Starting phenix.real_space_refine on Mon Jul 28 15:58:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plt_13501/07_2025/7plt_13501.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plt_13501/07_2025/7plt_13501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7plt_13501/07_2025/7plt_13501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plt_13501/07_2025/7plt_13501.map" model { file = "/net/cci-nas-00/data/ceres_data/7plt_13501/07_2025/7plt_13501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plt_13501/07_2025/7plt_13501.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6467 2.51 5 N 1723 2.21 5 O 1892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10148 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 4 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.10, per 1000 atoms: 0.70 Number of scatterers: 10148 At special positions: 0 Unit cell: (103.88, 133.56, 150.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 2 15.00 Mg 1 11.99 O 1892 8.00 N 1723 7.00 C 6467 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 14 sheets defined 56.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.190A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.698A pdb=" N MET A 135 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.594A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.810A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.236A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.645A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 292 removed outlier: 4.094A pdb=" N GLY A 291 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 4.435A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.571A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 removed outlier: 4.076A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.577A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 515 removed outlier: 3.822A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.543A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.619A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.059A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.776A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.666A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.793A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.277A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.873A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.633A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 4.371A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.649A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.715A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.659A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.379A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 355 removed outlier: 6.013A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.670A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.937A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.199A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.570A pdb=" N LEU A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.606A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY A 227 " --> pdb=" O GLY A 236 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.532A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.580A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.622A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.371A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28 528 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1698 1.31 - 1.44: 2744 1.44 - 1.56: 5816 1.56 - 1.69: 3 1.69 - 1.81: 102 Bond restraints: 10363 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.439 0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.190 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " ideal model delta sigma weight residual 1.409 1.353 0.056 1.70e-02 3.46e+03 1.10e+01 bond pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 1.530 1.465 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.458 0.067 2.10e-02 2.27e+03 1.03e+01 ... (remaining 10358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 13450 2.63 - 5.25: 479 5.25 - 7.88: 53 7.88 - 10.51: 10 10.51 - 13.14: 2 Bond angle restraints: 13994 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 111.20 10.50 1.80e+00 3.09e-01 3.40e+01 angle pdb=" N PHE A 564 " pdb=" CA PHE A 564 " pdb=" CB PHE A 564 " ideal model delta sigma weight residual 110.16 118.59 -8.43 1.48e+00 4.57e-01 3.24e+01 angle pdb=" N ASN C 296 " pdb=" CA ASN C 296 " pdb=" C ASN C 296 " ideal model delta sigma weight residual 110.68 118.03 -7.35 1.39e+00 5.18e-01 2.79e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 