Starting phenix.real_space_refine on Tue Dec 31 00:11:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5u_33625/12_2024/7y5u_33625.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5u_33625/12_2024/7y5u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y5u_33625/12_2024/7y5u_33625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5u_33625/12_2024/7y5u_33625.map" model { file = "/net/cci-nas-00/data/ceres_data/7y5u_33625/12_2024/7y5u_33625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5u_33625/12_2024/7y5u_33625.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} 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: 5.43, per 1000 atoms: 0.61 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: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.09 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: 2.93 Time building geometry restraints manager: 2.81 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.690 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- 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= 0.161 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), 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 TRP 0.025 0.001 TRP C 345 HIS 0.032 0.002 HIS A 615 PHE 0.018 0.001 PHE B 269 TYR 0.017 0.001 TYR C 98 ARG 0.006 0.000 ARG C 129 *********************** 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 : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 171 LEU cc_start: 0.5853 (mt) cc_final: 0.5422 (mp) REVERT: C 333 LEU cc_start: 0.7613 (tp) cc_final: 0.7388 (tt) REVERT: C 391 CYS cc_start: 0.7292 (t) cc_final: 0.7027 (t) outliers start: 1 outliers final: 1 residues processed: 210 average time/residue: 0.2260 time to fit residues: 64.4123 Evaluate side-chains 129 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 95 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 HIS C 277 ASN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN B 70 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1936 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= 0.200 Angle : 0.641 10.169 12302 Z= 0.317 Chirality : 0.046 0.239 1364 Planarity : 0.004 0.040 1594 Dihedral : 4.103 25.643 1222 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.07 % Allowed : 11.11 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1121 helix: 2.36 (0.36), residues: 208 sheet: 0.00 (0.30), residues: 306 loop : -1.16 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 10 HIS 0.011 0.001 HIS B 347 PHE 0.016 0.002 PHE B 242 TYR 0.012 0.001 TYR D 41 ARG 0.005 0.001 ARG E 40 *********************** 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 157 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6940 (mm-30) REVERT: C 333 LEU cc_start: 0.7725 (tp) cc_final: 0.7322 (tt) REVERT: C 391 CYS cc_start: 0.7272 (t) cc_final: 0.7011 (t) outliers start: 10 outliers final: 5 residues processed: 149 average time/residue: 0.2180 time to fit residues: 45.5491 Evaluate side-chains 134 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 B 115 ASN B 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9064 Z= 0.292 Angle : 0.648 9.763 12302 Z= 0.329 Chirality : 0.045 0.194 1364 Planarity : 0.004 0.035 1594 Dihedral : 4.279 24.620 1220 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.46 % Allowed : 11.75 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1121 helix: 2.43 (0.37), residues: 208 sheet: -0.16 (0.30), residues: 309 loop : -1.10 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 10 HIS 0.004 0.001 HIS C 328 PHE 0.022 0.002 PHE D 67 TYR 0.011 0.001 TYR B 330 ARG 0.008 0.001 ARG E 92 *********************** 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 161 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 ARG cc_start: 0.7925 (ptp-110) cc_final: 0.7622 (ttm110) REVERT: E 52 GLU cc_start: 0.7179 (pp20) cc_final: 0.6781 (pp20) REVERT: E 84 MET cc_start: 0.7052 (tpp) cc_final: 0.6738 (tpp) outliers start: 23 outliers final: 17 residues processed: 146 average time/residue: 0.2318 time to fit residues: 46.9447 Evaluate side-chains 137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain B residue 1 MET 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 189 LEU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 30.0000 chunk 49 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN E 75 HIS ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9064 Z= 0.246 Angle : 0.639 11.306 12302 Z= 0.317 Chirality : 0.045 0.196 1364 Planarity : 0.004 0.036 1594 Dihedral : 4.249 24.101 1220 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1121 helix: 2.51 (0.37), residues: 202 sheet: -0.13 (0.30), residues: 300 loop : -1.07 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 10 HIS 0.004 0.001 HIS C 200 PHE 0.016 0.002 PHE A 707 TYR 0.013 0.001 TYR B 330 ARG 0.005 0.000 ARG E 95 *********************** 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 153 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 94 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6988 (mm-30) REVERT: E 40 ARG cc_start: 0.7927 (ptp-110) cc_final: 0.7613 (ttm110) REVERT: E 52 GLU cc_start: 0.7164 (pp20) cc_final: 0.6877 (pp20) REVERT: E 53 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7230 (mm-30) REVERT: E 67 ARG cc_start: 0.7183 (ttp80) cc_final: 0.6975 (ttp-110) REVERT: E 84 MET cc_start: 0.7018 (tpp) cc_final: 0.6742 (tpp) REVERT: B 96 ASN cc_start: 0.5951 (OUTLIER) cc_final: 0.5628 (m110) REVERT: B 236 PHE cc_start: 0.8130 (t80) cc_final: 0.7783 (t80) outliers start: 18 outliers final: 13 residues processed: 145 average time/residue: 0.2450 time to fit residues: 49.0456 Evaluate side-chains 133 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain C residue 183 LEU 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 96 ASN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** C 64 HIS ** 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 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9064 Z= 0.384 Angle : 0.711 10.346 12302 Z= 0.361 Chirality : 0.046 0.204 1364 Planarity : 0.004 0.036 1594 Dihedral : 4.597 23.094 1220 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.88 % Allowed : 16.45 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1121 helix: 2.14 (0.37), residues: 202 sheet: -0.34 (0.30), residues: 290 loop : -1.08 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 10 HIS 0.006 0.001 HIS C 200 PHE 0.025 0.002 PHE D 67 TYR 0.017 0.002 TYR C 21 ARG 0.010 0.001 ARG E 95 *********************** 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 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 40 ARG cc_start: 0.7979 (ptp-110) cc_final: 0.7661 (ttm110) REVERT: E 52 GLU cc_start: 0.7263 (pp20) cc_final: 0.6734 (pp20) REVERT: E 53 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7312 (mm-30) REVERT: E 84 MET cc_start: 0.7216 (tpp) cc_final: 0.6996 (tpp) REVERT: C 36 MET cc_start: 0.6916 (ttt) cc_final: 0.6637 (ttt) outliers start: 27 outliers final: 20 residues processed: 144 average time/residue: 0.2206 time to fit residues: 44.5302 Evaluate side-chains 135 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 ASP Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 62 LEU 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 96 ASN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 706 GLN ** C 64 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9064 Z= 0.193 Angle : 0.657 13.628 12302 Z= 0.323 Chirality : 0.045 0.196 1364 Planarity : 0.004 0.036 1594 Dihedral : 4.336 23.177 1220 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.03 % Allowed : 18.70 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1121 helix: 2.25 (0.37), residues: 202 sheet: -0.29 (0.31), residues: 284 loop : -0.97 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 10 HIS 0.004 0.001 HIS E 75 PHE 0.018 0.002 PHE D 67 TYR 0.014 0.001 TYR B 330 ARG 0.005 0.000 ARG E 95 *********************** 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 153 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 40 ARG cc_start: 0.7905 (ptp-110) cc_final: 0.7635 (ttm110) REVERT: E 52 GLU cc_start: 0.7268 (pp20) cc_final: 0.7009 (pp20) REVERT: E 84 MET cc_start: 0.7074 (tpp) cc_final: 0.6776 (tpp) REVERT: C 36 MET cc_start: 0.7005 (ttt) cc_final: 0.6802 (ttt) REVERT: C 253 MET cc_start: 0.7653 (mmm) cc_final: 0.6976 (mtt) REVERT: C 333 LEU cc_start: 0.8273 (tp) cc_final: 0.7940 (tt) REVERT: B 96 ASN cc_start: 0.6225 (OUTLIER) cc_final: 0.5851 (m110) REVERT: B 351 ASP cc_start: 0.8305 (t0) cc_final: 0.7960 (t0) outliers start: 19 outliers final: 14 residues processed: 145 average time/residue: 0.2268 time to fit residues: 45.7395 Evaluate side-chains 137 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 62 LEU 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 96 ASN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 249 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 40.0000 chunk 62 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9064 Z= 0.418 Angle : 0.752 12.770 12302 Z= 0.377 Chirality : 0.047 0.209 1364 Planarity : 0.005 0.039 1594 Dihedral : 4.563 22.548 1220 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.67 % Allowed : 19.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1121 helix: 2.04 (0.37), residues: 202 sheet: -0.47 (0.30), residues: 283 loop : -1.02 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 10 HIS 0.005 0.001 HIS B 280 PHE 0.018 0.002 PHE D 67 TYR 0.013 0.002 TYR B 330 ARG 0.006 0.001 ARG E 95 *********************** 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 147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: E 52 GLU cc_start: 0.7278 (pp20) cc_final: 0.6711 (pp20) REVERT: E 53 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7227 (mm-30) REVERT: E 84 MET cc_start: 0.7210 (tpp) cc_final: 0.6941 (tpp) REVERT: C 36 MET cc_start: 0.7127 (ttt) cc_final: 0.6842 (ttt) REVERT: C 253 MET cc_start: 0.7617 (mmm) cc_final: 0.6983 (mtt) REVERT: B 191 CYS cc_start: 0.7761 (t) cc_final: 0.7328 (t) REVERT: B 351 ASP cc_start: 0.8261 (t0) cc_final: 0.7846 (t0) outliers start: 25 outliers final: 21 residues processed: 139 average time/residue: 0.2219 time to fit residues: 42.9949 Evaluate side-chains 138 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 ASP 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 E residue 96 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 96 ASN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 256 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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 64 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** B 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4097 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= 0.209 Angle : 0.707 15.055 12302 Z= 0.343 Chirality : 0.046 0.195 1364 Planarity : 0.004 0.036 1594 Dihedral : 4.387 23.657 1220 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.82 % Allowed : 20.09 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1121 helix: 2.13 (0.37), residues: 202 sheet: -0.36 (0.31), residues: 288 loop : -0.97 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 10 HIS 0.004 0.001 HIS E 75 PHE 0.018 0.001 PHE D 67 TYR 0.015 0.001 TYR B 330 ARG 0.007 0.000 ARG E 95 *********************** 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 142 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: E 52 GLU cc_start: 0.7353 (pp20) cc_final: 0.6887 (pp20) REVERT: E 53 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7275 (mm-30) REVERT: C 333 LEU cc_start: 0.8276 (tp) cc_final: 0.7965 (tt) REVERT: B 96 ASN cc_start: 0.6616 (OUTLIER) cc_final: 0.6121 (m110) REVERT: B 156 TRP cc_start: 0.7837 (m-10) cc_final: 0.7625 (m-10) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.2225 time to fit residues: 42.0738 Evaluate side-chains 132 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 96 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 249 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 0.0770 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- 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 64 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** B 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9064 Z= 0.242 Angle : 0.732 15.448 12302 Z= 0.356 Chirality : 0.046 0.209 1364 Planarity : 0.004 0.036 1594 Dihedral : 4.352 24.487 1220 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.71 % Allowed : 19.76 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1121 helix: 2.08 (0.37), residues: 202 sheet: -0.39 (0.30), residues: 290 loop : -0.93 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 10 HIS 0.004 0.001 HIS E 75 PHE 0.018 0.001 PHE D 67 TYR 0.019 0.001 TYR C 21 ARG 0.008 0.000 ARG E 95 *********************** 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 140 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 52 GLU cc_start: 0.7283 (pp20) cc_final: 0.6762 (pp20) REVERT: E 53 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7160 (mm-30) REVERT: C 333 LEU cc_start: 0.8338 (tp) cc_final: 0.8018 (tt) REVERT: B 96 ASN cc_start: 0.6618 (OUTLIER) cc_final: 0.6268 (m110) REVERT: B 351 ASP cc_start: 0.8167 (t0) cc_final: 0.7849 (t0) outliers start: 16 outliers final: 12 residues processed: 134 average time/residue: 0.2243 time to fit residues: 41.8242 Evaluate side-chains 136 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 62 LEU 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 66 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 256 VAL 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 50 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9064 Z= 0.266 Angle : 0.735 15.006 12302 Z= 0.361 Chirality : 0.046 0.202 1364 Planarity : 0.004 0.037 1594 Dihedral : 4.382 24.686 1220 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1121 helix: 1.94 (0.37), residues: 206 sheet: -0.36 (0.31), residues: 284 loop : -0.96 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 10 HIS 0.004 0.001 HIS B 280 PHE 0.016 0.002 PHE D 67 TYR 0.013 0.001 TYR B 330 ARG 0.008 0.000 ARG E 95 ********************** 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 139 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 52 GLU cc_start: 0.7310 (pp20) cc_final: 0.6779 (pp20) REVERT: E 53 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7145 (mm-30) REVERT: E 84 MET cc_start: 0.6930 (tpp) cc_final: 0.6601 (tpp) REVERT: B 96 ASN cc_start: 0.6604 (OUTLIER) cc_final: 0.6079 (m110) REVERT: B 351 ASP cc_start: 0.8153 (t0) cc_final: 0.7824 (t0) outliers start: 15 outliers final: 12 residues processed: 133 average time/residue: 0.2289 time to fit residues: 42.1020 Evaluate side-chains 131 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain E residue 62 LEU 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 66 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 256 VAL 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 82 optimal weight: 0.0770 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 11 optimal weight: 40.0000 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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** C 48 GLN ** C 64 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** C 385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.079111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.061546 restraints weight = 35150.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.063868 restraints weight = 20593.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.065433 restraints weight = 14549.384| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9064 Z= 0.202 Angle : 0.727 15.303 12302 Z= 0.354 Chirality : 0.046 0.216 1364 Planarity : 0.004 0.038 1594 Dihedral : 4.270 24.512 1220 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.60 % Allowed : 20.30 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1121 helix: 2.02 (0.37), residues: 202 sheet: -0.23 (0.31), residues: 287 loop : -0.99 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 156 HIS 0.004 0.001 HIS E 75 PHE 0.018 0.001 PHE D 67 TYR 0.019 0.001 TYR C 21 ARG 0.008 0.000 ARG E 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.65 seconds wall clock time: 36 minutes 27.77 seconds (2187.77 seconds total)