55 " --> pdb=" O VAL B 179 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1845 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: 7.04 Time building geometry restraints manager: 6.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10122 1.03 - 1.23: 32 1.23 - 1.42: 4258 1.42 - 1.62: 5935 1.62 - 1.81: 79 Bond restraints: 20426 Sorted by residual: bond pdb=" CA SER A 876 " pdb=" CB SER A 876 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.64e-02 3.72e+03 1.30e+01 bond pdb=" N LYS B 144 " pdb=" CA LYS B 144 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.32e-02 5.74e+03 8.03e+00 bond pdb=" C LYS B 144 " pdb=" O LYS B 144 " ideal model delta sigma weight residual 1.235 1.271 -0.036 1.33e-02 5.65e+03 7.27e+00 bond pdb=" N SER A 668 " pdb=" CA SER A 668 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.22e-02 6.72e+03 7.00e+00 bond pdb=" N GLY A 5 " pdb=" CA GLY A 5 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.27e+00 ... (remaining 20421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 35958 1.40 - 2.80: 959 2.80 - 4.20: 65 4.20 - 5.60: 27 5.60 - 7.00: 2 Bond angle restraints: 37011 Sorted by residual: angle pdb=" CA THR B 44 " pdb=" CB THR B 44 " pdb=" OG1 THR B 44 " ideal model delta sigma weight residual 109.60 104.65 4.95 1.50e+00 4.44e-01 1.09e+01 angle pdb=" CA THR B 44 " pdb=" C THR B 44 " pdb=" O THR B 44 " ideal model delta sigma weight residual 120.81 117.32 3.49 1.15e+00 7.56e-01 9.23e+00 angle pdb=" CA LYS B 143 " pdb=" C LYS B 143 " pdb=" O LYS B 143 " ideal model delta sigma weight residual 120.24 116.98 3.26 1.11e+00 8.12e-01 8.62e+00 angle pdb=" CA ASN A 230 " pdb=" C ASN A 230 " pdb=" O ASN A 230 " ideal model delta sigma weight residual 119.97 116.74 3.23 1.15e+00 7.56e-01 7.88e+00 angle pdb=" N ARG B 142 " pdb=" CA ARG B 142 " pdb=" C ARG B 142 " ideal model delta sigma weight residual 111.28 108.24 3.04 1.09e+00 8.42e-01 7.77e+00 ... (remaining 37006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.79: 9317 33.79 - 67.58: 203 67.58 - 101.37: 23 101.37 - 135.16: 0 135.16 - 168.95: 2 Dihedral angle restraints: 9545 sinusoidal: 5191 harmonic: 4354 Sorted by residual: dihedral pdb=" O3B GTP B 201 " pdb=" O3A GTP B 201 " pdb=" PB GTP B 201 " pdb=" PA GTP B 201 " ideal model delta sinusoidal sigma weight residual 291.08 122.13 168.95 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C8 GTP B 201 " pdb=" C1' GTP B 201 " pdb=" N9 GTP B 201 " pdb=" O4' GTP B 201 " ideal model delta sinusoidal sigma weight residual 104.59 -32.73 137.33 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" O5' GTP B 201 " pdb=" O3A GTP B 201 " pdb=" PA GTP B 201 " pdb=" PB GTP B 201 " ideal model delta sinusoidal sigma weight residual -85.88 -177.83 91.96 1 2.00e+01 2.50e-03 2.48e+01 ... (remaining 9542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1070 0.035 - 0.069: 380 0.069 - 0.104: 93 0.104 - 0.138: 37 0.138 - 0.173: 2 Chirality restraints: 1582 Sorted by residual: chirality pdb=" CA ILE A 898 " pdb=" N ILE A 898 " pdb=" C ILE A 898 " pdb=" CB ILE A 898 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA PRO A 647 " pdb=" N PRO A 647 " pdb=" C PRO A 647 " pdb=" CB PRO A 647 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ILE B 89 " pdb=" N ILE B 89 " pdb=" C ILE B 89 " pdb=" CB ILE B 89 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1579 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 230 " 0.129 2.00e-02 2.50e+03 1.39e-01 2.90e+02 pdb=" CG ASN A 230 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 230 " -0.126 2.00e-02 2.50e+03 pdb=" ND2 ASN A 230 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 230 " -0.203 2.00e-02 2.50e+03 pdb="HD22 ASN A 230 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 142 " -0.193 9.50e-02 1.11e+02 1.02e-01 1.44e+02 pdb=" NE ARG B 142 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG B 142 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 142 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 142 " 0.021 2.00e-02 2.50e+03 pdb="HH11 ARG B 142 " 0.157 2.00e-02 2.50e+03 pdb="HH12 ARG B 142 " -0.154 2.00e-02 2.50e+03 pdb="HH21 ARG B 142 " 0.059 2.00e-02 2.50e+03 pdb="HH22 ARG B 142 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 898 " -0.017 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" N PHE A 899 " 0.055 2.00e-02 2.50e+03 pdb=" CA PHE A 899 " -0.015 2.00e-02 2.50e+03 pdb=" H PHE A 899 " -0.024 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 593 2.14 - 