Starting phenix.real_space_refine on Tue Aug 4 22:02:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqi_62505/08_2026/9kqi_62505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqi_62505/08_2026/9kqi_62505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kqi_62505/08_2026/9kqi_62505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqi_62505/08_2026/9kqi_62505.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqi_62505/08_2026/9kqi_62505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqi_62505/08_2026/9kqi_62505.cif" } resolution = 3.02 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= 0.002 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 16 5.49 5 S 40 5.16 5 C 4836 2.51 5 N 1018 2.21 5 O 1170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7082 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3171 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364} Chain breaks: 1 Chain: "B" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3171 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364} Chain breaks: 1 Chain: "A" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 370 Unusual residues: {' CA': 1, 'C14': 1, 'D12': 1, 'LBN': 5, 'PSF': 2, 'T7X': 1} Inner-chain residues flagged as termini: ['pdbres="SER A 511 "'] Classifications: {'peptide': 1, 'undetermined': 11} Modifications used: {'COO': 1} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 370 Unusual residues: {' CA': 1, 'C14': 1, 'D12': 1, 'LBN': 5, 'PSF': 2, 'T7X': 1} Classifications: {'peptide': 1, 'undetermined': 11} Modifications used: {'COO': 1} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'LBN:plan-3': 2} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 1.86, per 1000 atoms: 0.26 Number of scatterers: 7082 At special positions: 0 Unit cell: (91.785, 108.665, 71.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 40 16.00 P 16 15.00 O 1170 8.00 N 1018 7.00 C 4836 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: 0.60 Conformation dependent library (CDL) restraints added in 317.1 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 76.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 14 through 23 removed outlier: 3.971A pdb=" N PHE A 21 " --> pdb=" O TYR A 17 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 22 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.783A pdb=" N PHE A 37 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG A 39 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 59 Processing helix chain 'A' and resid 64 through 88 removed outlier: 3.506A pdb=" N LEU A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 119 removed outlier: 3.652A pdb=" N VAL A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 135 through 140 removed outlier: 4.299A pdb=" N TYR A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 140' Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 185 through 204 removed outlier: 3.554A pdb=" N CYS A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.591A pdb=" N GLU A 301 " --> pdb=" O TRP A 297 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 344 removed outlier: 4.042A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.813A pdb=" N ARG A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 372 removed outlier: 3.562A pdb=" N ALA A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 408 removed outlier: 3.576A pdb=" N THR A 394 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 23 removed outlier: 3.995A pdb=" N PHE B 21 " --> pdb=" O TYR B 17 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.782A pdb=" N PHE B 37 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG B 39 " --> pdb=" O PHE B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 59 removed outlier: 3.614A pdb=" N ILE B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.616A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 69 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.522A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 135 through 140 removed outlier: 4.265A pdb=" N TYR B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 140' Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 166 through 184 removed outlier: 3.941A pdb=" N LEU B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 204 Processing helix chain 'B' and resid 213 through 219 removed outlier: 4.262A pdb=" N GLN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 283 through 311 removed outlier: 3.652A pdb=" N GLN B 298 " --> pdb=" O MET B 294 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 