Starting phenix.real_space_refine on Sun Jul 27 04:36:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nyb_0541/07_2025/6nyb_0541.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nyb_0541/07_2025/6nyb_0541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nyb_0541/07_2025/6nyb_0541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nyb_0541/07_2025/6nyb_0541.map" model { file = "/net/cci-nas-00/data/ceres_data/6nyb_0541/07_2025/6nyb_0541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nyb_0541/07_2025/6nyb_0541.cif" } resolution = 4.1 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= 0.001 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: 9 Type Number sf(0) Gaussians I 1 10.91 5 Zn 2 6.06 5 P 7 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 5583 2.51 5 N 1527 2.21 5 O 1668 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 8842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2819 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 2 Chain: "B" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2258 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 16, 'TRANS': 272} Chain breaks: 1 Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1846 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Chain: "D" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1833 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 223} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {' MG': 1, 'ADP': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 136 SG CYS A 248 61.072 29.426 55.042 1.00 69.52 S ATOM 161 SG CYS A 251 62.989 27.854 57.470 1.00 79.60 S ATOM 343 SG CYS A 272 60.523 25.561 55.470 1.00113.58 S ATOM 249 SG CYS A 261 53.756 37.009 46.317 1.00107.92 S ATOM 271 SG CYS A 264 53.994 38.015 49.372 1.00114.35 S ATOM 401 SG CYS A 280 50.374 39.002 48.986 1.00149.39 S Time building chain proxies: 5.81, per 1000 atoms: 0.66 Number of scatterers: 8842 At special positions: 0 Unit cell: (111.3, 93.28, 125.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) I 1 52.95 Zn 2 29.99 S 52 16.00 P 7 15.00 Mg 1 11.99 F 1 9.00 O 1668 8.00 N 1527 7.00 C 5583 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 272 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 248 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 251 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 280 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 235 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 264 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 261 " Number of angles added : 3 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 60.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 491 through 506 removed outlier: 3.651A pdb=" N GLN A 496 " --> pdb=" O PRO A 492 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 504 " --> pdb=" O ASN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 Processing helix chain 'A' and resid 549 through 570 Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 634 through 652 Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 686 through 697 removed outlier: 3.548A pdb=" N LEU A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 693 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 697 " --> pdb=" O MET A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.601A pdb=" N ALA A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 726 removed outlier: 3.763A pdb=" N ARG A 726 " --> pdb=" O LYS A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.537A pdb=" N GLN B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.529A pdb=" N LYS B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 184 removed outlier: 3.787A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 212 through 223 removed outlier: 3.521A pdb=" N ASN B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.540A pdb=" N GLN B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 259 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 351 through 357 removed outlier: 3.831A pdb=" N VAL B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 removed outlier: 3.516A pdb=" N ALA B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.758A pdb=" N THR C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 70 removed outlier: 3.933A pdb=" N ASN C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C 52 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 102 removed outlier: 4.169A pdb=" N GLN C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 131 Processing helix chain 'C' and resid 137 through 160 removed outlier: 3.676A pdb=" N VAL C 141 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 181 Processing helix chain 'C' and resid 184 through 202 removed outlier: 4.204A pdb=" N GLU C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 210 removed outlier: 3.558A pdb=" N SER C 210 " --> pdb=" O ASN C 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 210' Processing helix chain 'C' and resid 211 through 229 Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 19 through 31 removed outlier: 3.950A pdb=" N VAL D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 67 removed outlier: 3.814A pdb=" N LEU D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 67 " --> pdb=" O SER D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 89 removed outlier: 4.376A pdb=" N MET D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 104 removed outlier: 3.932A pdb=" N LEU D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 133 removed outlier: 3.784A pdb=" N GLU D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 160 removed outlier: 4.276A pdb=" N ASN D 139 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 181 Processing helix chain 'D' and resid 184 through 202 Processing helix chain 'D' and resid 212 through 230 removed