2.75: 38934 2.75 - 3.37: 60041 3.37 - 3.98: 74832 3.98 - 4.60: 120116 Nonbonded interactions: 294516 Sorted by model distance: nonbonded pdb=" OE1 GLU A 596 " pdb=" H GLU A 596 " model vdw 1.524 2.450 nonbonded pdb=" OE1 GLU A 218 " pdb=" H GLU A 218 " model vdw 1.546 2.450 nonbonded pdb=" HG1 THR B 56 " pdb=" O GLU B 177 " model vdw 1.606 2.450 nonbonded pdb=" O VAL A 818 " pdb=" HG SER A 821 " model vdw 1.608 2.450 nonbonded pdb=" O LEU A 697 " pdb="HE21 GLN A 797 " model vdw 1.616 2.450 ... (remaining 294511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.310 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 41.910 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 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 : 0.006 0.059 10279 Z= 0.271 Angle : 0.596 7.003 13930 Z= 0.336 Chirality : 0.039 0.173 1582 Planarity : 0.004 0.052 1733 Dihedral : 11.968 168.951 3828 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.24), residues: 1210 helix: 1.15 (0.18), residues: 857 sheet: 0.19 (0.69), residues: 50 loop : 0.43 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 807 HIS 0.004 0.001 HIS A 496 PHE 0.018 0.002 PHE A 570 TYR 0.016 0.002 TYR A 508 ARG 0.003 0.001 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.13247 ( 628) hydrogen bonds : angle 5.91809 ( 1845) covalent geometry : bond 0.00569 (10279) covalent geometry : angle 0.59586 (13930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 847 MET cc_start: 0.7455 (ptt) cc_final: 0.7152 (ptm) REVERT: B 105 ASN cc_start: 0.8789 (t0) cc_final: 0.7831 (t0) REVERT: B 109 ASP cc_start: 0.8680 (m-30) cc_final: 0.8175 (m-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.5960 time to fit residues: 45.6079 Evaluate side-chains 44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.068499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048515 restraints weight = 89936.766| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.11 r_work: 0.2786 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10279 Z= 0.163 Angle : 0.537 6.245 13930 Z= 0.288 Chirality : 0.038 0.128 1582 Planarity : 0.004 0.048 1733 Dihedral : 8.343 175.635 1333 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.18 % Allowed : 4.42 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.25), residues: 1210 helix: 1.46 (0.18), residues: 874 sheet: -0.03 (0.70), residues: 50 loop : 0.18 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 807 HIS 0.004 0.001 HIS B 32 PHE 0.013 0.001 PHE A 412 TYR 0.014 0.001 TYR A1105 ARG 0.003 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 628) hydrogen bonds : angle 4.80285 ( 1845) covalent geometry : bond 0.00356 (10279) covalent geometry : angle 0.53710 (13930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 847 MET cc_start: 0.7539 (ptt) cc_final: 0.7252 (ptm) REVERT: B 105 ASN cc_start: 0.8714 (t0) cc_final: 0.7853 (t0) REVERT: B 109 ASP cc_start: 0.8660 (m-30) cc_final: 0.8165 (m-30) outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.4879 time to fit residues: 34.5452 Evaluate side-chains 43 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.068264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.048340 restraints weight = 90628.430| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.10 r_work: 0.2782 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10279 Z= 0.173 Angle : 0.506 5.810 13930 Z= 0.269 Chirality : 0.037 0.130 1582 Planarity : 0.004 0.049 1733 Dihedral : 8.097 175.711 1333 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.83 (0.25), residues: 1210 helix: 1.70 (0.18), residues: 875 sheet: -0.25 (0.72), residues: 50 loop : 0.11 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 807 HIS 0.007 0.001 HIS B 32 PHE 0.012 0.001 PHE A 412 TYR 0.014 0.001 TYR A 863 ARG 0.003 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 628) hydrogen bonds : angle 4.51034 ( 1845) covalent geometry : bond 0.00387 (10279) covalent geometry : angle 0.50589 (13930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 ASN cc_start: 0.8695 (t0) cc_final: 0.7860 (t0) REVERT: B 109 ASP cc_start: 0.8663 (m-30) cc_final: 0.8161 (m-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.5018 time to fit residues: 31.9325 Evaluate side-chains 42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 105 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.068270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.048338 restraints weight = 91677.649| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.12 