301 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 344 removed outlier: 4.086A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.796A pdb=" N ARG B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 372 removed outlier: 3.705A pdb=" N ALA B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 408 removed outlier: 3.575A pdb=" N THR B 394 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 406 " --> pdb=" O MET B 402 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1167 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: 1.04 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 975 1.32 - 1.44: 2259 1.44 - 1.56: 3960 1.56 - 1.69: 32 1.69 - 1.81: 62 Bond restraints: 7288 Sorted by residual: bond pdb=" CG1 ILE A 192 " pdb=" CD1 ILE A 192 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.94e+00 bond pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CG1 ILE B 192 " pdb=" CD1 ILE B 192 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.42e+00 bond pdb=" CB CYS B 237 " pdb=" SG CYS B 237 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB VAL A 359 " pdb=" CG2 VAL A 359 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.49e-01 ... (remaining 7283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 9518 1.34 - 2.69: 213 2.69 - 4.03: 46 4.03 - 5.38: 10 5.38 - 6.72: 9 Bond angle restraints: 9796 Sorted by residual: angle pdb=" C ALA A 87 " pdb=" N PHE A 88 " pdb=" CA PHE A 88 " ideal model delta sigma weight residual 122.38 116.09 6.29 2.90e+00 1.19e-01 4.71e+00 angle pdb=" C SER B 63 " pdb=" N VAL B 64 " pdb=" CA VAL B 64 " ideal model delta sigma weight residual 123.43 121.07 2.36 1.10e+00 8.26e-01 4.62e+00 angle pdb=" C ALA B 87 " pdb=" N PHE B 88 " pdb=" CA PHE B 88 " ideal model delta sigma weight residual 122.38 116.17 6.21 2.90e+00 1.19e-01 4.59e+00 angle pdb=" C VAL B 64 " pdb=" CA VAL B 64 " pdb=" CB VAL B 64 " ideal model delta sigma weight residual 110.37 112.64 -2.27 1.07e+00 8.73e-01 4.50e+00 angle pdb=" CB MET A 402 " pdb=" CG MET A 402 " pdb=" SD MET A 402 " ideal model delta sigma weight residual 112.70 118.98 -6.28 3.00e+00 1.11e-01 4.39e+00 ... (remaining 9791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 3962 33.92 - 67.83: 230 67.83 - 101.75: 41 101.75 - 135.66: 15 135.66 - 169.58: 12 Dihedral angle restraints: 4260 sinusoidal: 2038 harmonic: 2222 Sorted by residual: dihedral pdb=" O5 LBN A 505 " pdb=" C2 LBN A 505 " pdb=" C3 LBN A 505 " pdb=" O7 LBN A 505 " ideal model delta sinusoidal sigma weight residual 62.67 -127.75 -169.58 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O5 LBN B 506 " pdb=" C2 LBN B 506 " pdb=" C3 LBN B 506 " pdb=" O7 LBN B 506 " ideal model delta sinusoidal sigma weight residual 62.67 -128.75 -168.58 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" O5 LBN B 505 " pdb=" C2 LBN B 505 " pdb=" C3 LBN B 505 " pdb=" O7 LBN B 505 " ideal model delta sinusoidal sigma weight residual 62.67 -102.17 164.84 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 4257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 602 0.033 - 0.066: 295 0.066 - 0.099: 83 0.099 - 0.133: 19 0.133 - 0.166: 5 Chirality restraints: 1004 Sorted by residual: chirality pdb=" CG LEU B 207 " pdb=" CB LEU B 207 " pdb=" CD1 LEU B 207 " pdb=" CD2 LEU B 207 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CB VAL A 359 " pdb=" CA VAL A 359 " pdb=" CG1 VAL A 359 " pdb=" CG2 VAL A 359 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" C2 LBN B 509 " pdb=" C1 LBN B 509 " pdb=" C3 LBN B 509 " pdb=" O7 LBN B 509 " both_signs ideal model delta sigma weight residual False -2.36 -2.22 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 1001 not shown) Planarity restraints: 1128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 332 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 333 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 333 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 333 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 332 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 333 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 64 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO B 65 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 65 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 65 " -0.020 5.00e-02 4.00e+02 ... (remaining 1125 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 849 2.74 - 3.28: 6641 3.28 - 3.82: 11702 3.82 - 4.36: 14768 4.36 - 4.90: 24919 Nonbonded interactions: 58879 Sorted by model