Starting phenix.real_space_refine on Wed Mar 4 14:43:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5u_33625/03_2026/7y5u_33625.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5u_33625/03_2026/7y5u_33625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y5u_33625/03_2026/7y5u_33625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5u_33625/03_2026/7y5u_33625.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y5u_33625/03_2026/7y5u_33625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5u_33625/03_2026/7y5u_33625.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Anisotropic ADP refinement not supported. Converting 6842 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 5599 2.51 5 N 1553 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8865 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1256 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ARG:plan': 5, 'TRP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 123 Chain: "D" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 898 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 642 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3165 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 378} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2904 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 1.73, per 1000 atoms: 0.20 Number of scatterers: 8865 At special positions: 0 Unit cell: (81, 98, 133, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1675 8.00 N 1553 7.00 C 5599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 353.7 milliseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 16 sheets defined 20.5% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 652 through 674 Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 63 through 79 removed outlier: 3.836A pdb=" N PHE D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 114 Processing helix chain 'D' and resid 120 through 132 Processing helix chain 'E' and resid 25 through 29 removed outlier: 4.361A pdb=" N ILE E 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 41 Processing helix chain 'E' and resid 49 through 76 removed outlier: 4.450A pdb=" N GLU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'C' and resid 12 through 32 Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.534A pdb=" N PHE C 93 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.199A pdb=" N TYR C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 410' Processing sheet with id=AA1, first strand: chain 'A' and resid 570 through 572 removed outlier: 6.360A pdb=" N LEU A 559 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N THR C 37 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN A 561 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ALA C 39 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 684 through 686 removed outlier: 3.807A pdb=" N TYR B 340 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG B 316 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL B 296 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL B 318 " --> pdb=" O CYS B 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 710 through 711 removed outlier: 5.742A pdb=" N TYR B 267 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE B 269 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU B 250 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.560A pdb=" N ILE D 119 " --> pdb=" O ARG E 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 54 removed outlier: 7.632A pdb=" N LEU C 50 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL C 67 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP C 52 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG C 65 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN C 77 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN C 122 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU C 79 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS C 120 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C 81 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 130 through 133 removed outlier: 10.266A pdb=" N ARG C 131 " --> pdb=" O CYS C 138 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N CYS C 138 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET C 133 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG C 172 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 182 through 185 removed outlier: 4.105A pdb=" N GLY C 182 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 230 through 235 Processing sheet with id=AA9, first strand: chain 'C' and resid 276 through 281 removed outlier: 6.862A pdb=" N GLY C 292 " --> pdb=" O ASN C 277 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 279 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA C 290 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE C 288 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS C 311 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 320 through 325 removed outlier: 5.722A pdb=" N ASP C 346 