outlier: 4.018A pdb=" N SER D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 237 through 240 Processing sheet with id=AA2, first strand: chain 'A' and resid 458 through 465 removed outlier: 7.356A pdb=" N GLY A 460 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LYS A 475 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG A 462 " --> pdb=" O LYS A 473 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A 473 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 582 through 585 Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 75 removed outlier: 5.966A pdb=" N LYS B 70 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER B 86 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL B 82 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B 144 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE B 129 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 196 through 198 478 hydrogen bonds defined for protein. 1398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 3024 1.37 - 1.55: 5889 1.55 - 1.74: 11 1.74 - 1.92: 84 1.92 - 2.11: 2 Bond restraints: 9010 Sorted by residual: bond pdb=" C4 AGS A 801 " pdb=" C5 AGS A 801 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C5 AGS A 801 " pdb=" C6 AGS A 801 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.33e+01 bond pdb=" PG AGS A 801 " pdb=" S1G AGS A 801 " ideal model delta sigma weight residual 1.949 2.074 -0.125 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C18 LCJ B 901 " pdb=" N09 LCJ B 901 " ideal model delta sigma weight residual 1.349 1.458 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 9005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 10198 2.45 - 4.89: 1861 4.89 - 7.34: 85 7.34 - 9.79: 12 9.79 - 12.24: 1 Bond angle restraints: 12157 Sorted by residual: angle pdb=" C5 AGS A 801 " pdb=" C4 AGS A 801 " pdb=" N3 AGS A 801 " ideal model delta sigma weight residual 126.80 119.45 7.35 7.41e-01 1.82e+00 9.84e+01 angle pdb=" C4 AGS A 801 " pdb=" C5 AGS A 801 " pdb=" N7 AGS A 801 " ideal model delta sigma weight residual 110.73 106.42 4.31 4.52e-01 4.89e+00 9.11e+01 angle pdb=" C5 AGS A 801 " pdb=" N7 AGS A 801 " pdb=" C8 AGS A 801 " ideal model delta sigma weight residual 103.67 107.48 -3.81 4.26e-01 5.51e+00 7.99e+01 angle pdb=" N1 AGS A 801 " pdb=" C2 AGS A 801 " pdb=" N3 AGS A 801 " ideal model delta sigma weight residual 128.80 123.21 5.59 8.41e-01 1.41e+00 4.42e+01 angle pdb=" C4 AGS A 801 " pdb=" N9 AGS A 801 " pdb=" C8 AGS A 801 " ideal model delta sigma weight residual 105.70 108.67 -2.97 4.55e-01 4.83e+00 4.25e+01 ... (remaining 12152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.85: 5040 18.85 - 37.70: 342 37.70 - 56.56: 96 56.56 - 75.41: 24 75.41 - 94.26: 5 Dihedral angle restraints: 5507 sinusoidal: 2301 harmonic: 3206 Sorted by residual: dihedral pdb=" C ASP A 587 " pdb=" N ASP A 587 " pdb=" CA ASP A 587 " pdb=" CB ASP A 587 " ideal model delta harmonic sigma weight residual -122.60 -139.54 16.94 0 2.50e+00 1.60e-01 4.59e+01 dihedral pdb=" N ASP A 587 " pdb=" C ASP A 587 " pdb=" CA ASP A 587 " pdb=" CB ASP A 587 " ideal model delta harmonic sigma weight residual 122.80 138.29 -15.49 0 2.50e+00 1.60e-01 3.84e+01 dihedral pdb=" C ASP B 190 " pdb=" N ASP B 190 " pdb=" CA ASP B 190 " pdb=" CB ASP B 190 " ideal model delta harmonic sigma weight residual -122.60 -135.64 13.04 0 2.50e+00 1.60e-01 2.72e+01 ... (remaining 5504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 1209 0.138 - 0.277: 121 0.277 - 0.415: 2 0.415 - 0.554: 1 0.554 - 0.692: 1 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CA ASP A 587 " pdb=" N ASP A 587 " pdb=" C ASP A 587 " pdb=" CB ASP A 587 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ASP B 190 " pdb=" N ASP B 190 " pdb=" C ASP B 190 " pdb=" CB ASP B 190 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CA ASP A 576 " pdb=" N ASP A 576 " pdb=" C ASP A 576 " pdb=" CB ASP A 576 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 1331 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 726 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.21e+00 pdb=" C ARG A 726 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG A 726 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 727 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 628 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C GLN A 628 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN A 628 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 629 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 104 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C HIS D 104 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS D 104 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 105 " -0.014 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.65: 89 2.65 - 3.23: 7940 3.23 - 3.80: 13875 3.80 - 4.38: 18945 4.38 - 4.96: 31445 Nonbonded interactions: 72294 Sorted by model distance: nonbonded pdb=" O2B ADP B 601 " pdb="MG MG B 602 " model vdw 2.070 2.170 nonbonded pdb=" O3P SEP A 729 " pdb=" NH2 ARG D 56 " model vdw 2.247 3.120 nonbonded pdb=" O PHE A 468 " pdb=" N ASN A 486 " model vdw 2.256 3.120 nonbonded pdb=" NZ LYS D 88 " pdb=" OE2 GLU D 92 " model vdw 2.350 3.120 nonbonded pdb=" O SER A 520 " pdb=" O GLN A 524 " model vdw 2.367 3.040 ... (remaining 72289 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 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 through 201 or (resid \ 202 and (name N or name CA or name C or name O or name CB )) or resid 203 throug \ h 230)) selection = chain 'D' } 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 group one per residue 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: 0.480 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.200 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.018 