distance: nonbonded pdb=" O PHE B 48 " pdb=" OG SER B 52 " model vdw 2.205 3.040 nonbonded pdb=" O LEU B 240 " pdb=" OH TYR B 245 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR B 44 " pdb=" O3 LBN B 501 " model vdw 2.247 3.040 nonbonded pdb=" O GLY B 187 " pdb=" OG1 THR B 191 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR A 44 " pdb=" O3 LBN A 512 " model vdw 2.261 3.040 ... (remaining 58874 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 408 or resid 502 or resid 505)) selection = (chain 'B' and (resid 14 through 408 or resid 502 or (resid 505 and (name C1 or \ name C12 or name C15 or name C18 or name C2 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C30 or name C34 or name C35 or name C \ 36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C6 or nam \ e C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 or name O \ 6 or name O7 or name O8 or name P1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.990 Find NCS groups from input model: 0.140 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.005 0.054 7288 Z= 0.194 Angle : 0.557 6.721 9796 Z= 0.269 Chirality : 0.042 0.166 1004 Planarity : 0.004 0.041 1128 Dihedral : 24.255 169.578 2820 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.44 % Allowed : 21.18 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.77 (0.29), residues: 746 helix: -0.38 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.42 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 TYR 0.007 0.001 TYR B 139 PHE 0.013 0.001 PHE A 79 TRP 0.012 0.001 TRP A 321 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.19 ( 7288) covalent geometry : angle 0.55716 / 0.27 ( 9796) hydrogen bonds : bond 0.21439 / 14.29 ( 393) hydrogen bonds : angle 8.01893 / 5.91 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.250 Fit side-chains REVERT: B 67 ASP cc_start: 0.7266 (t70) cc_final: 0.6826 (m-30) outliers start: 3 outliers final: 1 residues processed: 92 average time/residue: 0.0887 time to fit residues: 11.0270 Evaluate side-chains 91 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN A 309 HIS B 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.175551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135407 restraints weight = 6755.487| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.75 r_work: 0.3378 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7288 Z= 0.135 Angle : 0.547 7.698 9796 Z= 0.269 Chirality : 0.040 0.155 1004 Planarity : 0.004 0.038 1128 Dihedral : 24.669 167.314 1410 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.53 % Allowed : 18.97 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.49 (0.30), residues: 746 helix: 0.74 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.59 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.012 0.001 TYR B 291 PHE 0.011 0.001 PHE A 79 TRP 0.016 0.001 TRP A 321 HIS 0.003 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 ( 7288) covalent geometry : angle 0.54664 / 0.27 ( 9796) hydrogen bonds : bond 0.04318 / 2.87 ( 393) hydrogen bonds : angle 4.74857 / 3.43 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.149 Fit side-chains REVERT: A 19 MET cc_start: 0.7733 (ttt) cc_final: 0.7530 (ttt) REVERT: A 22 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7756 (mtp85) REVERT: A 71 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6011 (mmp-170) REVERT: A 387 TRP cc_start: 0.4945 (OUTLIER) cc_final: 0.3728 (t60) REVERT: B 170 PHE cc_start: 0.6386 (OUTLIER) cc_final: 0.4630 (m-80) REVERT: B 387 TRP cc_start: 0.4769 (OUTLIER) cc_final: 0.3713 (t60) REVERT: B 393 PHE cc_start: 0.7043 (m-10) cc_final: 0.6583 (m-10) outliers start: 24 outliers final: 9 residues processed: 100 average time/residue: 0.0964 time to fit residues: 12.5525 Evaluate side-chains 99 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.0060 chunk 37 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 HIS B 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.184662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143074 restraints weight = 6726.150| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.83 r_work: 0.3422 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7288 Z= 0.118 Angle : 0.514 9.354 9796 Z= 0.248 Chirality : 0.039 0.151 1004 Planarity : 0.003 0.036 1128 Dihedral : 22.518 166.476 1408 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.24 % Allowed : 20.44 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.06 (0.31), residues: 746 helix: 1.19 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.51 