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU C 366 " --> pdb=" O ASP C 346 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5 removed outlier: 6.957A pdb=" N PHE B 360 " --> pdb=" O TRP B 354 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP B 354 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 362 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE B 352 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER B 364 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.721A pdb=" N ALA B 35 " --> pdb=" O TYR B 17 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU B 19 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 33 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 41 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN B 61 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 43 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 47 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE B 55 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.997A pdb=" N GLY B 84 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 94 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL B 121 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 132 through 137 removed outlier: 6.436A pdb=" N ASP B 157 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS B 163 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 174 through 179 removed outlier: 4.217A pdb=" N GLY B 176 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER B 199 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 205 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 211 through 213 315 hydrogen bonds defined for protein. 855 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: 1.42 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2880 1.34 - 1.46: 1276 1.46 - 1.57: 4851 1.57 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 9064 Sorted by residual: bond pdb=" CA ASP B 150 " pdb=" C ASP B 150 " ideal model delta sigma weight residual 1.522 1.576 -0.054 1.72e-02 3.38e+03 9.88e+00 bond pdb=" N ASN B 12 " pdb=" CA ASN B 12 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.89e+00 bond pdb=" CA PHE E 100 " pdb=" CB PHE E 100 " ideal model delta sigma weight residual 1.528 1.510 0.019 1.39e-02 5.18e+03 1.82e+00 bond pdb=" CA PHE E 100 " pdb=" C PHE E 100 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.31e-02 5.83e+03 1.75e+00 bond pdb=" CB LYS B 286 " pdb=" CG LYS B 286 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.68e+00 ... (remaining 9059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 12111 2.07 - 4.15: 157 4.15 - 6.22: 27 6.22 - 8.29: 4 8.29 - 10.36: 3 Bond angle restraints: 12302 Sorted by residual: angle pdb=" N GLU D 97 " pdb=" CA GLU D 97 " pdb=" CB GLU D 97 " ideal model delta sigma weight residual 110.16 116.20 -6.04 1.48e+00 4.57e-01 1.66e+01 angle pdb=" CB LYS B 286 " pdb=" CG LYS B 286 " pdb=" CD LYS B 286 " ideal model delta sigma weight residual 111.30 120.13 -8.83 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA MET C 133 " pdb=" CB MET C 133 " pdb=" CG MET C 133 " ideal model delta sigma weight residual 114.10 121.36 -7.26 2.00e+00 2.50e-01 1.32e+01 angle pdb=" C HIS B 347 " pdb=" CA HIS B 347 " pdb=" CB HIS B 347 " ideal model delta sigma weight residual 110.45 116.39 -5.94 1.73e+00 3.34e-01 1.18e+01 angle pdb=" C SER A 614 " pdb=" N HIS A 615 " pdb=" CA HIS A 615 " ideal model delta sigma weight residual 122.32 128.01 -5.69 1.76e+00 3.23e-01 1.05e+01 ... (remaining 12297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 4968 16.57 - 33.13: 359 33.13 - 49.70: 72 49.70 - 66.26: 8 66.26 - 82.83: 7 Dihedral angle restraints: 5414 sinusoidal: 2107 harmonic: 3307 Sorted by residual: dihedral pdb=" CA MET C 133 " pdb=" C MET C 133 " pdb=" N PRO C 134 " pdb=" CA PRO C 134 " ideal model delta harmonic sigma weight residual 180.00 -151.78 -28.22 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA PHE B 236 " pdb=" C PHE B 236 " pdb=" N PHE B 237 " pdb=" CA PHE B 237 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP C 52 " pdb=" CB ASP C 52 " pdb=" CG ASP C 52 " pdb=" OD1 ASP C 52 " ideal model delta sinusoidal sigma weight residual -30.00 -89.73 59.73 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 5411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 911 0.037 - 0.073: 299 0.073 - 0.110: 109 0.110 - 0.147: 43 0.147 - 0.183: 2 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CA THR C 28 " pdb=" N THR C 28 " pdb=" C THR C 28 " pdb=" CB THR C 28 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA GLU D 97 " pdb=" N GLU D 97 " pdb=" C GLU D 97 " pdb=" CB GLU D 97 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA LEU D 65 " pdb=" N LEU D 65 " pdb=" C LEU D 65 " pdb=" CB LEU D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1361 not shown) Planarity restraints: 1594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 615 " 0.020 2.00e-02 2.50e+03 2.55e-02 9.72e+00 pdb=" CG HIS A 615 " -0.054 2.00e-02 2.50e+03 pdb=" ND1 HIS A 615 