0.574 9017 Z= 1.097 Angle : 1.861 57.150 12160 Z= 1.323 Chirality : 0.091 0.692 1334 Planarity : 0.003 0.029 1548 Dihedral : 14.523 94.262 3433 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.39 % Favored : 94.43 % Rotamer: Outliers : 3.66 % Allowed : 5.02 % Favored : 91.32 % Cbeta Deviations : 0.29 % 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: -3.02 (0.22), residues: 1077 helix: -1.43 (0.18), residues: 596 sheet: -2.52 (0.58), residues: 57 loop : -2.65 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.007 0.002 HIS A 269 PHE 0.015 0.002 PHE A 250 TYR 0.020 0.002 TYR C 179 ARG 0.004 0.001 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.21547 ( 478) hydrogen bonds : angle 8.30541 ( 1398) metal coordination : bond 0.40281 ( 7) metal coordination : angle 40.20144 ( 3) covalent geometry : bond 0.01369 ( 9010) covalent geometry : angle 1.75074 (12157) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 406 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 LYS cc_start: 0.8456 (tttt) cc_final: 0.8076 (tttm) REVERT: A 501 GLU cc_start: 0.8098 (tp30) cc_final: 0.7565 (tp30) REVERT: A 544 ILE cc_start: 0.8968 (pt) cc_final: 0.8048 (mp) REVERT: A 640 TYR cc_start: 0.8918 (t80) cc_final: 0.8599 (t80) REVERT: A 698 LYS cc_start: 0.8373 (mmtp) cc_final: 0.8081 (mmmm) REVERT: A 715 GLU cc_start: 0.8006 (tt0) cc_final: 0.7764 (tp30) REVERT: A 723 LYS cc_start: 0.5281 (OUTLIER) cc_final: 0.4903 (pttt) REVERT: B 63 LEU cc_start: 0.6488 (mt) cc_final: 0.5636 (mp) REVERT: B 114 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8679 (tt0) REVERT: B 130 TYR cc_start: 0.9032 (m-80) cc_final: 0.7895 (m-10) REVERT: B 146 MET cc_start: 0.8515 (mmm) cc_final: 0.8090 (mmm) REVERT: B 160 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.8106 (ptm-80) REVERT: B 163 GLU cc_start: 0.7441 (tt0) cc_final: 0.6981 (tm-30) REVERT: B 195 ASN cc_start: 0.8701 (m-40) cc_final: 0.8293 (m-40) REVERT: B 207 CYS cc_start: 0.9338 (p) cc_final: 0.8574 (t) REVERT: B 230 MET cc_start: 0.7535 (tpp) cc_final: 0.7270 (mmt) REVERT: B 253 LEU cc_start: 0.9635 (mt) cc_final: 0.9292 (mm) REVERT: B 255 GLU cc_start: 0.8018 (tt0) cc_final: 0.7724 (tt0) REVERT: B 308 MET cc_start: 0.8177 (mmp) cc_final: 0.7733 (mmm) REVERT: B 333 GLU cc_start: 0.9430 (mp0) cc_final: 0.9086 (mp0) REVERT: B 337 PHE cc_start: 0.9124 (t80) cc_final: 0.8881 (t80) REVERT: B 341 CYS cc_start: 0.8925 (m) cc_final: 0.8248 (m) REVERT: B 342 LEU cc_start: 0.8780 (mt) cc_final: 0.8453 (mt) REVERT: B 358 HIS cc_start: 0.6902 (t-90) cc_final: 0.6398 (t-90) REVERT: B 374 TRP cc_start: 0.8372 (t60) cc_final: 0.7892 (t60) REVERT: C 14 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8252 (tm-30) REVERT: C 27 LYS cc_start: 0.8849 (tttt) cc_final: 0.8644 (ttpp) REVERT: C 30 THR cc_start: 0.8892 (m) cc_final: 0.8667 (t) REVERT: C 100 LEU cc_start: 0.8404 (mt) cc_final: 0.7985 (mt) REVERT: C 149 TYR cc_start: 0.8207 (m-10) cc_final: 0.7835 (m-10) REVERT: C 179 TYR cc_start: 0.9029 (t80) cc_final: 0.8768 (t80) REVERT: C 194 GLN cc_start: 0.8542 (tt0) cc_final: 0.8222 (tm-30) REVERT: D 167 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8015 (ttt-90) outliers start: 35 outliers final: 8 residues processed: 426 average time/residue: 0.2377 time to fit residues: 132.1133 Evaluate side-chains 243 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 234 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 709 GLN B 87 HIS B 243 GLN C 8 GLN C 173 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.108956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.082277 restraints weight = 22294.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.084773 restraints weight = 14066.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.086536 restraints weight = 10338.488| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9017 Z= 0.164 Angle : 0.674 9.369 12160 Z= 0.346 Chirality : 0.042 0.178 1334 Planarity : 0.005 0.085 1548 Dihedral : 7.242 91.377 1240 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.10 % Allowed : 2.72 % Favored : 97.18 % 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: -0.60 (0.25), residues: 1077 helix: 0.64 (0.20), residues: 601 sheet: -1.68 (0.61), residues: 63 loop : -1.73 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 476 HIS 0.012 0.002 HIS B 184 PHE 0.026 0.002 PHE B 371 TYR 0.019 0.002 TYR D 82 ARG 0.026 0.001 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 478) hydrogen bonds : angle 4.69992 ( 1398) metal coordination : bond 0.02197 ( 7) metal coordination : angle 7.21090 ( 3) covalent geometry : bond 0.00358 ( 9010) covalent geometry : angle 0.66449 (12157) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 286 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 MET cc_start: 0.8485 (mtp) cc_final: 0.7966 (mtt) REVERT: A 501 GLU cc_start: 0.8323 (tp30) cc_final: 0.7929 (tp30) REVERT: A 505 LEU cc_start: 0.9274 (mt) cc_final: 0.8559 (mt) REVERT: A 544 ILE cc_start: 0.8363 (pt) cc_final: 0.8146 (mp) REVERT: A 564 MET cc_start: 0.8435 (tpt) cc_final: 0.8126 (tpp) REVERT: A 591 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7765 (mtpt) REVERT: A 608 HIS cc_start: 0.6271 (p90) cc_final: 0.5840 (m90) REVERT: A 640 TYR cc_start: 0.9213 (t80) cc_final: 0.8823 (t80) REVERT: A 698 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8649 (mmmm) REVERT: A 699 LYS cc_start: 0.8480 (mttp) cc_final: 0.8229 (mmtp) REVERT: A 715 GLU cc_start: 0.7996 (tt0) cc_final: 0.7614 (tp30) REVERT: A 723 LYS cc_start: 0.6984 (ptmt) cc_final: 0.6724 (pttt) REVERT: B 108 ARG cc_start: 0.9068 (ptt180) cc_final: 0.8694 (ptt90) REVERT: B 114 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8702 (tp30) REVERT: B 146 MET cc_start: 0.8949 (mmm) cc_final: 0.8177 (mmm) REVERT: