Starting phenix.real_space_refine on Fri Jun 13 20:09:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q6v_18199/06_2025/8q6v_18199.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q6v_18199/06_2025/8q6v_18199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q6v_18199/06_2025/8q6v_18199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q6v_18199/06_2025/8q6v_18199.map" model { file = "/net/cci-nas-00/data/ceres_data/8q6v_18199/06_2025/8q6v_18199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q6v_18199/06_2025/8q6v_18199.cif" } resolution = 3.23 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 29 5.16 5 C 5100 2.51 5 N 1341 2.21 5 O 1438 1.98 5 H 7497 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15406 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5714 Classifications: {'peptide': 370} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 9691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 9691 Classifications: {'peptide': 651} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 49, 'TRANS': 601} Chain breaks: 6 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 11, 'TYR:plan': 2, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 200 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.17, per 1000 atoms: 0.47 Number of scatterers: 15406 At special positions: 0 Unit cell: (71.724, 86.736, 131.772, 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 29 16.00 Mg 1 11.99 O 1438 8.00 N 1341 7.00 C 5100 6.00 H 7497 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 47.0% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 79 through 92 removed outlier: 4.116A pdb=" N HIS A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.776A pdb=" N GLY A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.881A pdb=" N ILE A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 250 through 270 removed outlier: 3.640A pdb=" N THR A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 255 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 311 through 328 removed outlier: 3.692A pdb=" N GLU A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'B' and resid 4 through 14 removed outlier: 3.940A pdb=" N ARG B 8 " --> pdb=" O PRO B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 63 Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 72 through 92 Processing helix chain 'B' and resid 106 through 128 removed outlier: 3.988A pdb=" N GLN B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.529A pdb=" N THR B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 185 removed outlier: 4.090A pdb=" N ARG B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 203 through 217 Processing helix chain 'B' and resid 235 through 244 removed outlier: 3.934A pdb=" N HIS B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 removed outlier: 3.695A pdb=" N GLU B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 330 Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 373 through 398 removed outlier: 3.991A pdb=" N THR B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY B 389 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASP B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 614 removed outlier: 5.242A pdb=" N THR B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 645 removed outlier: 3.594A pdb=" N TYR B 642 " --> pdb=" O VAL B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.592A pdb=" N PHE B 664 " --> pdb=" O ALA B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 690 Processing helix chain 'B' and resid 691 through 698 removed outlier: 4.438A pdb=" N HIS B 696 " --> pdb=" O ALA B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 708 removed outlier: 3.857A pdb=" N ARG B 703 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU B 705 " --> pdb=" O ILE B 701 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 742 through 752 Processing helix chain 'B' and resid 753 through 757 Processing helix chain 'B' and resid 758 through 763 Processing helix chain 'B' and resid 780 through 789 Processing helix chain 'B' and resid 838 through 842 Processing helix chain 'B' and resid 873 through 882 Processing helix chain 'B' and resid 920 through 928 removed outlier: 3.811A pdb=" N PHE B 925 " --> pdb=" O TYR B 921 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 926 " --> pdb=" O