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS A 615 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS A 615 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A 615 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 347 " 0.017 2.00e-02 2.50e+03 2.00e-02 5.97e+00 pdb=" CG HIS B 347 " -0.043 2.00e-02 2.50e+03 pdb=" ND1 HIS B 347 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS B 347 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 HIS B 347 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 347 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 283 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO B 284 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " 0.031 5.00e-02 4.00e+02 ... (remaining 1591 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 850 2.75 - 3.29: 8672 3.29 - 3.82: 15009 3.82 - 4.36: 17059 4.36 - 4.90: 29554 Nonbonded interactions: 71144 Sorted by model distance: nonbonded pdb=" OG1 THR C 72 " pdb=" O GLU C 75 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP B 180 " pdb=" NH2 ARG B 271 " model vdw 2.239 3.120 nonbonded pdb=" OG SER C 44 " pdb=" O THR C 46 " model vdw 2.260 3.040 nonbonded pdb=" O LEU D 48 " pdb=" OH TYR B 369 " model vdw 2.266 3.040 nonbonded pdb=" NH1 ARG B 73 " pdb=" O ILE B 135 " model vdw 2.284 3.120 ... (remaining 71139 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 9.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 0.002 0.056 9064 Z= 0.123 Angle : 0.622 10.363 12302 Z= 0.323 Chirality : 0.044 0.183 1364 Planarity : 0.004 0.056 1594 Dihedral : 12.266 82.829 3268 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.25), residues: 1121 helix: 2.60 (0.36), residues: 202 sheet: -0.03 (0.31), residues: 299 loop : -1.15 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 129 TYR 0.017 0.001 TYR C 98 PHE 0.018 0.001 PHE B 269 TRP 0.025 0.001 TRP C 345 HIS 0.032 0.002 HIS A 615 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9064) covalent geometry : angle 0.62186 (12302) hydrogen bonds : bond 0.09348 ( 315) hydrogen bonds : angle 5.97794 ( 855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 171 LEU cc_start: 0.5853 (mt) cc_final: 0.5419 (mp) REVERT: C 333 LEU cc_start: 0.7613 (tp) cc_final: 0.7387 (tt) REVERT: C 391 CYS cc_start: 0.7292 (t) cc_final: 0.7060 (t) outliers start: 1 outliers final: 1 residues processed: 210 average time/residue: 0.0906 time to fit residues: 25.9502 Evaluate side-chains 127 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN B 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.073846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.055661 restraints weight = 36958.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.057823 restraints weight = 21612.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059265 restraints weight = 15367.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.060281 restraints weight = 12309.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061010 restraints weight = 10556.771| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.078 9064 Z= 0.464 Angle : 0.885 10.983 12302 Z= 0.456 Chirality : 0.051 0.325 1364 Planarity : 0.006 0.047 1594 Dihedral : 5.060 25.721 1222 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.88 % Allowed : 13.03 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.25), residues: 1121 helix: 1.81 (0.36), residues: 201 sheet: -0.39 (0.30), residues: 299 loop : -1.20 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 316 TYR 0.015 0.002 TYR B 133 PHE 0.020 0.003 PHE B 319 TRP 0.027 0.003 TRP A 690 HIS 0.010 0.002 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00962 ( 9064) covalent geometry : angle 0.88457 (12302) hydrogen bonds : bond 0.04356 ( 315) hydrogen bonds : angle 6.09491 ( 855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 94 GLU cc_start: 0.9382 (tp30) cc_final: 0.9109 (mm-30) REVERT: D 97 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: D 120 MET cc_start: 0.8069 (mmm) cc_final: 0.7781 (mmm) REVERT: E 74 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8205 (tm-30) REVERT: E 78 ARG cc_start: 0.8931 (mtp-110) cc_final: 0.8360 (mtm180) REVERT: E 97 LEU cc_start: 0.9547 (tp) cc_final: 0.9256 (tt) REVERT: C 253 MET cc_start: 0.8160 (mmm) cc_final: 0.7619 (mmm) REVERT: C 399 MET cc_start: 0.8673 (tmm) cc_final: 0.7991 (tmm) REVERT: B 1 MET cc_start: 0.8438 (ttp) cc_final: 0.8236 (ttp) REVERT: B 14 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8653 (mm-30) REVERT: B 227 MET cc_start: 0.8945 (ptp) cc_final: 0.8130 (pmm) REVERT: B 236 PHE cc_start: 0.9422 (m-80) cc_final: 0.8453 (t80) REVERT: B 385 LYS cc_start: 0.9210 (mmtt) cc_final: 0.8814 (mmmt) outliers start: 27 outliers final: 20 residues processed: 146 average time/residue: 0.0958 time to fit residues: 19.4116 Evaluate side-chains 129 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 688 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.0000 chunk 40 optimal weight: 6.