B 160 ARG cc_start: 0.8788 (mtm-85) cc_final: 0.8329 (ptm-80) REVERT: B 195 ASN cc_start: 0.8694 (m-40) cc_final: 0.8192 (m-40) REVERT: B 197 LEU cc_start: 0.8361 (mm) cc_final: 0.7906 (mm) REVERT: B 230 MET cc_start: 0.7515 (tpp) cc_final: 0.7312 (mmt) REVERT: B 233 GLU cc_start: 0.6785 (pp20) cc_final: 0.6032 (pp20) REVERT: B 242 VAL cc_start: 0.8548 (m) cc_final: 0.8053 (p) REVERT: B 245 ASP cc_start: 0.8840 (m-30) cc_final: 0.8612 (m-30) REVERT: B 255 GLU cc_start: 0.8195 (tt0) cc_final: 0.7899 (tt0) REVERT: B 319 ASN cc_start: 0.9255 (t0) cc_final: 0.8877 (t0) REVERT: B 342 LEU cc_start: 0.8898 (mt) cc_final: 0.8629 (mt) REVERT: C 100 LEU cc_start: 0.8447 (mt) cc_final: 0.8229 (mt) REVERT: C 111 ASN cc_start: 0.8414 (t0) cc_final: 0.8176 (t0) REVERT: C 194 GLN cc_start: 0.8926 (tt0) cc_final: 0.8583 (tm-30) REVERT: C 198 ASP cc_start: 0.8441 (p0) cc_final: 0.8148 (p0) REVERT: C 202 GLU cc_start: 0.8319 (mp0) cc_final: 0.8017 (mp0) REVERT: D 26 MET cc_start: 0.9076 (mmp) cc_final: 0.8774 (mpp) REVERT: D 59 TRP cc_start: 0.9259 (t60) cc_final: 0.8928 (t60) REVERT: D 111 ASN cc_start: 0.9112 (t0) cc_final: 0.8765 (t0) REVERT: D 167 ARG cc_start: 0.8856 (ttt180) cc_final: 0.7889 (ttt-90) REVERT: D 197 ASP cc_start: 0.8871 (m-30) cc_final: 0.8664 (m-30) REVERT: D 224 ASN cc_start: 0.9014 (m-40) cc_final: 0.8807 (m110) outliers start: 1 outliers final: 0 residues processed: 287 average time/residue: 0.2331 time to fit residues: 89.4757 Evaluate side-chains 210 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 ASN B 87 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 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 = 0.3554 r_free = 0.3554 target = 0.101740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076196 restraints weight = 23821.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077264 restraints weight = 14530.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078411 restraints weight = 11424.123| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9017 Z= 0.264 Angle : 0.755 15.747 12160 Z= 0.384 Chirality : 0.045 0.190 1334 Planarity : 0.005 0.055 1548 Dihedral : 7.169 95.876 1240 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % 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: -0.16 (0.25), residues: 1077 helix: 0.88 (0.21), residues: 617 sheet: -1.01 (0.60), residues: 58 loop : -1.51 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 374 HIS 0.008 0.002 HIS A 568 PHE 0.030 0.003 PHE C 196 TYR 0.025 0.002 TYR C 128 ARG 0.006 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04670 ( 478) hydrogen bonds : angle 4.74320 ( 1398) metal coordination : bond 0.02255 ( 7) metal coordination : angle 9.32760 ( 3) covalent geometry : bond 0.00584 ( 9010) covalent geometry : angle 0.74070 (12157) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 LEU cc_start: 0.9181 (mt) cc_final: 0.8953 (mt) REVERT: A 501 GLU cc_start: 0.8402 (tp30) cc_final: 0.7956 (tp30) REVERT: A 505 LEU cc_start: 0.9376 (mt) cc_final: 0.8687 (mt) REVERT: A 544 ILE cc_start: 0.8734 (pt) cc_final: 0.7679 (tt) REVERT: A 565 ASP cc_start: 0.8787 (t0) cc_final: 0.8453 (t0) REVERT: A 640 TYR cc_start: 0.9228 (t80) cc_final: 0.8722 (t80) REVERT: A 698 LYS cc_start: 0.9228 (mmtp) cc_final: 0.8843 (mmmm) REVERT: A 699 LYS cc_start: 0.8819 (mttp) cc_final: 0.8592 (mmtp) REVERT: B 114 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8825 (tp30) REVERT: B 146 MET cc_start: 0.9068 (mmm) cc_final: 0.8471 (mmm) REVERT: B 180 LEU cc_start: 0.9101 (mt) cc_final: 0.8847 (mt) REVERT: B 181 ARG cc_start: 0.8570 (mmp-170) cc_final: 0.8259 (mmm160) REVERT: B 188 HIS cc_start: 0.7992 (t-90) cc_final: 0.7730 (t-90) REVERT: B 195 ASN cc_start: 0.8736 (m-40) cc_final: 0.8133 (m-40) REVERT: B 197 LEU cc_start: 0.8324 (mm) cc_final: 0.7872 (mm) REVERT: B 233 GLU cc_start: 0.7192 (pp20) cc_final: 0.6649 (pp20) REVERT: B 242 VAL cc_start: 0.9034 (m) cc_final: 0.8417 (p) REVERT: B 249 MET cc_start: 0.9255 (tmm) cc_final: 0.8949 (tmm) REVERT: B 255 GLU cc_start: 0.8193 (tt0) cc_final: 0.7986 (tt0) REVERT: B 319 ASN cc_start: 0.9311 (t0) cc_final: 0.8871 (t0) REVERT: B 337 PHE cc_start: 0.9275 (t80) cc_final: 0.8879 (t80) REVERT: B 341 CYS cc_start: 0.8625 (m) cc_final: 0.8193 (m) REVERT: B 342 LEU cc_start: 0.8625 (mt) cc_final: 0.8315 (mt) REVERT: B 374 TRP cc_start: 0.8825 (t60) cc_final: 0.8415 (t60) REVERT: C 74 ARG cc_start: 0.8215 (ptt180) cc_final: 0.7591 (ptt180) REVERT: C 92 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: C 100 LEU cc_start: 0.8616 (mt) cc_final: 0.8391 (mt) REVERT: C 202 GLU cc_start: 0.8584 (mp0) cc_final: 0.8329 (mp0) REVERT: C 207 ASN cc_start: 0.8979 (p0) cc_final: 0.8756 (p0) REVERT: C 224 ASN cc_start: 0.9555 (m-40) cc_final: 0.9317 (m-40) REVERT: D 26 MET cc_start: 0.9195 (mmp) cc_final: 0.8849 (mpp) REVERT: D 111 ASN cc_start: 0.9073 (t0) cc_final: 0.8822 (t0) REVERT: D 224 ASN cc_start: 0.9020 (m-40) cc_final: 0.8817 (m110) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1890 time to fit residues: 61.1000 Evaluate side-chains 170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 16 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 ASN ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.080863 restraints weight = 23123.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.080238 restraints weight = 13932.