ARG B 922 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 4.803A pdb=" N PHE A 104 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLU A 139 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 101 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLY A 219 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR A 103 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU A 221 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 25 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG A 208 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU A 23 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 177 removed outlier: 6.806A pdb=" N ASN A 44 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS A 224 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 275 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY A 279 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 276 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU A 292 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 290 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE A 280 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.665A pdb=" N HIS B 227 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU B 251 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 229 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS B 228 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN B 49 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TYR B 230 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR B 51 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU B 47 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL B 96 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN B 49 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL B 98 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR B 51 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN B 192 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS B 95 " --> pdb=" O GLN B 192 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 194 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 97 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 193 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 771 " --> pdb=" O TYR B 848 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 723 through 724 343 hydrogen bonds defined for protein. 939 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: 6.14 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 7483 1.12 - 1.30: 1312 1.30 - 1.47: 3183 1.47 - 1.65: 3585 1.65 - 1.82: 44 Bond restraints: 15607 Sorted by residual: bond pdb=" N ALA B 928 " pdb=" H ALA B 928 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N LEU B 182 " pdb=" H LEU B 182 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA B 760 " pdb=" H ALA B 760 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N VAL B 307 " pdb=" H VAL B 307 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ARG B 624 " pdb=" H ARG B 624 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 15602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 24635 2.84 - 5.68: 2725 5.68 - 8.52: 752 8.52 - 11.36: 6 11.36 - 14.21: 14 Bond angle restraints: 28132 Sorted by residual: angle pdb=" C GLY A 133 " pdb=" N GLN A 134 " pdb=" CA GLN A 134 " ideal model delta sigma weight residual 121.75 132.46 -10.71 1.73e+00 3.34e-01 3.84e+01 angle pdb=" C PHE B 600 " pdb=" N GLU B 601 " pdb=" CA GLU B 601 " ideal model delta sigma weight residual 120.58 127.24 -6.66 1.32e+00 5.74e-01 2.55e+01 angle pdb=" OE1 GLN B 913 " pdb=" CD GLN B 913 " pdb=" NE2 GLN B 913 " ideal model delta sigma weight residual 122.60 117.65 4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" CB HIS B 337 " pdb=" CG HIS B 337 " pdb=" CD2 HIS B 337 " ideal model delta sigma weight residual 131.20 124.85 6.35 1.30e+00 5.92e-01 2.38e+01 angle pdb=" N VAL B 96 " pdb=" CA VAL B 96 " pdb=" C VAL B 96 " ideal model delta sigma weight residual 108.42 115.36 -6.94 1.43e+00 4.89e-01 2.36e+01 ... (remaining 28127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6845 17.69 - 35.38: 407 35.38 - 53.07: 105 53.07 - 70.76: 110 70.76 - 88.45: 7 Dihedral angle restraints: 7474 sinusoidal: 3874 harmonic: 3600 Sorted by residual: dihedral pdb=" CA LEU A 353 " pdb=" C LEU A 353 " pdb=" N ARG A 354 " pdb=" CA ARG A 354 