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.076952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.058600 restraints weight = 36005.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060949 restraints weight = 20002.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.062594 restraints weight = 13831.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.063734 restraints weight = 10857.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.064506 restraints weight = 9169.593| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9064 Z= 0.139 Angle : 0.645 11.565 12302 Z= 0.322 Chirality : 0.046 0.197 1364 Planarity : 0.004 0.039 1594 Dihedral : 4.505 23.832 1220 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.92 % Allowed : 14.74 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.25), residues: 1121 helix: 2.35 (0.37), residues: 201 sheet: -0.24 (0.31), residues: 286 loop : -1.17 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 238 TYR 0.013 0.001 TYR B 330 PHE 0.018 0.002 PHE A 707 TRP 0.013 0.002 TRP B 93 HIS 0.004 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9064) covalent geometry : angle 0.64457 (12302) hydrogen bonds : bond 0.03165 ( 315) hydrogen bonds : angle 5.33503 ( 855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 50 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8909 (tm-30) REVERT: D 67 PHE cc_start: 0.9460 (t80) cc_final: 0.9209 (t80) REVERT: D 93 GLN cc_start: 0.8976 (mm110) cc_final: 0.8565 (mm110) REVERT: D 94 GLU cc_start: 0.9366 (tp30) cc_final: 0.8805 (mm-30) REVERT: D 97 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8267 (pm20) REVERT: E 40 ARG cc_start: 0.9319 (ttm110) cc_final: 0.9091 (ttm110) REVERT: E 52 GLU cc_start: 0.8719 (pp20) cc_final: 0.8489 (pp20) REVERT: E 63 GLU cc_start: 0.9317 (mt-10) cc_final: 0.8964 (mt-10) REVERT: E 67 ARG cc_start: 0.8810 (ttm110) cc_final: 0.8524 (ttp-110) REVERT: E 71 THR cc_start: 0.8474 (m) cc_final: 0.8065 (p) REVERT: E 74 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8217 (tm-30) REVERT: E 78 ARG cc_start: 0.8874 (mtp-110) cc_final: 0.8459 (mtm180) REVERT: E 88 TYR cc_start: 0.9293 (m-10) cc_final: 0.9043 (m-10) REVERT: E 92 ARG cc_start: 0.9160 (ttt90) cc_final: 0.8947 (ttm-80) REVERT: E 95 ARG cc_start: 0.9430 (ttm110) cc_final: 0.8825 (ttm110) REVERT: E 97 LEU cc_start: 0.9450 (tp) cc_final: 0.9181 (tt) REVERT: C 253 MET cc_start: 0.8259 (mmm) cc_final: 0.7688 (mmm) REVERT: C 399 MET cc_start: 0.8748 (tmm) cc_final: 0.8177 (tmm) REVERT: B 14 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8703 (mm-30) REVERT: B 131 ASP cc_start: 0.8648 (m-30) cc_final: 0.8173 (m-30) REVERT: B 154 ILE cc_start: 0.8394 (tt) cc_final: 0.7829 (mt) REVERT: B 227 MET cc_start: 0.8888 (ptp) cc_final: 0.8257 (pmm) REVERT: B 236 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8434 (t80) REVERT: B 385 LYS cc_start: 0.9218 (mmtt) cc_final: 0.8792 (mmmt) outliers start: 18 outliers final: 10 residues processed: 150 average time/residue: 0.0970 time to fit residues: 20.1017 Evaluate side-chains 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 353 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 0.0060 chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 HIS C 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.076511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.058361 restraints weight = 36054.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060701 restraints weight = 20017.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.062322 restraints weight = 13788.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063432 restraints weight = 10780.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.064185 restraints weight = 9091.306| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9064 Z= 0.147 Angle : 0.625 12.127 12302 Z= 0.309 Chirality : 0.045 0.197 1364 Planarity : 0.004 0.038 1594 Dihedral : 4.312 23.094 1220 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.03 % Allowed : 16.56 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.25), residues: 1121 helix: 2.19 (0.37), residues: 208 sheet: -0.24 (0.31), residues: 283 loop : -1.15 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 131 TYR 0.013 0.001 TYR B 330 PHE 0.015 0.001 PHE A 707 TRP 0.012 0.002 TRP B 93 HIS 0.004 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9064) covalent geometry : angle 0.62508 (12302) hydrogen bonds : bond 0.03035 ( 315) hydrogen bonds : angle 5.20798 ( 855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: D 93 GLN cc_start: 0.8947 (mm110) cc_final: 0.8672 (tp40) REVERT: D 94 GLU cc_start: 0.9372 (tp30) cc_final: 0.8821 (mm-30) REVERT: D 97 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: D 120 MET cc_start: 0.8078 (mmm) cc_final: 0.7842 (mmm) REVERT: E 40 ARG cc_start: 0.9352 (ttm110) cc_final: 0.9028 (ttm110) REVERT: E 52 GLU cc_start: 0.8761 (pp20) cc_final: 0.7982 (pp20) REVERT: E 53 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8826 (mm-30) REVERT: E 60 VAL cc_start: 0.9493 (t) cc_final: 0.9258 (p) REVERT: E 63 