r_work: 0.2783 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10279 Z= 0.172 Angle : 0.508 9.352 13930 Z= 0.267 Chirality : 0.037 0.128 1582 Planarity : 0.003 0.044 1733 Dihedral : 8.018 179.346 1333 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.18 % Allowed : 4.77 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.89 (0.25), residues: 1210 helix: 1.79 (0.18), residues: 877 sheet: -0.40 (0.72), residues: 50 loop : 0.01 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 807 HIS 0.004 0.001 HIS B 32 PHE 0.012 0.001 PHE A 412 TYR 0.013 0.001 TYR A 863 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 628) hydrogen bonds : angle 4.33513 ( 1845) covalent geometry : bond 0.00385 (10279) covalent geometry : angle 0.50825 (13930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 ASN cc_start: 0.8660 (t0) cc_final: 0.7845 (t0) REVERT: B 109 ASP cc_start: 0.8634 (m-30) cc_final: 0.8119 (m-30) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.4756 time to fit residues: 33.6607 Evaluate side-chains 44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 121 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048752 restraints weight = 91382.431| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.13 r_work: 0.2796 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10279 Z= 0.136 Angle : 0.486 8.228 13930 Z= 0.253 Chirality : 0.036 0.130 1582 Planarity : 0.003 0.047 1733 Dihedral : 7.882 178.786 1333 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.18 % Allowed : 5.57 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.25), residues: 1210 helix: 1.93 (0.18), residues: 877 sheet: -0.54 (0.72), residues: 50 loop : 0.02 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 807 HIS 0.005 0.001 HIS A1019 PHE 0.015 0.001 PHE A 412 TYR 0.012 0.001 TYR A 863 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 628) hydrogen bonds : angle 4.18675 ( 1845) covalent geometry : bond 0.00304 (10279) covalent geometry : angle 0.48585 (13930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 ASN cc_start: 0.8632 (t0) cc_final: 0.7831 (t0) REVERT: B 109 ASP cc_start: 0.8618 (m-30) cc_final: 0.8103 (m-30) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.4789 time to fit residues: 33.0750 Evaluate side-chains 45 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.069216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.050536 restraints weight = 89947.315| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.94 r_work: 0.2800 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10279 Z= 0.149 Angle : 0.489 9.210 13930 Z= 0.255 Chirality : 0.036 0.130 1582 Planarity : 0.003 0.043 1733 Dihedral : 7.787 177.713 1333 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.25), residues: 1210 helix: 1.99 (0.18), residues: 877 sheet: -0.62 (0.72), residues: 50 loop : -0.01 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 807 HIS 0.003 0.001 HIS A 652 PHE 0.015 0.001 PHE A1037 TYR 0.019 0.001 TYR A1105 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 628) hydrogen bonds : angle 4.12752 ( 1845) covalent geometry : bond 0.00335 (10279) covalent geometry : angle 0.48919 (13930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.5023 time to fit residues: 33.4133 Evaluate side-chains 43 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.069425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.050755 restraints weight = 88971.081| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.92 r_work: 0.2806 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10279 Z= 0.136 Angle : 0.486 10.438 13930 Z= 0.252 Chirality : 0.036 0.130 1582 Planarity : 0.003 0.044 1733 Dihedral : 7.701 176.202 1333 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.18 % Allowed : 6.10 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.25), residues: 1210 helix: 2.05 (0.18), residues: 876 sheet: -0.71 (0.71), residues: 50 loop : -0.01 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 75 HIS 0.003 0.001 HIS A 652 PHE 0.014 0.001 PHE A 412 TYR 0.012 0.001 TYR A 863 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 628) hydrogen bonds : angle 4.06605 ( 1845) covalent geometry : bond 0.00306 (10279) covalent geometry : angle 0.48641 (13930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 0.4939 time to fit residues: 35.2429 Evaluate side-chains 44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 32 optimal weight: 0.0030 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 