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA PRO B 770 " pdb=" C PRO B 770 " pdb=" N VAL B 771 " pdb=" CA VAL B 771 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA THR B 364 " pdb=" C THR B 364 " pdb=" N TYR B 365 " pdb=" CA TYR B 365 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 7471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 735 0.072 - 0.144: 372 0.144 - 0.216: 97 0.216 - 0.288: 14 0.288 - 0.360: 3 Chirality restraints: 1221 Sorted by residual: chirality pdb=" CA HIS B 244 " pdb=" N HIS B 244 " pdb=" C HIS B 244 " pdb=" CB HIS B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA PRO B 836 " pdb=" N PRO B 836 " pdb=" C PRO B 836 " pdb=" CB PRO B 836 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA LYS B 845 " pdb=" N LYS B 845 " pdb=" C LYS B 845 " pdb=" CB LYS B 845 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1218 not shown) Planarity restraints: 2382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 285 " 0.247 2.00e-02 2.50e+03 9.63e-02 2.78e+02 pdb=" CG TYR A 285 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 285 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 285 " -0.092 2.00e-02 2.50e+03 pdb=" CE1 TYR A 285 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR A 285 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 285 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 285 " 0.153 2.00e-02 2.50e+03 pdb=" HD1 TYR A 285 " -0.045 2.00e-02 2.50e+03 pdb=" HD2 TYR A 285 " -0.067 2.00e-02 2.50e+03 pdb=" HE1 TYR A 285 " -0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR A 285 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 803 " 0.144 2.00e-02 2.50e+03 1.35e-01 2.75e+02 pdb=" CD GLN B 803 " -0.049 2.00e-02 2.50e+03 pdb=" OE1 GLN B 803 " -0.088 2.00e-02 2.50e+03 pdb=" NE2 GLN B 803 " -0.122 2.00e-02 2.50e+03 pdb="HE21 GLN B 803 " -0.112 2.00e-02 2.50e+03 pdb="HE22 GLN B 803 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 42 " -0.120 2.00e-02 2.50e+03 1.17e-01 2.04e+02 pdb=" CG ASN A 42 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 42 " 0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN A 42 " 0.117 2.00e-02 2.50e+03 pdb="HD21 ASN A 42 " 0.093 2.00e-02 2.50e+03 pdb="HD22 ASN A 42 " -0.195 2.00e-02 2.50e+03 ... (remaining 2379 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 980 2.20 - 2.80: 27098 2.80 - 3.40: 42155 3.40 - 4.00: 54827 4.00 - 4.60: 80294 Nonbonded interactions: 205354 Sorted by model distance: nonbonded pdb=" HH TYR B 657 " pdb=" OD2 ASP B 724 " model vdw 1.596 2.450 nonbonded pdb=" O ILE A 251 " pdb=" HG1 THR A 254 " model vdw 1.608 2.450 nonbonded pdb=" OD1 ASP A 58 " pdb=" HG SER A 60 " model vdw 1.617 2.450 nonbonded pdb=" OE2 GLU A 23 " pdb=" HG SER A 205 " model vdw 1.621 2.450 nonbonded pdb=" HH TYR B 221 " pdb=" OE1 GLU B 245 " model vdw 1.627 2.450 ... (remaining 205349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.280 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 34.500 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 : 0.012 0.044 8110 Z= 0.699 Angle : 1.713 10.714 11033 Z= 1.155 Chirality : 0.087 0.360 1221 Planarity : 0.015 0.124 1429 Dihedral : 13.171 88.451 2888 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -1.06 (0.25), residues: 1003 helix: -0.80 (0.23), residues: 381 sheet: -0.00 (0.46), residues: 114 loop : -0.67 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.022 TRP B 355 HIS 0.009 0.002 HIS A 338 PHE 0.062 0.011 PHE A 344 TYR 0.215 0.022 TYR A 285 ARG 0.010 0.001 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.16837 ( 343) hydrogen bonds : angle 7.31462 ( 939) covalent geometry : bond 0.01181 ( 8110) covalent geometry : angle 1.71293 (11033) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.249 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.5389 (mtt) cc_final: 0.5123 (mtp) REVERT: B 87 VAL cc_start: 0.9185 (t) cc_final: 0.8704 (t) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.4615 time to fit residues: 97.5042 Evaluate side-chains 90 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN B 192 GLN B 793 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.072266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.057006 restraints weight = 78819.724| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 5.07 