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8971 (mt-10) REVERT: E 67 ARG cc_start: 0.8820 (ttm110) cc_final: 0.8479 (ttp-110) REVERT: E 71 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8059 (p) REVERT: E 74 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8174 (tm-30) REVERT: E 78 ARG cc_start: 0.8927 (mtp-110) cc_final: 0.8518 (mtm180) REVERT: E 88 TYR cc_start: 0.9197 (m-10) cc_final: 0.8976 (m-10) REVERT: E 95 ARG cc_start: 0.9389 (ttm110) cc_final: 0.8761 (ttm110) REVERT: E 97 LEU cc_start: 0.9449 (tp) cc_final: 0.9195 (tt) REVERT: C 131 ARG cc_start: 0.9067 (mmt90) cc_final: 0.8227 (mmp80) REVERT: C 253 MET cc_start: 0.8325 (mmm) cc_final: 0.7685 (mmm) REVERT: C 399 MET cc_start: 0.8858 (tmm) cc_final: 0.8061 (tmm) REVERT: B 14 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8704 (mm-30) REVERT: B 131 ASP cc_start: 0.8633 (m-30) cc_final: 0.8045 (m-30) REVERT: B 227 MET cc_start: 0.8977 (ptp) cc_final: 0.8261 (pmm) REVERT: B 236 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8445 (t80) REVERT: B 385 LYS cc_start: 0.9241 (mmtt) cc_final: 0.8813 (mmmt) outliers start: 19 outliers final: 11 residues processed: 138 average time/residue: 0.1019 time to fit residues: 19.3365 Evaluate side-chains 135 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 353 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN D 93 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.075461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.057192 restraints weight = 36475.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.059468 restraints weight = 20640.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.061026 restraints weight = 14414.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.062127 restraints weight = 11382.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.062836 restraints weight = 9663.158| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9064 Z= 0.194 Angle : 0.650 11.671 12302 Z= 0.320 Chirality : 0.045 0.201 1364 Planarity : 0.004 0.037 1594 Dihedral : 4.353 22.820 1220 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.56 % Allowed : 18.06 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.25), residues: 1121 helix: 2.25 (0.37), residues: 208 sheet: -0.31 (0.31), residues: 278 loop : -1.09 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 238 TYR 0.014 0.001 TYR B 330 PHE 0.028 0.002 PHE D 67 TRP 0.013 0.002 TRP B 93 HIS 0.004 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 9064) covalent geometry : angle 0.65008 (12302) hydrogen bonds : bond 0.03068 ( 315) hydrogen bonds : angle 5.26514 ( 855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 94 GLU cc_start: 0.9363 (tp30) cc_final: 0.8850 (mm-30) REVERT: D 120 MET cc_start: 0.8188 (mmm) cc_final: 0.7895 (mmm) REVERT: E 40 ARG cc_start: 0.9390 (ttm110) cc_final: 0.9057 (ttm110) REVERT: E 52 GLU cc_start: 0.8795 (pp20) cc_final: 0.8490 (pp20) REVERT: E 60 VAL cc_start: 0.9475 (t) cc_final: 0.9244 (p) REVERT: E 63 GLU cc_start: 0.9319 (mt-10) cc_final: 0.9007 (mt-10) REVERT: E 67 ARG cc_start: 0.8889 (ttm110) cc_final: 0.8563 (ttm110) REVERT: E 71 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8065 (p) REVERT: E 74 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8295 (tm-30) REVERT: E 78 ARG cc_start: 0.8986 (mtp-110) cc_final: 0.8414 (mtm180) REVERT: E 97 LEU cc_start: 0.9485 (tp) cc_final: 0.9207 (tt) REVERT: C 36 MET cc_start: 0.8300 (tpt) cc_final: 0.7750 (ttt) REVERT: C 253 MET cc_start: 0.8442 (mmm) cc_final: 0.7918 (mmm) REVERT: C 399 MET cc_start: 0.8797 (tmm) cc_final: 0.7905 (tmm) REVERT: B 14 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8732 (mm-30) REVERT: B 131 ASP cc_start: 0.8570 (m-30) cc_final: 0.8007 (m-30) REVERT: B 144 MET cc_start: 0.8085 (tpp) cc_final: 0.7633 (mmm) REVERT: B 227 MET cc_start: 0.9123 (ptp) cc_final: 0.8331 (pmm) REVERT: B 236 PHE cc_start: 0.9358 (m-80) cc_final: 0.8466 (t80) REVERT: B 385 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8827 (mmmt) outliers start: 24 outliers final: 18 residues processed: 146 average time/residue: 0.0935 time to fit residues: 19.1099 Evaluate side-chains 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 353 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN D 93 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 HIS ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.074984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.056990 restraints weight = 36547.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059184 restraints weight = 21591.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060671 restraints weight = 15425.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061746 restraints weight = 12337.