0.0000 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.067516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.048232 restraints weight = 89621.174| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.07 r_work: 0.2755 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10279 Z= 0.112 Angle : 0.474 8.207 13930 Z= 0.243 Chirality : 0.036 0.132 1582 Planarity : 0.003 0.043 1733 Dihedral : 7.573 174.425 1333 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.32 (0.25), residues: 1210 helix: 2.16 (0.18), residues: 876 sheet: -0.77 (0.71), residues: 50 loop : 0.05 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 75 HIS 0.002 0.001 HIS A 652 PHE 0.014 0.001 PHE A 412 TYR 0.014 0.001 TYR A1105 ARG 0.003 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 628) hydrogen bonds : angle 3.97863 ( 1845) covalent geometry : bond 0.00249 (10279) covalent geometry : angle 0.47362 (13930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1023 MET cc_start: 0.8751 (ttm) cc_final: 0.8545 (mtm) REVERT: A 1077 TYR cc_start: 0.8546 (t80) cc_final: 0.8177 (t80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.4709 time to fit residues: 31.5293 Evaluate side-chains 42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.067336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.048033 restraints weight = 89668.887| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.07 r_work: 0.2752 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10279 Z= 0.130 Angle : 0.486 11.698 13930 Z= 0.249 Chirality : 0.036 0.131 1582 Planarity : 0.003 0.043 1733 Dihedral : 7.525 173.923 1333 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.25), residues: 1210 helix: 2.20 (0.18), residues: 876 sheet: -0.81 (0.71), residues: 50 loop : 0.06 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 807 HIS 0.003 0.001 HIS A 652 PHE 0.016 0.001 PHE A1037 TYR 0.013 0.001 TYR A1105 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 628) hydrogen bonds : angle 3.99233 ( 1845) covalent geometry : bond 0.00292 (10279) covalent geometry : angle 0.48566 (13930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1077 TYR cc_start: 0.8581 (t80) cc_final: 0.8218 (t80) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.5184 time to fit residues: 34.1658 Evaluate side-chains 42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.068034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.047925 restraints weight = 90124.159| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.20 r_work: 0.2751 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10279 Z= 0.110 Angle : 0.479 10.031 13930 Z= 0.245 Chirality : 0.036 0.132 1582 Planarity : 0.003 0.043 1733 Dihedral : 7.448 172.336 1333 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.25), residues: 1210 helix: 2.25 (0.18), residues: 877 sheet: -0.81 (0.71), residues: 50 loop : 0.04 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 75 HIS 0.002 0.001 HIS A1019 PHE 0.014 0.001 PHE A1037 TYR 0.011 0.001 TYR A 863 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 628) hydrogen bonds : angle 3.92062 ( 1845) covalent geometry : bond 0.00246 (10279) covalent geometry : angle 0.47868 (13930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1077 TYR cc_start: 0.8560 (t80) cc_final: 0.8196 (t80) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.4626 time to fit residues: 31.6426 Evaluate side-chains 42 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1018 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.068746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.048629 restraints weight = 89915.424| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.20 r_work: 0.2759 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10279 Z= 0.102 Angle : 0.477 10.071 13930 Z= 0.244 Chirality : 0.036 0.133 1582 Planarity : 0.003 0.043 1733 Dihedral : 7.366 170.979 1333 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1210 helix: 2.32 (0.18), residues: 877 sheet: -0.80 (0.71), residues: 50 loop : 0.03 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 75 HIS 0.002 0.000 HIS B 107 PHE 0.014 0.001 PHE A 412 TYR 0.011 0.001 TYR A 863 ARG 0.002 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 628) hydrogen bonds : angle 3.90422 ( 1845) covalent geometry : bond 0.00231 (10279) covalent geometry : angle 0.47719 (13930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8243.85 seconds wall clock time: 140 minutes 53.98 seconds (8453.98 seconds total)