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081900 restraints weight = 11483.479| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9017 Z= 0.147 Angle : 0.642 12.057 12160 Z= 0.329 Chirality : 0.042 0.188 1334 Planarity : 0.004 0.049 1548 Dihedral : 6.878 97.979 1240 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: 0.08 (0.26), residues: 1077 helix: 1.07 (0.21), residues: 614 sheet: -0.89 (0.59), residues: 58 loop : -1.36 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 247 HIS 0.006 0.001 HIS A 542 PHE 0.061 0.002 PHE B 360 TYR 0.017 0.002 TYR C 178 ARG 0.006 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 478) hydrogen bonds : angle 4.41087 ( 1398) metal coordination : bond 0.01570 ( 7) metal coordination : angle 6.28383 ( 3) covalent geometry : bond 0.00313 ( 9010) covalent geometry : angle 0.63476 (12157) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 GLU cc_start: 0.8282 (tp30) cc_final: 0.7735 (tp30) REVERT: A 544 ILE cc_start: 0.8697 (pt) cc_final: 0.7716 (tt) REVERT: A 565 ASP cc_start: 0.8556 (t0) cc_final: 0.8257 (t0) REVERT: A 608 HIS cc_start: 0.6848 (p90) cc_final: 0.6153 (m170) REVERT: A 640 TYR cc_start: 0.9161 (t80) cc_final: 0.8704 (t80) REVERT: A 698 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8584 (mmmm) REVERT: A 699 LYS cc_start: 0.8750 (mttp) cc_final: 0.8528 (mmtm) REVERT: A 723 LYS cc_start: 0.7561 (ptmt) cc_final: 0.7326 (pttt) REVERT: B 94 MET cc_start: 0.4364 (pmm) cc_final: 0.3942 (pmm) REVERT: B 146 MET cc_start: 0.8962 (mmm) cc_final: 0.8329 (mmm) REVERT: B 180 LEU cc_start: 0.9096 (mt) cc_final: 0.8878 (mt) REVERT: B 181 ARG cc_start: 0.8693 (mmp-170) cc_final: 0.8356 (mmm160) REVERT: B 195 ASN cc_start: 0.8709 (m-40) cc_final: 0.8321 (m-40) REVERT: B 197 LEU cc_start: 0.8252 (mm) cc_final: 0.8007 (mm) REVERT: B 207 CYS cc_start: 0.9078 (p) cc_final: 0.8770 (p) REVERT: B 233 GLU cc_start: 0.7116 (pp20) cc_final: 0.6462 (pp20) REVERT: B 242 VAL cc_start: 0.8930 (m) cc_final: 0.8355 (p) REVERT: B 249 MET cc_start: 0.9182 (tmm) cc_final: 0.8890 (tmm) REVERT: B 319 ASN cc_start: 0.9290 (t0) cc_final: 0.8814 (t0) REVERT: B 341 CYS cc_start: 0.8668 (m) cc_final: 0.8384 (m) REVERT: B 342 LEU cc_start: 0.8651 (mt) cc_final: 0.8315 (mt) REVERT: B 374 TRP cc_start: 0.8731 (t60) cc_final: 0.8504 (t60) REVERT: C 17 GLU cc_start: 0.7367 (mp0) cc_final: 0.7014 (mp0) REVERT: C 74 ARG cc_start: 0.8221 (ptt180) cc_final: 0.7650 (ptt180) REVERT: C 100 LEU cc_start: 0.8554 (mt) cc_final: 0.8321 (mt) REVERT: C 218 MET cc_start: 0.9029 (mmm) cc_final: 0.8763 (mmt) REVERT: C 228 TRP cc_start: 0.8986 (m-10) cc_final: 0.8573 (m-90) REVERT: D 59 TRP cc_start: 0.9222 (t60) cc_final: 0.8939 (t60) REVERT: D 111 ASN cc_start: 0.9089 (t0) cc_final: 0.8821 (t0) REVERT: D 224 ASN cc_start: 0.9001 (m-40) cc_final: 0.8780 (m-40) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2207 time to fit residues: 73.6928 Evaluate side-chains 182 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.102936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076181 restraints weight = 23561.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078767 restraints weight = 14133.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080439 restraints weight = 10162.646| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9017 Z= 0.157 Angle : 0.625 9.303 12160 Z= 0.316 Chirality : 0.041 0.164 1334 Planarity : 0.004 0.066 1548 Dihedral : 6.833 100.521 1240 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.10 % Allowed : 1.67 % Favored : 98.22 % 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: 0.24 (0.26), residues: 1077 helix: 1.17 (0.21), residues: 611 sheet: -0.70 (0.59), residues: 58 loop : -1.26 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 247 HIS 0.013 0.001 HIS B 188 PHE 0.043 0.002 PHE B 360 TYR 0.022 0.002 TYR C 178 ARG 0.007 0.000 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 478) hydrogen bonds : angle 4.26319 ( 1398) metal coordination : bond 0.01922 ( 7) metal coordination : angle 5.83301 ( 3) covalent geometry : bond 0.00351 ( 9010) covalent geometry : angle 0.61807 (12157) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 GLU cc_start: 0.8355 (tp30) cc_final: 0.7876 (tp30) REVERT: A 505 LEU cc_start: 0.9364 (mt) cc_final: 0.8696 (mt) REVERT: A 544 ILE cc_start: 0.8691 (pt) cc_final: 0.7647 (tt) REVERT: A 564 MET cc_start: 0.8129 (mmt) cc_final: 0.7868 (mmm) REVERT: A 565 ASP cc_start: 0.8452 (t0) cc_final: 0.8189 (t0) REVERT: A 591 LYS cc_start: 0.8476 (mmtt) cc_final: 0.7800 (mttp) REVERT: A 608 HIS cc_start: 0.6313 (p90) cc_final: 0.5904 (m170) REVERT: A 640 TYR cc_start: 0.9240 (t80) cc_final: 0.8808 (t80) REVERT: A 698 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8408 (mmmm) REVERT: B 94 MET cc_start: 0.4217 (pmm) cc_final: 0.3773 (pmm) REVERT: B 146 MET cc_start: 0.8971 (mmm) cc_final: 0.8342 (mmm) REVERT: B 180 LEU cc_start: 0.9073 (mt) cc_final: 0.8823 (mt) REVERT: B 181 ARG cc_start: 0.8678 (mmp-170) cc_final: 0.8325 (mmm160) REVERT: B 187 MET cc_start: 0.6273 (ttm) cc_final: 0.6054 (ttm) REVERT: B 195 ASN cc_start: 0.8763 (m-40) cc_final: 0.8541 (m-40) REVERT: B 197 LEU cc_start: 0.8173 (mm) cc_final: 0.7895 (mm) REVERT: B 233 GLU cc_start: 0.7151 (pp20) cc_final: 0.6473 (pp20) REVERT: B 242 VAL cc_start: 0.9104 (m) cc_final: 0.8802 (m) REVERT: B 249 MET cc_start: 0.9179 (tmm) cc_final: 0.8931 (tmm) REVERT: B 319 ASN cc_start: 0.9268 (t0) cc_final: 0.8744 (t0) REVERT: B 341 CYS cc_start: 0.8578 (m) cc_final: 0.8361 (m) REVERT: B 374 TRP cc_start: 0.8743 (t60) cc_final: 0.8536 (t60) REVERT: C 17 GLU cc_start: 0.7329 (mp0) cc_final: 0.7006 (mp0) REVERT: C 74 ARG cc_start: 0.8143 (ptt180) cc_final: 0.7588 (ptt180) REVERT: C 100 LEU cc_start: 0.8567 (mt) cc_final: 0.8351 (mt) REVERT: C 207 ASN cc_start: 0.9000 (p0) cc_final: 0.8699 (p0) REVERT: C 218 MET cc_start: 0.9060 (mmm) cc_final: 0.8759 (mmt) REVERT: C 224 ASN cc_start: 0.9544 (m-40) cc_final: 0.7984 (m-40) REVERT: C 228 TRP cc_start: 0.8976 (m-10) cc_final: 0.8521 (m-90) REVERT: D 26 MET cc_start: 0.9142 (mmp) cc_final: 0.8792 (mpp) REVERT: D 59 TRP cc_start: 0.9279 (t60) cc_final: 0.8986 (t60) REVERT: D 111 ASN cc_start: 0.9068 (t0) cc_final: 0.8805 (t0) REVERT: D 224 ASN cc_start: 0.9010 (m-40) cc_final: 0.8782 (m-40) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.2050 time to fit residues: 66.1885 Evaluate side-chains 178 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 0.0070 chunk 96 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.103279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.078595 restraints weight = 23904.