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.062459 restraints weight = 10524.010| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9064 Z= 0.222 Angle : 0.667 12.308 12302 Z= 0.334 Chirality : 0.046 0.204 1364 Planarity : 0.004 0.039 1594 Dihedral : 4.480 22.249 1220 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.99 % Allowed : 18.70 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.25), residues: 1121 helix: 2.24 (0.37), residues: 208 sheet: -0.40 (0.31), residues: 278 loop : -1.04 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 95 TYR 0.019 0.001 TYR C 21 PHE 0.025 0.002 PHE D 67 TRP 0.013 0.002 TRP B 93 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 9064) covalent geometry : angle 0.66743 (12302) hydrogen bonds : bond 0.03255 ( 315) hydrogen bonds : angle 5.36139 ( 855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 589 GLN cc_start: 0.8840 (pp30) cc_final: 0.8611 (mm-40) REVERT: D 97 GLU cc_start: 0.8814 (pm20) cc_final: 0.8555 (pm20) REVERT: D 120 MET cc_start: 0.8348 (mmm) cc_final: 0.8018 (mmm) REVERT: E 52 GLU cc_start: 0.8752 (pp20) cc_final: 0.7868 (pp20) REVERT: E 53 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8621 (mm-30) REVERT: E 60 VAL cc_start: 0.9537 (t) cc_final: 0.9288 (p) REVERT: E 63 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8933 (mt-10) REVERT: E 67 ARG cc_start: 0.8871 (ttm110) cc_final: 0.8626 (ttm110) REVERT: E 74 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8234 (tm-30) REVERT: E 97 LEU cc_start: 0.9506 (tp) cc_final: 0.9256 (tt) REVERT: C 36 MET cc_start: 0.8419 (tpt) cc_final: 0.7832 (ttt) REVERT: C 253 MET cc_start: 0.8502 (mmm) cc_final: 0.8050 (mmm) REVERT: C 399 MET cc_start: 0.8717 (tmm) cc_final: 0.7929 (tmm) REVERT: B 1 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8351 (tmm) REVERT: B 14 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8648 (mm-30) REVERT: B 131 ASP cc_start: 0.8534 (m-30) cc_final: 0.8206 (m-30) REVERT: B 144 MET cc_start: 0.8193 (tpp) cc_final: 0.7904 (mmm) REVERT: B 227 MET cc_start: 0.9090 (ptp) cc_final: 0.8418 (pmm) REVERT: B 236 PHE cc_start: 0.9317 (m-80) cc_final: 0.8634 (t80) REVERT: B 385 LYS cc_start: 0.9206 (mmtt) cc_final: 0.8784 (mmmt) outliers start: 28 outliers final: 21 residues processed: 152 average time/residue: 0.0973 time to fit residues: 20.2407 Evaluate side-chains 143 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 18 optimal weight: 0.0870 chunk 45 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.078842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.060776 restraints weight = 35802.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.063142 restraints weight = 20862.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064750 restraints weight = 14763.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.065841 restraints weight = 11730.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.066545 restraints weight = 9997.085| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9064 Z= 0.116 Angle : 0.663 14.723 12302 Z= 0.320 Chirality : 0.046 0.203 1364 Planarity : 0.004 0.050 1594 Dihedral : 4.262 23.169 1220 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.60 % Allowed : 20.62 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.25), residues: 1121 helix: 2.33 (0.36), residues: 208 sheet: -0.20 (0.30), residues: 290 loop : -1.01 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 95 TYR 0.014 0.001 TYR B 330 PHE 0.026 0.001 PHE D 67 TRP 0.018 0.002 TRP B 156 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9064) covalent geometry : angle 0.66346 (12302) hydrogen bonds : bond 0.02931 ( 315) hydrogen bonds : angle 5.09754 ( 855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 93 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8478 (mm110) REVERT: D 94 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8847 (mm-30) REVERT: E 40 ARG cc_start: 0.9330 (ttm110) cc_final: 0.8987 (ttm110) REVERT: E 52 GLU cc_start: 0.8745 (pp20) cc_final: 0.8385 (pp20) REVERT: E 60 VAL cc_start: 0.9500 (t) cc_final: 0.9260 (p) REVERT: E 63 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8899 (mt-10) REVERT: E 67 ARG cc_start: 0.8834 (ttm110) cc_final: 0.8522 (ttm110) REVERT: E 68 ASP cc_start: 0.8577 (m-30) cc_final: 0.8368 (m-30) REVERT: E 71 THR cc_start: 0.8571 (m) cc_final: 0.8208 (p) REVERT: E 74 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8233 (tm-30) REVERT: E 97 LEU cc_start: 0.9506 (tp) cc_final: 0.9253 (tt) REVERT: C 36 MET cc_start: 0.8389 (tpt) cc_final: 0.7937 (ttt) REVERT: C 253 MET cc_start: 0.8459 (mmm) cc_final: 0.8059 (mmm) REVERT: C 399 MET cc_start: 0.8744 (tmm) cc_final: 0.8056 (tmm) REVERT: B 1 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8212 (tmm) REVERT: B 14 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8638 (mm-30) REVERT: B 131 ASP cc_start: 0.8335 (m-30) cc_final: 0.7866 (m-30) REVERT: B 144 MET cc_start: 0.8192 (tpp) cc_final: 0.7935 (mmm) REVERT: B 227 MET cc_start: 0.8826 (ptp) cc_final: 0.8331 (pmm) REVERT: B 236 PHE cc_start: 0.9186 (m-80) cc_final: 0.8504 (t80) REVERT: B 385 LYS cc_start: 0.9181 (mmtt) cc_final: 0.8753 (mmmt) outliers start: 15 outliers final: 9 residues processed: 140 average time/residue: 0.0933 time to fit residues: 18.2116 Evaluate side-chains 138 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 88 optimal weight: 0.2980 chunk 64 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN D 93 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.077318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.060389 restraints weight = 35841.