100.47 9.63 1.90e+00 2.77e-01 2.57e+01 angle pdb=" C GLY A 563 " pdb=" N PHE A 564 " pdb=" CA PHE A 564 " ideal model delta sigma weight residual 120.29 113.34 6.95 1.42e+00 4.96e-01 2.40e+01 ... (remaining 13989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.12: 6108 32.12 - 64.24: 118 64.24 - 96.36: 31 96.36 - 128.48: 1 128.48 - 160.60: 2 Dihedral angle restraints: 6260 sinusoidal: 2567 harmonic: 3693 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 100.59 -160.60 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 164.34 135.66 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 56.94 -116.94 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 6257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 886 0.054 - 0.108: 474 0.108 - 0.162: 141 0.162 - 0.216: 24 0.216 - 0.269: 4 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CA PHE A 564 " pdb=" N PHE A 564 " pdb=" C PHE A 564 " pdb=" CB PHE A 564 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ASN C 296 " pdb=" N ASN C 296 " pdb=" C ASN C 296 " pdb=" CB ASN C 296 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA TYR A 711 " pdb=" N TYR A 711 " pdb=" C TYR A 711 " pdb=" CB TYR A 711 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1526 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 564 " -0.058 2.00e-02 2.50e+03 5.41e-02 5.12e+01 pdb=" CG PHE A 564 " 0.125 2.00e-02 2.50e+03 pdb=" CD1 PHE A 564 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE A 564 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 564 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 564 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 564 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " -0.089 9.50e-02 1.11e+02 5.27e-02 1.57e+01 pdb=" NE ARG A 213 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.095 9.50e-02 1.11e+02 5.44e-02 1.55e+01 pdb=" NE ARG A 278 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.018 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 14 2.36 - 3.00: 5719 3.00 - 3.63: 14612 3.63 - 4.27: 22564 4.27 - 4.90: 38412 Nonbonded interactions: 81321 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.727 3.620 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.098 2.170 nonbonded pdb=" OE1 GLU A 144 " pdb=" OH TYR A 179 " model vdw 2.142 3.040 nonbonded pdb=" OE2 GLU A 476 " pdb=" NH1 ARG A 701 " model vdw 2.160 3.120 nonbonded pdb=" O TRP H 1 " pdb=" O1 EEP H 2 " model vdw 2.191 3.040 ... (remaining 81316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.780 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 : 0.014 0.133 10365 Z= 0.609 Angle : 1.149 13.135 14000 Z= 0.654 Chirality : 0.068 0.269 1529 Planarity : 0.008 0.095 1791 Dihedral : 14.644 160.598 3874 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1237 helix: -1.68 (0.17), residues: 615 sheet: 0.00 (0.36), residues: 172 loop : -0.22 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.006 TRP C 356 HIS 0.016 0.003 HIS A 418 PHE 0.125 0.004 PHE A 564 TYR 0.031 0.006 TYR A 439 ARG 0.066 0.010 ARG A 213 Details of bonding type rmsd link_TRANS : bond 0.02040 ( 2) link_TRANS : angle 4.84086 ( 6) hydrogen bonds : bond 0.15376 ( 526) hydrogen bonds : angle 6.75776 ( 1437) covalent geometry : bond 0.01437 (10363) covalent geometry : angle 1.14503 (13994) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 MET cc_start: 0.8375 (mmm) cc_final: 0.8171 (mmt) REVERT: C 360 GLN cc_start: 0.7925 (tp40) cc_final: 0.7191 (tp40) REVERT: B 66 ASP cc_start: 0.9237 (p0) cc_final: 0.8896 (p0) REVERT: B 93 PHE cc_start: 0.9258 (m-80) cc_final: 0.8850 (m-80) REVERT: B 110 ARG cc_start: 0.9019 (mtt-85) cc_final: 0.8733 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3029 time to fit residues: 48.4657 Evaluate side-chains 68 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 264 GLN A 398 ASN A 410 ASN A 458 ASN A 463 GLN A 464 GLN A 481 GLN A 497 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 121 GLN C 296 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 147 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049380 restraints weight = 31412.265| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.44 r_work: 0.2669 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10365 Z= 0.154 Angle : 0.633 6.800 14000 Z= 0.336 Chirality : 0.044 0.210 1529 Planarity : 0.005 0.055 1791 Dihedral : 8.892 163.813 1397 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.83 % Allowed : 4.25 % Favored : 94.92 % 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: 0.66 (0.23), residues: 1237 helix: 0.51 (0.20), residues: 614 sheet: 0.44 (0.38), residues: 161 