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.079689 restraints weight = 13808.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.080868 restraints weight = 10898.503| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9017 Z= 0.134 Angle : 0.625 9.237 12160 Z= 0.316 Chirality : 0.041 0.181 1334 Planarity : 0.004 0.042 1548 Dihedral : 6.685 103.257 1240 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 0.38 (0.26), residues: 1077 helix: 1.32 (0.21), residues: 609 sheet: -1.02 (0.59), residues: 62 loop : -1.18 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 247 HIS 0.011 0.001 HIS A 235 PHE 0.053 0.002 PHE B 360 TYR 0.028 0.002 TYR C 178 ARG 0.006 0.000 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 478) hydrogen bonds : angle 4.25863 ( 1398) metal coordination : bond 0.02984 ( 7) metal coordination : angle 6.04236 ( 3) covalent geometry : bond 0.00295 ( 9010) covalent geometry : angle 0.61823 (12157) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 GLU cc_start: 0.8387 (tp30) cc_final: 0.7927 (tp30) REVERT: A 505 LEU cc_start: 0.9304 (mt) cc_final: 0.8607 (mt) REVERT: A 544 ILE cc_start: 0.8687 (pt) cc_final: 0.7678 (tt) REVERT: A 565 ASP cc_start: 0.8281 (t0) cc_final: 0.8057 (t0) REVERT: A 591 LYS cc_start: 0.8515 (mmtt) cc_final: 0.7929 (mttp) REVERT: A 608 HIS cc_start: 0.6879 (p90) cc_final: 0.6218 (m170) REVERT: A 640 TYR cc_start: 0.9116 (t80) cc_final: 0.8620 (t80) REVERT: A 698 LYS cc_start: 0.8928 (mmtp) cc_final: 0.8365 (mmmm) REVERT: A 703 GLU cc_start: 0.8569 (tt0) cc_final: 0.8368 (tt0) REVERT: B 94 MET cc_start: 0.4665 (pmm) cc_final: 0.4132 (pmm) REVERT: B 146 MET cc_start: 0.8917 (mmm) cc_final: 0.8146 (mmm) REVERT: B 181 ARG cc_start: 0.8613 (mmp-170) cc_final: 0.8382 (mmm160) REVERT: B 209 PHE cc_start: 0.9222 (p90) cc_final: 0.8916 (p90) REVERT: B 233 GLU cc_start: 0.7217 (pp20) cc_final: 0.6538 (pp20) REVERT: B 242 VAL cc_start: 0.9040 (m) cc_final: 0.8718 (m) REVERT: B 249 MET cc_start: 0.9150 (tmm) cc_final: 0.8890 (tmm) REVERT: B 319 ASN cc_start: 0.9224 (t0) cc_final: 0.8690 (t0) REVERT: B 341 CYS cc_start: 0.8498 (m) cc_final: 0.8197 (m) REVERT: C 5 GLU cc_start: 0.8836 (pt0) cc_final: 0.8608 (pt0) REVERT: C 17 GLU cc_start: 0.7219 (mp0) cc_final: 0.6952 (mp0) REVERT: C 207 ASN cc_start: 0.9049 (p0) cc_final: 0.8758 (p0) REVERT: C 218 MET cc_start: 0.8967 (mmm) cc_final: 0.8480 (mmm) REVERT: C 224 ASN cc_start: 0.9541 (m-40) cc_final: 0.8007 (m-40) REVERT: C 228 TRP cc_start: 0.8984 (m-10) cc_final: 0.8512 (m-90) REVERT: D 26 MET cc_start: 0.9146 (mmp) cc_final: 0.8915 (mpp) REVERT: D 59 TRP cc_start: 0.9259 (t60) cc_final: 0.8927 (t60) REVERT: D 111 ASN cc_start: 0.9042 (t0) cc_final: 0.8784 (t0) REVERT: D 147 LYS cc_start: 0.9404 (mttt) cc_final: 0.9039 (mppt) REVERT: D 224 ASN cc_start: 0.8984 (m-40) cc_final: 0.8740 (m-40) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1906 time to fit residues: 60.8578 Evaluate side-chains 179 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 27 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.103440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076469 restraints weight = 23718.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.079067 restraints weight = 14534.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.080788 restraints weight = 10541.125| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9017 Z= 0.149 Angle : 0.654 11.191 12160 Z= 0.332 Chirality : 0.041 0.175 1334 Planarity : 0.004 0.041 1548 Dihedral : 6.727 105.904 1240 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 0.44 (0.26), residues: 1077 helix: 1.34 (0.21), residues: 609 sheet: -0.64 (0.60), residues: 56 loop : -1.16 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 374 HIS 0.013 0.002 HIS D 164 PHE 0.055 0.002 PHE C 174 TYR 0.021 0.002 TYR A 656 ARG 0.004 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 478) hydrogen bonds : angle 4.28817 ( 1398) metal coordination : bond 0.00738 ( 7) metal coordination : angle 4.45253 ( 3) covalent geometry : bond 0.00332 ( 9010) covalent geometry : angle 0.65047 (12157) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 GLU cc_start: 0.8408 (tp30) cc_final: 0.7974 (tp30) REVERT: A 505 LEU cc_start: 0.9324 (mt) cc_final: 0.8746 (mt) REVERT: A 544 ILE cc_start: 0.8632 (pt) cc_final: 0.8278 (tt) REVERT: A 565 ASP cc_start: 0.8480 (t0) cc_final: 0.8198 (t0) REVERT: A 591 LYS cc_start: 0.8554 (mmtt) cc_final: 0.7938 (mttp) REVERT: A 608 HIS cc_start: 0.6340 (p90) cc_final: 0.5918 (m170) REVERT: A 638 ASP cc_start: 0.8163 (t0) cc_final: 0.7713 (t0) REVERT: A 640 TYR cc_start: 0.9158 (t80) cc_final: 0.8747 (t80) REVERT: A 698 LYS cc_start: 0.9037 (mmtp) cc_final: 0.8487 (mmmm) REVERT: A 703 GLU cc_start: 0.8600 (tt0) cc_final: 0.8390 (tt0) REVERT: B 94 MET cc_start: 0.4570 (pmm) cc_final: 0.4029 (pmm) REVERT: B 146 MET cc_start: 0.8932 (mmm) cc_final: 0.8174 (mmm) REVERT: B 195 ASN cc_start: 0.8378 (m110) cc_final: 0.7876 (t0) REVERT: B 219 MET cc_start: 0.8864 (mtm) cc_final: 0.8447 (mtm) REVERT: B 233 GLU cc_start: 0.7258 (pp20) cc_final: 0.6582 (pp20) REVERT: B 247 TRP cc_start: 0.9319 (t-100) cc_final: 0.9108 (t-100) REVERT: B 249 MET cc_start: 0.9198 (tmm) cc_final: 0.8925 (tmm) REVERT: B 319 ASN cc_start: 0.9130 (t0) cc_final: 0.8571 (t0) REVERT: B 341 CYS cc_start: 0.8396 (m) cc_final: 0.8036 (m) REVERT: C 5 GLU cc_start: 0.8871 (pt0) cc_final: 0.8649 (pt0) REVERT: C 17 GLU cc_start: 0.7217 (mp0) cc_final: 0.6965 (mp0) REVERT: C 111 ASN cc_start: 0.8508 (t0) cc_final: 0.8110 (t0) REVERT: C 207 ASN cc_start: 0.9060 (p0) cc_final: 0.8761 (p0) REVERT: C 218 MET cc_start: 0.9060 (mmm) cc_final: 0.8541 (mmm) REVERT: C 228 TRP cc_start: 0.8965 (m-10) cc_final: 0.8656 (m-90) REVERT: D 59 TRP cc_start: 0.9250 (t60) cc_final: 0.8902 (t60) REVERT: D 111 ASN cc_start: 0.9003 (t0) cc_final: 0.8706 (t0) REVERT: D 147 LYS cc_start: 0.9375 (mttt) cc_final: 0.9038 (mppt) REVERT: D 224 ASN cc_start: 0.8996 (m-40) cc_final: 0.8728 (m-40) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1767 time to fit residues: 54.4004 Evaluate side-chains 173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 101 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.075070 restraints weight = 23624.