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8110 Z= 0.143 Angle : 0.653 6.179 11033 Z= 0.352 Chirality : 0.043 0.161 1221 Planarity : 0.004 0.037 1429 Dihedral : 6.456 70.053 1104 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.00 % Allowed : 7.22 % Favored : 91.78 % 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: -0.10 (0.26), residues: 1003 helix: 0.55 (0.25), residues: 388 sheet: -0.55 (0.41), residues: 128 loop : -0.32 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 291 HIS 0.004 0.001 HIS A 199 PHE 0.019 0.002 PHE A 344 TYR 0.024 0.002 TYR A 285 ARG 0.004 0.001 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.05345 ( 343) hydrogen bonds : angle 5.55161 ( 939) covalent geometry : bond 0.00314 ( 8110) covalent geometry : angle 0.65334 (11033) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 1.288 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: A 127 ARG cc_start: 0.8269 (mtt90) cc_final: 0.8021 (mtt90) REVERT: A 267 GLN cc_start: 0.9394 (tt0) cc_final: 0.8764 (tp-100) REVERT: B 54 MET cc_start: 0.9567 (tpt) cc_final: 0.9348 (tpp) REVERT: B 349 ASP cc_start: 0.9416 (p0) cc_final: 0.9193 (p0) REVERT: B 640 MET cc_start: 0.8969 (ttm) cc_final: 0.8568 (ttp) REVERT: B 842 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9086 (mm) REVERT: B 912 THR cc_start: 0.9374 (m) cc_final: 0.8875 (t) outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.4762 time to fit residues: 66.8028 Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 268 CYS Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 842 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 63 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.070575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.055046 restraints weight = 80685.742| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 5.05 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8110 Z= 0.199 Angle : 0.591 5.352 11033 Z= 0.318 Chirality : 0.041 0.158 1221 Planarity : 0.004 0.046 1429 Dihedral : 5.835 69.726 1104 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.87 % Allowed : 8.72 % Favored : 90.41 % 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 (0.26), residues: 1003 helix: 1.03 (0.26), residues: 389 sheet: -0.70 (0.40), residues: 129 loop : -0.34 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 291 HIS 0.004 0.001 HIS B 396 PHE 0.023 0.001 PHE A 131 TYR 0.023 0.002 TYR A 285 ARG 0.005 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 343) hydrogen bonds : angle 5.16255 ( 939) covalent geometry : bond 0.00433 ( 8110) covalent geometry : angle 0.59114 (11033) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 1.270 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: A 127 ARG cc_start: 0.8295 (mtt90) cc_final: 0.7863 (mtt90) REVERT: A 267 GLN cc_start: 0.9431 (tt0) cc_final: 0.8890 (tp-100) REVERT: B 76 MET cc_start: 0.8805 (mtp) cc_final: 0.8476 (mtt) REVERT: B 706 MET cc_start: 0.8543 (mtp) cc_final: 0.8198 (mtp) REVERT: B 912 THR cc_start: 0.9434 (m) cc_final: 0.9019 (t) outliers start: 7 outliers final: 6 residues processed: 84 average time/residue: 0.4248 time to fit residues: 50.8264 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 96 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.069782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.054411 restraints weight = 81371.682| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 5.04 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8110 Z= 0.212 Angle : 0.573 4.894 11033 Z= 0.306 Chirality : 0.041 0.151 1221 Planarity : 0.004 0.035 1429 Dihedral : 5.611 70.719 1104 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.25 % Allowed : 9.96 % Favored : 88.79 % 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: 0.20 (0.27), residues: 1003 helix: 1.27 (0.26), residues: 389 sheet: -0.88 (0.41), residues: 128 loop : -0.44 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 291 HIS 0.004 0.001 HIS A 338 PHE 0.011 0.001 PHE A 131 TYR 0.021 0.002 TYR A 285 ARG 0.005 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 343) hydrogen bonds : angle 5.09529 ( 939) covalent geometry : bond 0.00457 ( 8110) covalent geometry : angle 0.57256 (11033) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.790 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: A 127 ARG cc_start: 0.8315 (mtt90) cc_final: 0.8097 (mtt90) REVERT: A 278 TYR cc_start: 0.8602 (m-80) cc_final: 0.8288 (m-80) REVERT: B 76 MET cc_start: 0.8849 (mtp) cc_final: 0.8519 (mtt) REVERT: B 640 MET cc_start: 0.9066 (ttt) cc_final: 0.8726 (ttp) REVERT: B 912 THR cc_start: 0.9436 (m) cc_final: 0.9062 (t) outliers start: 10 outliers final: 9 residues processed: 78 average time/residue: 0.4189 time to fit residues: 47.6482 Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 771 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.068505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053357 restraints weight = 83460.168| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.97 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 8110 Z= 0.245 Angle : 0.587 4.711 11033 Z= 0.314 Chirality : 0.041 0.161 1221 Planarity : 0.004 0.043 1429 Dihedral : 5.571 73.338 1104 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.87 % Allowed : 10.34 % Favored : 87.80 % 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: 0.03 (0.26), residues: 1003 helix: 1.24 (0.26), residues: 390 sheet: -1.05 (0.41), residues: 128 loop : -0.63 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 306 HIS 0.005 0.001 HIS B 383 PHE 0.027 0.001 PHE A 131 TYR 0.022 0.002 TYR A 285 ARG 0.007 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 343) hydrogen bonds : angle 5.08549 ( 939) covalent geometry : bond 0.00525 ( 8110) covalent geometry : angle 0.58719 (11033) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.243 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: A 127 ARG cc_start: 0.8298 (mtt90) cc_final: 0.8053 (mtt90) REVERT: A 278 TYR cc_start: 0.8592 (m-80) cc_final: 0.8285 (m-10) REVERT: B 76 MET cc_start: 0.8898 (mtp) cc_final: 0.8554 (mtt) REVERT: B 706 MET cc_start: 0.8376 (mtp) cc_final: 0.7826 (mmm) REVERT: B 717 TYR cc_start: 0.8473 (m-10) cc_final: 0.8217 (m-80) REVERT: B 912 THR cc_start: 0.9426 (m) cc_final: 0.9063 (t) outliers start: 15 outliers final: 14 residues processed: 81 average time/residue: 0.3896 time to fit residues: 45.3098 Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 771 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 100 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 685 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.069081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053927 restraints weight = 81775.120| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.96 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8110 Z= 0.186 Angle : 0.546 4.581 11033 Z= 0.288 Chirality : 0.040 0.151 1221 Planarity : 0.004 0.037 1429 Dihedral : 5.419 74.115 1104 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.74 % Allowed : 10.83 % Favored : 87.42 % 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: 0.21 (0.27), residues: 1003 helix: 1.48 (0.26), residues: 391 sheet: -1.09 (0.41), residues: 128 loop : -0.58 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 291 HIS 0.003 0.001 HIS A 338 PHE 0.011 0.001 PHE A 131 TYR 0.019 0.001 TYR A 285 ARG 0.006 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 343) hydrogen bonds : angle 4.92552 ( 939) covalent geometry : bond 0.00401 ( 8110) covalent geometry : angle 0.54623 (11033) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.062 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: A 278 TYR cc_start: 0.8575 (m-80) cc_final: 0.8271 (m-10) REVERT: A 352 HIS cc_start: 0.9314 (m90) cc_final: 0.9105 (p90) REVERT: B 76 MET cc_start: 0.8871 (mtp) cc_final: 0.8506 (mtt) REVERT: B 640 MET cc_start: 0.9050 (ttt) cc_final: 0.8727 (ttp) REVERT: B 706 MET cc_start: 0.8306 (mtp) cc_final: 0.7962 (mtp) REVERT: B 912 THR cc_start: 0.9423 (m) cc_final: 0.9052 (t) outliers start: 14 outliers final: 12 residues processed: 83 average time/residue: 0.3878 time to fit residues: 46.9515 Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 771 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.070817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055552 restraints weight = 80239.321| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 5.03 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8110 Z= 0.098 Angle : 0.509 5.440 11033 Z= 0.262 Chirality : 0.040 0.153 1221 Planarity : 0.004 0.036 1429 Dihedral : 5.127 70.514 1104 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.75 % Allowed : 12.08 % Favored : 87.17 % 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: 0.63 (0.27), residues: 1003 helix: 1.88 (0.27), residues: 392 sheet: -0.96 (0.41), residues: 130 loop : -0.36 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 291 HIS 0.002 0.000 HIS B 383 PHE 0.016 0.001 PHE A 131 TYR 0.014 0.001 TYR A 285 ARG 0.003 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 343) hydrogen bonds : angle 4.66967 ( 939) covalent geometry : bond 0.00227 ( 8110) covalent geometry : angle 0.50872 (11033) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 1.195 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: A 278 TYR cc_start: 0.8505 (m-80) cc_final: 0.8270 (m-80) REVERT: B 76 MET cc_start: 0.8858 (mtp) cc_final: 0.8526 (mtt) REVERT: B 349 ASP cc_start: 0.9374 (p0) cc_final: 0.9065 (p0) REVERT: B 912 THR cc_start: 0.9418 (m) cc_final: 0.9023 (t) outliers start: 6 outliers final: 6 residues processed: 80 average time/residue: 0.3799 time to fit residues: 43.8512 Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.070479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.055083 restraints weight = 81083.048| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 5.07 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8110 Z= 0.132 Angle : 0.515 5.212 11033 Z= 0.266 Chirality : 0.040 0.144 1221 Planarity : 0.004 0.044 1429 Dihedral : 5.016 67.895 1104 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.87 % Allowed : 12.20 % Favored : 86.92 % 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: 0.63 (0.27), residues: 1003 helix: 1.95 (0.27), residues: 392 sheet: -1.01 (0.40), residues: 130 loop : -0.42 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 355 HIS 0.002 0.001 HIS A 338 PHE 0.015 0.001 PHE A 348 TYR 0.018 0.001 TYR B 717 ARG 0.004 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 343) hydrogen bonds : angle 4.66209 ( 939) covalent geometry : bond 0.00295 ( 8110) covalent geometry : angle 0.51453 (11033) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 1.577 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: A 278 TYR cc_start: 0.8579 (m-80) cc_final: 0.8362 (m-80) REVERT: B 76 MET cc_start: 0.8911 (mtp) cc_final: 0.8570 (mtt) REVERT: B 349 ASP cc_start: 0.9357 (p0) cc_final: 0.9055 (p0) REVERT: B 640 MET cc_start: 0.9015 (ttt) cc_final: 0.8704 (ttp) REVERT: B 912 THR cc_start: 0.9420 (m) cc_final: 0.9034 (t) outliers start: 7 outliers final: 7 residues processed: 76 average time/residue: 0.4122 time to fit residues: 45.2370 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.070448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.055072 restraints weight = 81325.728| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 5.07 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8110 Z= 0.126 Angle : 0.509 5.326 11033 Z= 0.263 Chirality : 0.040 0.144 1221 Planarity : 0.004 0.035 1429 Dihedral : 4.905 64.359 1104 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.87 % Allowed : 12.58 % Favored : 86.55 % 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: 0.68 (0.27), residues: 1003 helix: 2.03 (0.27), residues: 392 sheet: -1.07 (0.41), residues: 131 loop : -0.39 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 291 HIS 0.002 0.001 HIS A 338 PHE 0.012 0.001 PHE A 131 TYR 0.014 0.001 TYR A 285 ARG 0.004 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 343) hydrogen bonds : angle 4.59523 ( 939) covalent geometry : bond 0.00282 ( 8110) covalent geometry : angle 0.50889 (11033) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 1.311 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: A 278 TYR cc_start: 0.8577 (m-80) cc_final: 0.8362 (m-80) REVERT: B 76 MET cc_start: 0.8893 (mtp) cc_final: 0.8542 (mtt) REVERT: B 349 ASP cc_start: 0.9354 (p0) cc_final: 0.9072 (p0) REVERT: B 780 ASN cc_start: 0.9420 (m-40) cc_final: 0.9081 (t0) REVERT: B 912 THR cc_start: 0.9421 (m) cc_final: 0.9034 (t) outliers start: 7 outliers final: 7 residues processed: 75 average time/residue: 0.4316 time to fit residues: 47.0356 Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.069683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.054381 restraints weight = 82277.660| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 5.06 