loop : 0.61 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 523 HIS 0.007 0.001 HIS A 418 PHE 0.041 0.002 PHE A 564 TYR 0.017 0.001 TYR B 29 ARG 0.008 0.001 ARG C 372 Details of bonding type rmsd link_TRANS : bond 0.00206 ( 2) link_TRANS : angle 1.46809 ( 6) hydrogen bonds : bond 0.04339 ( 526) hydrogen bonds : angle 4.72416 ( 1437) covalent geometry : bond 0.00347 (10363) covalent geometry : angle 0.63279 (13994) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8800 (tptt) cc_final: 0.8566 (tptp) REVERT: A 135 MET cc_start: 0.9340 (mmm) cc_final: 0.9096 (mmm) REVERT: A 305 MET cc_start: 0.9117 (tpp) cc_final: 0.8791 (tpp) REVERT: A 717 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8439 (tp-100) REVERT: C 113 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9112 (tppp) REVERT: C 123 MET cc_start: 0.9345 (mmm) cc_final: 0.9082 (mmm) REVERT: B 36 MET cc_start: 0.8848 (mmt) cc_final: 0.8622 (mmt) REVERT: B 66 ASP cc_start: 0.9199 (p0) cc_final: 0.8967 (p0) REVERT: B 93 PHE cc_start: 0.9447 (m-80) cc_final: 0.8958 (m-80) REVERT: B 110 ARG cc_start: 0.9168 (mtt-85) cc_final: 0.8825 (ttm-80) outliers start: 9 outliers final: 4 residues processed: 87 average time/residue: 0.2594 time to fit residues: 32.0107 Evaluate side-chains 73 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 147 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 5 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 52 optimal weight: 0.0470 chunk 65 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 225 ASN B 8 GLN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.072514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.049038 restraints weight = 31976.378| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.42 r_work: 0.2663 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10365 Z= 0.164 Angle : 0.578 7.181 14000 Z= 0.300 Chirality : 0.043 0.168 1529 Planarity : 0.004 0.051 1791 Dihedral : 8.599 177.651 1397 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.20 % Allowed : 5.17 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1237 helix: 1.17 (0.21), residues: 615 sheet: 0.36 (0.39), residues: 161 loop : 0.65 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.007 0.001 HIS A 418 PHE 0.044 0.002 PHE B 12 TYR 0.012 0.001 TYR B 29 ARG 0.004 0.000 ARG A 41 Details of bonding type rmsd link_TRANS : bond 0.00054 ( 2) link_TRANS : angle 1.10624 ( 6) hydrogen bonds : bond 0.03850 ( 526) hydrogen bonds : angle 4.47070 ( 1437) covalent geometry : bond 0.00378 (10363) covalent geometry : angle 0.57753 (13994) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8849 (tptt) cc_final: 0.8568 (tptp) REVERT: A 135 MET cc_start: 0.9323 (mmm) cc_final: 0.9016 (mmm) REVERT: A 305 MET cc_start: 0.9090 (tpp) cc_final: 0.8847 (tpp) REVERT: A 478 MET cc_start: 0.9410 (mmm) cc_final: 0.9196 (mmm) REVERT: A 717 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8407 (tp-100) REVERT: B 66 ASP cc_start: 0.9167 (p0) cc_final: 0.8909 (p0) REVERT: B 93 PHE cc_start: 0.9485 (m-80) cc_final: 0.8995 (m-80) REVERT: B 110 ARG cc_start: 0.9132 (mtt-85) cc_final: 0.8801 (ttm-80) outliers start: 13 outliers final: 5 residues processed: 81 average time/residue: 0.3258 time to fit residues: 39.3605 Evaluate side-chains 73 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 57 optimal weight: 0.0970 chunk 41 optimal weight: 0.0870 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 0.0000 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 overall best weight: 0.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 HIS A 775 GLN C 225 ASN B 8 GLN B 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.050858 restraints weight = 31296.725| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.43 r_work: 0.2712 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10365 Z= 0.099 Angle : 0.520 8.367 14000 Z= 0.266 Chirality : 0.041 0.165 1529 Planarity : 0.004 0.048 1791 Dihedral : 7.605 151.667 1397 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.29 % Allowed : 5.54 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1237 helix: 1.66 (0.21), residues: 610 sheet: 0.23 (0.38), residues: 160 loop : 0.79 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.042 0.001 PHE B 12 TYR 0.008 0.001 TYR B 141 ARG 0.003 0.000 ARG A 278 Details of bonding type rmsd link_TRANS : bond 0.00133 ( 2) link_TRANS : angle 0.98265 ( 6) hydrogen bonds : bond 0.03165 ( 526) hydrogen bonds : angle 4.21547 ( 1437) covalent geometry : bond 0.00218 (10363) covalent geometry : angle 0.51994 (13994) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8879 (tptt) cc_final: 0.8573 (tppt) REVERT: A 135 MET cc_start: 0.9249 (mmm) cc_final: 0.8994 (tpp) REVERT: A 211 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8732 (t) REVERT: A 212 THR cc_start: 0.9309 (p) cc_final: 0.8984 (p) REVERT: A 594 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: A 717 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8362 (tp-100) REVERT: A 788 MET cc_start: 0.9582 (mmm) cc_final: 0.9369 (tpp) REVERT: C 44 MET cc_start: 0.9190 (mtp) cc_final: 0.8942 (mtm) REVERT: C 123 MET cc_start: 0.9012 (mmm) cc_final: 0.8722 (mmm) REVERT: B 42 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.7117 (t0) REVERT: B 66 ASP cc_start: 0.9203 (p0) cc_final: 0.8917 (p0) REVERT: B 93 PHE cc_start: 0.9484 (m-80) cc_final: 0.8982 (m-80) REVERT: B 110 ARG cc_start: 0.9111 (mtt-85) cc_final: 0.8785 (ttm-80) outliers start: 14 outliers final: 7 residues processed: 86 average time/residue: 0.2201 time to fit residues: 27.9850 Evaluate side-chains 78 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 52 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049233 restraints weight = 31605.328| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.42 r_work: 0.2671 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10365 Z= 0.166 Angle : 0.551 8.895 14000 Z= 0.280 Chirality : 0.041 0.172 1529 Planarity : 0.004 0.048 1791 Dihedral : 7.149 135.229 1397 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.75 % Allowed : 6.37 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1237 helix: 1.72 (0.22), residues: 616 sheet: 0.34 (0.40), residues: 159 loop : 0.61 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.046 0.001 PHE B 12 TYR 0.011 0.001 TYR A 259 ARG 0.002 0.000 ARG A 41 Details of bonding type rmsd link_TRANS : bond 0.00121 ( 2) link_TRANS : angle 0.82661 ( 6) hydrogen bonds : bond 0.03345 ( 526) hydrogen bonds : angle 4.21973 ( 1437) covalent geometry : bond 0.00384 (10363) covalent geometry : angle 0.55073 (13994) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8909 (tptt) cc_final: 0.8586 (tppt) REVERT: A 135 MET cc_start: 0.9225 (mmm) cc_final: 0.8889 (mmm) REVERT: A 211 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9010 (t) REVERT: A 594 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: A 717 GLN cc_start: 0.8705 (tp-100) cc_final: 0.8401 (tp-100) REVERT: C 44 MET cc_start: 0.9166 (mtp) cc_final: 0.8904 (mtm) REVERT: C 123 MET cc_start: 0.9131 (mmm) cc_final: 0.8917 (mmm) REVERT: B 66 ASP cc_start: 0.9197 (p0) cc_final: 0.8899 (p0) REVERT: B 70 PHE cc_start: 0.7151 (t80) cc_final: 0.6699 (t80) REVERT: B 93 PHE cc_start: 0.9484 (m-80) cc_final: 0.8996 (m-80) REVERT: B 110 ARG cc_start: 0.9103 (mtt-85) cc_final: 0.8804 (ttm-80) outliers start: 19 outliers final: 9 residues processed: 84 average time/residue: 0.2490 time to fit residues: 30.3798 Evaluate side-chains 77 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 58 optimal weight: 0.0010 chunk 81 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.049753 restraints weight = 31473.905| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.37 r_work: 0.2689 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10365 Z= 0.127 Angle : 0.527 9.871 14000 Z= 0.268 Chirality : 0.041 0.168 1529 Planarity : 0.004 0.048 1791 Dihedral : 6.680 116.715 1397 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.66 % Allowed : 6.46 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1237 helix: 1.94 (0.22), residues: 609 sheet: 0.34 (0.40), residues: 159 loop : 0.66 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.045 0.001 PHE B 12 TYR 0.009 0.001 TYR A 259 ARG 0.002 0.000 ARG A 41 Details of bonding type rmsd link_TRANS : bond 0.00104 ( 2) link_TRANS : angle 0.83440 ( 6) hydrogen bonds : bond 0.03163 ( 526) hydrogen bonds : angle 4.14206 ( 1437) covalent geometry : bond 0.00295 (10363) covalent geometry : angle 0.52672 (13994) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8930 (tptt) cc_final: 0.8616 (tppt) REVERT: A 135 MET cc_start: 0.9215 (mmm) cc_final: 0.8900 (mmm) REVERT: A 211 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8999 (t) REVERT: A 478 MET cc_start: 0.9469 (mmm) cc_final: 0.9180 (mmp) REVERT: A 594 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: A 717 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8352 (tp-100) REVERT: A 788 MET cc_start: 0.9520 (mmm) cc_final: 0.9283 (tpp) REVERT: C 64 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9166 (tt) REVERT: B 93 PHE cc_start: 0.9494 (m-80) cc_final: 0.9020 (m-80) outliers start: 18 outliers final: 10 residues processed: 85 average time/residue: 0.2297 time to fit residues: 28.2930 Evaluate side-chains 