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.062589 restraints weight = 20620.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064073 restraints weight = 14494.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.065092 restraints weight = 11465.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.065753 restraints weight = 9770.138| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9064 Z= 0.243 Angle : 0.713 13.818 12302 Z= 0.352 Chirality : 0.046 0.202 1364 Planarity : 0.004 0.047 1594 Dihedral : 4.414 22.595 1220 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.03 % Allowed : 20.51 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1121 helix: 2.10 (0.37), residues: 208 sheet: -0.43 (0.30), residues: 286 loop : -0.95 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 95 TYR 0.021 0.002 TYR C 21 PHE 0.021 0.002 PHE D 67 TRP 0.016 0.002 TRP B 10 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 9064) covalent geometry : angle 0.71310 (12302) hydrogen bonds : bond 0.03382 ( 315) hydrogen bonds : angle 5.38682 ( 855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 40 ARG cc_start: 0.9353 (ttm110) cc_final: 0.9003 (ttm110) REVERT: E 52 GLU cc_start: 0.8759 (pp20) cc_final: 0.8404 (pp20) REVERT: E 60 VAL cc_start: 0.9521 (t) cc_final: 0.9268 (p) REVERT: E 63 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8903 (mt-10) REVERT: E 67 ARG cc_start: 0.8887 (ttm110) cc_final: 0.8634 (ttm110) REVERT: E 74 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8278 (tm-30) REVERT: E 97 LEU cc_start: 0.9521 (tp) cc_final: 0.9306 (tt) REVERT: C 36 MET cc_start: 0.8449 (tpt) cc_final: 0.7983 (ttt) REVERT: C 253 MET cc_start: 0.8556 (mmm) cc_final: 0.8164 (mmm) REVERT: C 399 MET cc_start: 0.8704 (tmm) cc_final: 0.7967 (tmm) REVERT: B 1 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8329 (tmm) REVERT: B 14 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8675 (mm-30) REVERT: B 144 MET cc_start: 0.8178 (tpp) cc_final: 0.7967 (mmm) REVERT: B 227 MET cc_start: 0.9037 (ptp) cc_final: 0.8435 (pmm) REVERT: B 236 PHE cc_start: 0.9301 (m-80) cc_final: 0.8615 (t80) REVERT: B 385 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8767 (mmmt) outliers start: 19 outliers final: 14 residues processed: 139 average time/residue: 0.0923 time to fit residues: 17.9428 Evaluate side-chains 141 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 109 optimal weight: 0.0010 chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN C 48 GLN C 71 HIS ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.078191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060265 restraints weight = 35814.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.062577 restraints weight = 20991.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.064133 restraints weight = 14907.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.065252 restraints weight = 11879.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.066045 restraints weight = 10111.713| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9064 Z= 0.126 Angle : 0.697 15.787 12302 Z= 0.337 Chirality : 0.046 0.220 1364 Planarity : 0.004 0.055 1594 Dihedral : 4.306 24.625 1220 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.60 % Allowed : 21.69 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.25), residues: 1121 helix: 2.16 (0.37), residues: 208 sheet: -0.23 (0.30), residues: 290 loop : -0.93 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 95 TYR 0.015 0.001 TYR B 330 PHE 0.028 0.002 PHE D 67 TRP 0.020 0.002 TRP B 10 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9064) covalent geometry : angle 0.69748 (12302) hydrogen bonds : bond 0.03152 ( 315) hydrogen bonds : angle 5.17754 ( 855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 ARG cc_start: 0.9354 (ttm110) cc_final: 0.9006 (ttm110) REVERT: E 52 GLU cc_start: 0.8741 (pp20) cc_final: 0.7942 (pp20) REVERT: E 53 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8590 (mm-30) REVERT: E 60 VAL cc_start: 0.9497 (t) cc_final: 0.9254 (p) REVERT: E 63 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8897 (mt-10) REVERT: E 67 ARG cc_start: 0.8842 (ttm110) cc_final: 0.8489 (ttm110) REVERT: E 71 THR cc_start: 0.8638 (m) cc_final: 0.8269 (p) REVERT: E 74 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8224 (tm-30) REVERT: E 97 LEU cc_start: 0.9525 (tp) cc_final: 0.9289 (tt) REVERT: C 36 MET cc_start: 0.8440 (tpt) cc_final: 0.7953 (ttt) REVERT: C 253 MET cc_start: 0.8449 (mmm) cc_final: 0.8067 (mmm) REVERT: C 399 MET cc_start: 0.8700 (tmm) cc_final: 0.7937 (tmm) REVERT: B 1 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8239 (tmm) REVERT: B 14 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8656 (mm-30) REVERT: B 126 ARG cc_start: 0.8033 (mmt-90) cc_final: 0.7789 (mmt-90) REVERT: B 131 ASP cc_start: 0.8330 (m-30) cc_final: 0.7856 (m-30) REVERT: B 191 CYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8580 (m) REVERT: B 227 MET cc_start: 0.8770 (ptp) cc_final: 0.8339 (pmm) REVERT: B 236 PHE cc_start: 0.9190 (m-80) cc_final: 0.8569 (t80) REVERT: B 237 PHE cc_start: 0.8863 (m-80) cc_final: 0.8644 (m-10) REVERT: B 385 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8741 (mmmt) outliers start: 15 outliers final: 11 residues processed: 139 average time/residue: 0.0979 time to fit residues: 18.7796 Evaluate side-chains 143 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN A 706 GLN D 93 GLN ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.080087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.061256 restraints weight = 36556.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.063580 restraints weight = 20798.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065161 restraints weight = 14569.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.066252 restraints weight = 11514.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.066934 restraints weight = 9790.433| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9064 Z= 0.172 Angle : 0.703 14.357 12302 Z= 0.340 Chirality : 0.045 0.200 1364 Planarity : 0.004 0.055 1594 Dihedral : 4.304 24.352 1220 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.92 % Allowed : 21.47 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.25), residues: 1121 helix: 2.12 (0.37), residues: 208 sheet: -0.34 (0.30), residues: 292 loop : -0.89 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 95 TYR 0.019 0.001 TYR C 21 PHE 0.029 0.002 PHE D 67 TRP 0.020 0.002 TRP B 10 HIS 0.005 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9064) covalent geometry : angle 0.70252 (12302) hydrogen bonds : bond 0.03196 ( 315) hydrogen bonds : angle 5.23712 ( 855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 94 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9081 (mm-30) REVERT: E 52 GLU cc_start: 0.8772 (pp20) cc_final: 0.7917 (pp20) REVERT: E 53 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8639 (mm-30) REVERT: E 60 VAL cc_start: 0.9501 (t) cc_final: 0.9261 (p) REVERT: E 63 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8928 (mt-10) REVERT: E 67 ARG cc_start: 0.8872 (ttm110) cc_final: 0.8510 (ttm110) REVERT: E 71 THR cc_start: 0.8643 (m) cc_final: 0.8230 (p) REVERT: E 74 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8292 (tm-30) REVERT: E 97 LEU cc_start: 0.9539 (tp) cc_final: 0.9339 (tt) REVERT: C 36 MET cc_start: 0.8431 (tpt) cc_final: 0.7859 (ttt) REVERT: C 131 ARG cc_start: 0.8811 (mmt90) cc_final: 0.8375 (mmt180) REVERT: C 253 MET cc_start: 0.8528 (mmm) cc_final: 0.8117 (mmm) REVERT: C 399 MET cc_start: 0.8690 (tmm) cc_final: 0.7891 (tmm) REVERT: B 14 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8662 (mm-30) REVERT: B 134 ASP cc_start: 0.8763 (t70) cc_final: 0.7962 (t0) REVERT: B 191 CYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8634 (m) REVERT: B 227 MET cc_start: 0.8934 (ptp) cc_final: 0.8397 (pmm) REVERT: B 236 PHE cc_start: 0.9226 (m-80) cc_final: 0.8586 (t80) REVERT: B 385 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8736 (mmmt) outliers start: 18 outliers final: 12 residues processed: 135 average time/residue: 0.0893 time to fit residues: 16.9458 Evaluate side-chains 138 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 9 optimal weight: 0.1980 chunk 15 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 0.0020 chunk 58 optimal weight: 0.9980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.080398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.061422 restraints weight = 36596.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.063733 restraints weight = 21351.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.065299 restraints weight = 15185.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066366 restraints weight = 12113.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.067025 restraints weight = 10421.828| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 9064 Z= 0.218 Angle : 1.033 59.163 12302 Z= 0.564 Chirality : 0.048 0.639 1364 Planarity : 0.004 0.053 1594 Dihedral : 4.308 24.259 1220 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.39 % Allowed : 22.33 % Favored : 76.28 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.25), residues: 1121 helix: 2.10 (0.37), residues: 208 sheet: -0.34 (0.30), residues: 292 loop : -0.89 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 95 TYR 0.014 0.001 TYR B 330 PHE 0.028 0.002 PHE D 67 TRP 0.017 0.002 TRP B 10 HIS 0.005 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9064) covalent geometry : angle 1.03279 (12302) hydrogen bonds : bond 0.03402 ( 315) hydrogen bonds : angle 5.24894 ( 855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.65 seconds wall clock time: 26 minutes 42.59 seconds (1602.59 seconds total)