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8110 Z= 0.171 Angle : 0.526 5.047 11033 Z= 0.275 Chirality : 0.040 0.147 1221 Planarity : 0.004 0.036 1429 Dihedral : 4.898 61.872 1104 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.75 % Allowed : 12.95 % Favored : 86.30 % 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: 0.59 (0.27), residues: 1003 helix: 1.97 (0.27), residues: 392 sheet: -1.09 (0.41), residues: 130 loop : -0.47 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 382 HIS 0.003 0.001 HIS A 338 PHE 0.013 0.001 PHE A 348 TYR 0.016 0.001 TYR A 285 ARG 0.005 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 343) hydrogen bonds : angle 4.65739 ( 939) covalent geometry : bond 0.00376 ( 8110) covalent geometry : angle 0.52620 (11033) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue THR 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue LEU 322 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue ILE 331 is missing expected H atoms. Skipping. Residue LEU 368 is missing expected H atoms. Skipping. Residue LEU 386 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue VAL 3 is missing expected H atoms. Skipping. Residue LEU 22 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 363 is missing expected H atoms. Skipping. Residue VAL 597 is missing expected H atoms. Skipping. Residue LYS 598 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue MET 725 is missing expected H atoms. Skipping. Residue LYS 728 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue MET 730 is missing expected H atoms. Skipping. Residue LEU 756 is missing expected H atoms. Skipping. Residue LEU 757 is missing expected H atoms. Skipping. Residue LYS 786 is missing expected H atoms. Skipping. Residue LYS 791 is missing expected H atoms. Skipping. Residue LYS 801 is missing expected H atoms. Skipping. Residue LEU 822 is missing expected H atoms. Skipping. Residue LYS 825 is missing expected H atoms. Skipping. Residue ILE 826 is missing expected H atoms. Skipping. Residue LEU 838 is missing expected H atoms. Skipping. Residue THR 840 is missing expected H atoms. Skipping. Residue TYR 875 is missing expected H atoms. Skipping. Residue SER 879 is missing expected H atoms. Skipping. Residue MET 881 is missing expected H atoms. Skipping. Residue TYR 882 is missing expected H atoms. Skipping. Residue ILE 903 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 1.266 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 278 TYR cc_start: 0.8615 (m-80) cc_final: 0.8401 (m-80) REVERT: A 354 ARG cc_start: 0.7629 (ttp80) cc_final: 0.7061 (ttp80) REVERT: B 76 MET cc_start: 0.8895 (mtp) cc_final: 0.8531 (mtt) REVERT: B 349 ASP cc_start: 0.9361 (p0) cc_final: 0.9157 (p0) REVERT: B 640 MET cc_start: 0.9039 (ttt) cc_final: 0.8731 (ttp) REVERT: B 706 MET cc_start: 0.8202 (mtp) cc_final: 0.7988 (mmm) REVERT: B 780 ASN cc_start: 0.9432 (m-40) cc_final: 0.9079 (t0) REVERT: B 912 THR cc_start: 0.9418 (m) cc_final: 0.9039 (t) outliers start: 6 outliers final: 6 residues processed: 74 average time/residue: 0.4853 time to fit residues: 50.5368 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 PHE Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 638 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.071415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055971 restraints weight = 80445.647| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 5.10 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8110 Z= 0.090 Angle : 0.497 5.529 11033 Z= 0.252 Chirality : 0.040 0.144 1221 Planarity : 0.004 0.035 1429 Dihedral : 4.617 54.599 1104 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.75 % Allowed : 13.08 % Favored : 86.18 % 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: 0.90 (0.28), residues: 1003 helix: 2.22 (0.27), residues: 392 sheet: -1.00 (0.41), residues: 131 loop : -0.26 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 382 HIS 0.001 0.000 HIS A 352 PHE 0.012 0.001 PHE A 131 TYR 0.011 0.001 TYR A 285 ARG 0.002 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 343) hydrogen bonds : angle 4.43869 ( 939) covalent geometry : bond 0.00210 ( 8110) covalent geometry : angle 0.49665 (11033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5484.49 seconds wall clock time: 98 minutes 30.89 seconds (5910.89 seconds total)