79 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.072247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.048901 restraints weight = 32009.823| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.44 r_work: 0.2659 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10365 Z= 0.168 Angle : 0.552 8.456 14000 Z= 0.280 Chirality : 0.041 0.171 1529 Planarity : 0.004 0.047 1791 Dihedral : 6.556 111.639 1397 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.57 % Allowed : 6.74 % Favored : 91.69 % 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: 1.74 (0.24), residues: 1237 helix: 1.92 (0.22), residues: 612 sheet: 0.31 (0.41), residues: 159 loop : 0.57 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.006 0.001 HIS A 418 PHE 0.049 0.002 PHE B 12 TYR 0.012 0.001 TYR A 259 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd link_TRANS : bond 0.00153 ( 2) link_TRANS : angle 0.78677 ( 6) hydrogen bonds : bond 0.03248 ( 526) hydrogen bonds : angle 4.16661 ( 1437) covalent geometry : bond 0.00392 (10363) covalent geometry : angle 0.55205 (13994) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8954 (tptt) cc_final: 0.8636 (tppt) REVERT: A 211 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.9016 (t) REVERT: A 478 MET cc_start: 0.9455 (mmm) cc_final: 0.9158 (mmp) REVERT: A 594 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: A 717 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8365 (tp-100) REVERT: C 64 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9155 (tt) REVERT: C 123 MET cc_start: 0.9411 (mmm) cc_final: 0.9096 (mmm) REVERT: B 70 PHE cc_start: 0.7248 (t80) cc_final: 0.6957 (t80) REVERT: B 93 PHE cc_start: 0.9496 (m-80) cc_final: 0.9014 (m-80) REVERT: B 120 MET cc_start: 0.6486 (mmt) cc_final: 0.6215 (mmt) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 0.2281 time to fit residues: 27.4345 Evaluate side-chains 81 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 74 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 50 optimal weight: 0.0470 chunk 83 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.072762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049548 restraints weight = 31725.767| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.41 r_work: 0.2683 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10365 Z= 0.127 Angle : 0.551 11.846 14000 Z= 0.277 Chirality : 0.041 0.169 1529 Planarity : 0.003 0.047 1791 Dihedral : 6.461 107.300 1397 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.66 % Allowed : 7.39 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.25), residues: 1237 helix: 1.96 (0.22), residues: 613 sheet: 0.30 (0.41), residues: 159 loop : 0.58 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.005 0.001 HIS A 418 PHE 0.051 0.001 PHE B 12 TYR 0.010 0.001 TYR A 259 ARG 0.004 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00119 ( 2) link_TRANS : angle 0.81053 ( 6) hydrogen bonds : bond 0.03088 ( 526) hydrogen bonds : angle 4.14596 ( 1437) covalent geometry : bond 0.00295 (10363) covalent geometry : angle 0.55075 (13994) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 1.258 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 46 LYS cc_start: 0.8964 (tptt) cc_final: 0.8651 (tppt) REVERT: A 211 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9019 (t) REVERT: A 478 MET cc_start: 0.9417 (mmm) cc_final: 0.9212 (tpp) REVERT: A 594 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: A 717 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8324 (tp-100) REVERT: C 64 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9155 (tt) REVERT: C 167 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8472 (mp0) REVERT: B 93 PHE cc_start: 0.9477 (m-80) cc_final: 0.9006 (m-80) REVERT: B 120 MET cc_start: 0.6612 (mmt) cc_final: 0.6337 (mmt) outliers start: 18 outliers final: 11 residues processed: 86 average time/residue: 0.2355 time to fit residues: 29.6881 Evaluate side-chains 83 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 120 optimal weight: 10.0000 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.049891 restraints weight = 31714.107| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.40 r_work: 0.2687 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10365 Z= 0.116 Angle : 0.549 10.907 14000 Z= 0.277 Chirality : 0.041 0.191 1529 Planarity : 0.003 0.047 1791 Dihedral : 6.320 103.556 1397 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.66 % Allowed : 7.66 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.25), residues: 1237 helix: 1.98 (0.22), residues: 615 sheet: 0.28 (0.41), residues: 159 loop : 0.61 