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.077466 restraints weight = 14826.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079081 restraints weight = 10904.795| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9017 Z= 0.183 Angle : 0.689 11.162 12160 Z= 0.346 Chirality : 0.043 0.173 1334 Planarity : 0.004 0.041 1548 Dihedral : 6.828 107.835 1240 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: 0.49 (0.26), residues: 1077 helix: 1.41 (0.21), residues: 610 sheet: -0.54 (0.61), residues: 56 loop : -1.20 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 374 HIS 0.013 0.002 HIS D 164 PHE 0.038 0.002 PHE B 360 TYR 0.028 0.002 TYR A 656 ARG 0.003 0.000 ARG A 735 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 478) hydrogen bonds : angle 4.40447 ( 1398) metal coordination : bond 0.02096 ( 7) metal coordination : angle 6.74326 ( 3) covalent geometry : bond 0.00407 ( 9010) covalent geometry : angle 0.68095 (12157) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 GLU cc_start: 0.8381 (tp30) cc_final: 0.8074 (tp30) REVERT: A 505 LEU cc_start: 0.9360 (mt) cc_final: 0.8858 (mt) REVERT: A 544 ILE cc_start: 0.8639 (pt) cc_final: 0.7650 (tt) REVERT: A 565 ASP cc_start: 0.8517 (t0) cc_final: 0.8193 (t0) REVERT: A 591 LYS cc_start: 0.8589 (mmtt) cc_final: 0.7913 (mttp) REVERT: A 608 HIS cc_start: 0.6323 (p90) cc_final: 0.5912 (m170) REVERT: A 640 TYR cc_start: 0.9213 (t80) cc_final: 0.8705 (t80) REVERT: A 698 LYS cc_start: 0.9137 (mmtp) cc_final: 0.8631 (mmmm) REVERT: A 703 GLU cc_start: 0.8673 (tt0) cc_final: 0.8464 (tt0) REVERT: B 94 MET cc_start: 0.4758 (pmm) cc_final: 0.4224 (pmm) REVERT: B 146 MET cc_start: 0.8960 (mmm) cc_final: 0.8271 (mmm) REVERT: B 209 PHE cc_start: 0.9144 (p90) cc_final: 0.8824 (p90) REVERT: B 233 GLU cc_start: 0.7368 (pp20) cc_final: 0.6696 (pp20) REVERT: B 247 TRP cc_start: 0.9311 (t-100) cc_final: 0.9059 (t-100) REVERT: B 249 MET cc_start: 0.9203 (tmm) cc_final: 0.8934 (tmm) REVERT: B 319 ASN cc_start: 0.9085 (t0) cc_final: 0.8511 (t0) REVERT: B 334 PHE cc_start: 0.9193 (t80) cc_final: 0.8890 (t80) REVERT: B 341 CYS cc_start: 0.8424 (m) cc_final: 0.8161 (m) REVERT: C 17 GLU cc_start: 0.7276 (mp0) cc_final: 0.7008 (mp0) REVERT: C 111 ASN cc_start: 0.8557 (t0) cc_final: 0.8151 (t0) REVERT: C 203 LEU cc_start: 0.9133 (mt) cc_final: 0.8791 (mt) REVERT: C 207 ASN cc_start: 0.9121 (p0) cc_final: 0.8738 (p0) REVERT: C 218 MET cc_start: 0.9042 (mmm) cc_final: 0.8444 (mmm) REVERT: C 224 ASN cc_start: 0.9480 (m-40) cc_final: 0.7486 (m-40) REVERT: C 228 TRP cc_start: 0.8982 (m-10) cc_final: 0.8486 (m-90) REVERT: D 59 TRP cc_start: 0.9255 (t60) cc_final: 0.8872 (t60) REVERT: D 111 ASN cc_start: 0.9021 (t0) cc_final: 0.8712 (t0) REVERT: D 224 ASN cc_start: 0.8989 (m-40) cc_final: 0.8739 (m-40) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2099 time to fit residues: 62.2256 Evaluate side-chains 167 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 105 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.076136 restraints weight = 23379.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.078632 restraints weight = 13908.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.080373 restraints weight = 10003.115| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9017 Z= 0.140 Angle : 0.666 10.167 12160 Z= 0.333 Chirality : 0.042 0.165 1334 Planarity : 0.004 0.043 1548 Dihedral : 6.763 108.951 1240 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.53 (0.26), residues: 1077 helix: 1.45 (0.21), residues: 609 sheet: -0.72 (0.62), residues: 51 loop : -1.17 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 374 HIS 0.011 0.001 HIS D 164 PHE 0.040 0.002 PHE A 707 TYR 0.026 0.002 TYR D 178 ARG 0.005 0.000 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 478) hydrogen bonds : angle 4.37307 ( 1398) metal coordination : bond 0.01088 ( 7) metal coordination : angle 6.04985 ( 3) covalent geometry : bond 0.00312 ( 9010) covalent geometry : angle 0.65934 (12157) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 GLU cc_start: 0.8354 (tp30) cc_final: 0.8097 (tp30) REVERT: A 505 LEU cc_start: 0.9391 (mt) cc_final: 0.8862 (mt) REVERT: A 517 MET cc_start: 0.7792 (mmt) cc_final: 0.7466 (mmt) REVERT: A 544 ILE cc_start: 0.8579 (pt) cc_final: 0.8255 (tt) REVERT: A 591 LYS cc_start: 0.8581 (mmtt) cc_final: 0.7864 (mttp) REVERT: A 608 HIS cc_start: 0.6209 (p90) cc_final: 0.5910 (m170) REVERT: A 640 TYR cc_start: 0.9174 (t80) cc_final: 0.8601 (t80) REVERT: A 698 LYS cc_start: 0.9085 (mmtp) cc_final: 0.8577 (mmmm) REVERT: A 703 GLU cc_start: 0.8652 (tt0) cc_final: 0.8406 (tt0) REVERT: B 94 MET cc_start: 0.4710 (pmm) cc_final: 0.4156 (pmm) REVERT: B 146 MET cc_start: 0.8931 (mmm) cc_final: 0.8232 (mmm) REVERT: B 195 ASN cc_start: 0.8749 (m110) cc_final: 0.8337 (m-40) REVERT: B 209 PHE cc_start: 0.9118 (p90) cc_final: 0.8767 (p90) REVERT: B 233 GLU cc_start: 0.7298 (pp20) cc_final: 0.6576 (pp20) REVERT: B 247 TRP cc_start: 0.9277 (t-100) cc_final: 0.9003 (t-100) REVERT: B 249 MET cc_start: 0.9179 (tmm) cc_final: 0.8905 (tmm) REVERT: B 319 ASN cc_start: 0.9049 (t0) cc_final: 0.8577 (p0) REVERT: B 334 PHE cc_start: 0.9221 (t80) cc_final: 0.8928 (t80) REVERT: B 341 CYS cc_start: 0.8398 (m) cc_final: 0.8018 (m) REVERT: C 17 GLU cc_start: 0.7276 (mp0) cc_final: 0.7025 (mp0) REVERT: C 111 ASN cc_start: 0.8551 (t0) cc_final: 0.8142 (t0) REVERT: C 207 ASN cc_start: 0.9152 (p0) cc_final: 0.8739 (p0) REVERT: C 218 MET cc_start: 0.9109 (mmm) cc_final: 0.8667 (mmm) REVERT: C 224 ASN cc_start: 0.9468 (m-40) cc_final: 0.7828 (m-40) REVERT: C 228 TRP cc_start: 0.8954 (m-10) cc_final: 0.8526 (m-90) REVERT: D 26 MET cc_start: 0.9294 (mmt) cc_final: 0.8694 (mpp) REVERT: D 59 TRP cc_start: 0.9242 (t60) cc_final: 0.8835 (t60) REVERT: D 111 ASN cc_start: 0.9040 (t0) cc_final: 0.8735 (t0) REVERT: D 224 ASN cc_start: 0.8959 (m-40) cc_final: 0.8694 (m-40) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1919 time to fit residues: 57.1731 Evaluate side-chains 170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 HIS ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS D 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.103403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076869 restraints weight = 23126.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079410 restraints weight = 13863.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.081036 restraints weight = 10029.162| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9017 Z= 0.141 Angle : 0.692 10.449 12160 Z= 0.347 Chirality : 0.043 0.247 1334 Planarity : 0.004 0.050 1548 Dihedral : 6.731 111.184 1240 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.53 (0.26), residues: 1077 helix: 1.44 (0.21), residues: 612 sheet: -0.63 (0.67), residues: 48 loop : -1.18 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 374 HIS 0.010 0.001 HIS D 164 PHE 0.054 0.002 PHE C 174 TYR 0.029 0.002 TYR C 179 ARG 0.005 0.000 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 478) hydrogen bonds : angle 4.34342 ( 1398) metal coordination : bond 0.00841 ( 7) metal coordination : angle 5.27875 ( 3) covalent geometry : bond 0.00313 ( 9010) covalent geometry : angle 0.68721 (12157) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 GLU cc_start: 0.8336 (tp30) cc_final: 0.8101 (tp30) REVERT: A 505 LEU cc_start: 0.9376 (mt) cc_final: 0.8819 (mt) REVERT: A 517 MET cc_start: 0.7966 (mmt) cc_final: 0.7588 (mmt) REVERT: A 544 ILE cc_start: 0.8525 (pt) cc_final: 0.8190 (tp) REVERT: A 591 LYS cc_start: 0.8568 (mmtt) cc_final: 0.7853 (mttp) REVERT: A 608 HIS cc_start: 0.6203 (p90) cc_final: 0.5927 (m170) REVERT: A 673 TYR cc_start: 0.9006 (m-10) cc_final: 0.8740 (m-10) REVERT: A 698 LYS cc_start: 0.9068 (mmtp) cc_final: 0.8559 (mmmm) REVERT: A 703 GLU cc_start: 0.8679 (tt0) cc_final: 0.8426 (tt0) REVERT: B 94 MET cc_start: 0.4692 (pmm) cc_final: 0.4120 (pmm) REVERT: B 146 MET cc_start: 0.8942 (mmm) cc_final: 0.8259 (mmm) REVERT: B 195 ASN cc_start: 0.8724 (m110) cc_final: 0.8347 (m-40) REVERT: B 209 PHE cc_start: 0.9031 (p90) cc_final: 0.8688 (p90) REVERT: B 223 PHE cc_start: 0.6133 (m-10) cc_final: 0.5809 (m-10) REVERT: B 233 GLU cc_start: 0.7384 (pp20) cc_final: 0.6666 (pp20) REVERT: B 247 TRP cc_start: 0.9246 (t-100) cc_final: 0.9020 (t-100) REVERT: B 249 MET cc_start: 0.9192 (tmm) cc_final: 0.8922 (tmm) REVERT: B 308 MET cc_start: 0.7526 (ttp) cc_final: 0.7079 (ppp) REVERT: B 311 PHE cc_start: 0.8133 (t80) cc_final: 0.7904 (t80) REVERT: B 319 ASN cc_start: 0.9002 (t0) cc_final: 0.8547 (p0) REVERT: B 334 PHE cc_start: 0.9227 (t80) cc_final: 0.8959 (t80) REVERT: B 341 CYS cc_start: 0.8357 (m) cc_final: 0.7869 (m) REVERT: C 17 GLU cc_start: 0.7267 (mp0) cc_final: 0.7015 (mp0) REVERT: C 100 LEU cc_start: 0.8649 (mt) cc_final: 0.8382 (mt) REVERT: C 111 ASN cc_start: 0.8530 (t0) cc_final: 0.8136 (t0) REVERT: C 207 ASN cc_start: 0.9168 (p0) cc_final: 0.8706 (p0) REVERT: C 218 MET cc_start: 0.8998 (mmm) cc_final: 0.8392 (mmm) REVERT: C 224 ASN cc_start: 0.9437 (m-40) cc_final: 0.7804 (m-40) REVERT: C 228 TRP cc_start: 0.8906 (m-10) cc_final: 0.8371 (m-90) REVERT: D 26 MET cc_start: 0.9298 (mmt) cc_final: 0.8610 (mpp) REVERT: D 111 ASN cc_start: 0.9021 (t0) cc_final: 0.8707 (t0) REVERT: D 224 ASN cc_start: 0.8947 (m-40) cc_final: 0.8681 (m-40) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1620 time to fit residues: 49.7649 Evaluate side-chains 173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 0.0030 chunk 74 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 79 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.077464 restraints weight = 23637.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.080056 restraints weight = 14143.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.081715 restraints weight = 10240.531| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9017 Z= 0.124 Angle : 0.650 9.947 12160 Z= 0.329 Chirality : 0.042 0.231 1334 Planarity : 0.004 0.042 1548 Dihedral : 6.607 112.849 1240 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.61 (0.26), residues: 1077 helix: 1.49 (0.21), residues: 612 sheet: -0.56 (0.68), residues: 49 loop : -1.12 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 374 HIS 0.008 0.001 HIS D 164 PHE 0.026 0.002 PHE B 360 TYR 0.022 0.002 TYR D 178 ARG 0.009 0.000 ARG C 74 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 478) hydrogen bonds : angle 4.29359 ( 1398) metal coordination : bond 0.00647 ( 7) metal coordination : angle 4.70560 ( 3) covalent geometry : bond 0.00267 ( 9010) covalent geometry : angle 0.64586 (12157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3083.57 seconds wall clock time: 54 minutes 52.25 seconds (3292.25 seconds total)