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.005 0.001 HIS A 418 PHE 0.052 0.001 PHE B 12 TYR 0.011 0.001 TYR A 787 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00110 ( 2) link_TRANS : angle 0.80485 ( 6) hydrogen bonds : bond 0.03112 ( 526) hydrogen bonds : angle 4.12901 ( 1437) covalent geometry : bond 0.00268 (10363) covalent geometry : angle 0.54936 (13994) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8938 (tptt) cc_final: 0.8617 (tppt) REVERT: A 211 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9030 (t) REVERT: A 594 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7973 (mp10) REVERT: A 717 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8410 (tp-100) REVERT: C 44 MET cc_start: 0.8985 (mtm) cc_final: 0.8734 (ttm) REVERT: C 64 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9182 (tt) REVERT: C 167 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8517 (mp0) REVERT: B 70 PHE cc_start: 0.7383 (t80) cc_final: 0.7145 (t80) REVERT: B 93 PHE cc_start: 0.9483 (m-80) cc_final: 0.9005 (m-80) REVERT: B 110 ARG cc_start: 0.9078 (mtt-85) cc_final: 0.8799 (ttm-80) REVERT: B 120 MET cc_start: 0.6620 (mmt) cc_final: 0.6364 (mmt) outliers start: 18 outliers final: 12 residues processed: 86 average time/residue: 0.3430 time to fit residues: 42.3553 Evaluate side-chains 86 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 4.9990 chunk 18 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 84 optimal weight: 0.0770 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.073562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.050515 restraints weight = 31708.642| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.44 r_work: 0.2711 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10365 Z= 0.103 Angle : 0.569 12.259 14000 Z= 0.285 Chirality : 0.041 0.223 1529 Planarity : 0.003 0.046 1791 Dihedral : 6.158 97.660 1397 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.48 % Allowed : 7.76 % Favored : 90.77 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1237 helix: 2.10 (0.22), residues: 609 sheet: 0.22 (0.40), residues: 161 loop : 0.68 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS A 418 PHE 0.054 0.001 PHE B 12 TYR 0.008 0.001 TYR C 133 ARG 0.002 0.000 ARG A 41 Details of bonding type rmsd link_TRANS : bond 0.00120 ( 2) link_TRANS : angle 0.81431 ( 6) hydrogen bonds : bond 0.02996 ( 526) hydrogen bonds : angle 4.13811 ( 1437) covalent geometry : bond 0.00234 (10363) covalent geometry : angle 0.56931 (13994) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.9112 (mmm) cc_final: 0.8900 (tpp) REVERT: A 211 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.9000 (t) REVERT: A 511 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8730 (tm-30) REVERT: A 594 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: A 717 GLN cc_start: 0.8781 (tp-100) cc_final: 0.8447 (tp-100) REVERT: C 47 MET cc_start: 0.8008 (ppp) cc_final: 0.7321 (ppp) REVERT: C 64 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9179 (tt) REVERT: C 167 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: B 93 PHE cc_start: 0.9446 (m-80) cc_final: 0.8967 (m-80) REVERT: B 110 ARG cc_start: 0.9099 (mtt-85) cc_final: 0.8826 (ttm-80) REVERT: B 120 MET cc_start: 0.6630 (mmt) cc_final: 0.6368 (mmt) outliers start: 16 outliers final: 12 residues processed: 87 average time/residue: 0.3653 time to fit residues: 47.7444 Evaluate side-chains 85 residues out of total 1094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 594 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 55 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.049406 restraints weight = 31692.748| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.44 r_work: 0.2679 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10365 Z= 0.152 Angle : 0.592 12.015 14000 Z= 0.294 Chirality : 0.041 0.197 1529 Planarity : 0.004 0.046 1791 Dihedral : 6.202 99.931 1397 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.57 % Allowed : 8.13 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1237 helix: 1.97 (0.22), residues: 620 sheet: 0.23 (0.40), residues: 161 loop : 0.66 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.005 0.001 HIS A 418 PHE 0.054 0.001 PHE B 12 TYR 0.011 0.001 TYR A 259 ARG 0.003 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00143 ( 2) link_TRANS : angle 0.75019 ( 6) hydrogen bonds : bond 0.03178 ( 526) hydrogen bonds : angle 4.17578 ( 1437) covalent geometry : bond 0.00354 (10363) covalent geometry : angle 0.59171 (13994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5532.25 seconds wall clock time: 101 minutes 26.74 seconds (6086.74 seconds total)