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 184 TYR 0.009 0.001 TYR B 291 PHE 0.010 0.001 PHE A 79 TRP 0.016 0.001 TRP B 321 HIS 0.003 0.000 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7288) covalent geometry : angle 0.51429 / 0.25 ( 9796) hydrogen bonds : bond 0.03943 / 2.63 ( 393) hydrogen bonds : angle 4.38302 / 3.13 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.241 Fit side-chains REVERT: A 19 MET cc_start: 0.7806 (ttt) cc_final: 0.7555 (ttt) REVERT: A 22 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7720 (mtp85) REVERT: A 387 TRP cc_start: 0.5075 (OUTLIER) cc_final: 0.3705 (t60) REVERT: A 393 PHE cc_start: 0.7051 (m-10) cc_final: 0.6609 (m-10) REVERT: B 71 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.5994 (mmp-170) REVERT: B 170 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.6166 (t80) REVERT: B 387 TRP cc_start: 0.4987 (OUTLIER) cc_final: 0.3781 (t60) REVERT: B 393 PHE cc_start: 0.7061 (m-10) cc_final: 0.6581 (m-10) outliers start: 22 outliers final: 11 residues processed: 105 average time/residue: 0.0965 time to fit residues: 13.1718 Evaluate side-chains 103 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 309 HIS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.0470 chunk 47 optimal weight: 2.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN B 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.171647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.131638 restraints weight = 6977.165| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.74 r_work: 0.3373 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7288 Z= 0.176 Angle : 0.557 8.228 9796 Z= 0.266 Chirality : 0.042 0.236 1004 Planarity : 0.003 0.038 1128 Dihedral : 22.597 166.716 1408 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.12 % Allowed : 20.44 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.03 (0.30), residues: 746 helix: 1.18 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.54 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.007 0.001 TYR B 186 PHE 0.012 0.001 PHE A 79 TRP 0.017 0.001 TRP B 321 HIS 0.010 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 7288) covalent geometry : angle 0.55742 / 0.27 ( 9796) hydrogen bonds : bond 0.04178 / 2.76 ( 393) hydrogen bonds : angle 4.38449 / 3.14 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.142 Fit side-chains REVERT: A 19 MET cc_start: 0.7790 (ttt) cc_final: 0.7573 (ttt) REVERT: A 71 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6103 (mmp-170) REVERT: A 387 TRP cc_start: 0.5259 (OUTLIER) cc_final: 0.3895 (t60) REVERT: A 393 PHE cc_start: 0.7025 (m-10) cc_final: 0.6594 (m-10) REVERT: B 71 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6029 (mmp-170) REVERT: B 170 PHE cc_start: 0.6410 (OUTLIER) cc_final: 0.6124 (t80) REVERT: B 387 TRP cc_start: 0.5122 (OUTLIER) cc_final: 0.3862 (t60) REVERT: B 393 PHE cc_start: 0.7055 (m-10) cc_final: 0.6603 (m-10) outliers start: 28 outliers final: 14 residues processed: 107 average time/residue: 0.0931 time to fit residues: 12.9303 Evaluate side-chains 107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN B 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.159927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.119500 restraints weight = 7042.031| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.69 r_work: 0.3123 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7288 Z= 0.138 Angle : 0.526 9.019 9796 Z= 0.252 Chirality : 0.041 0.205 1004 Planarity : 0.003 0.036 1128 Dihedral : 22.243 167.139 1408 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.68 % Allowed : 20.44 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.20 (0.30), residues: 746 helix: 1.29 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.45 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.007 0.001 TYR B 186 PHE 0.010 0.001 PHE A 79 TRP 0.017 0.001 TRP B 321 HIS 0.003 0.000 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 7288) covalent geometry : angle 0.52607 / 0.25 ( 9796) hydrogen bonds : bond 0.03868 / 2.57 ( 393) hydrogen bonds : angle 4.26255 / 3.05 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.166 Fit side-chains REVERT: A 19 MET cc_start: 0.7684 (ttt) cc_final: 0.7450 (ttt) REVERT: A 71 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.5621 (mmp-170) REVERT: A 298 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: A 387 TRP cc_start: 0.5118 (OUTLIER) cc_final: 0.3718 (t60) REVERT: A 393 PHE cc_start: 0.6748 (m-10) cc_final: 0.6338 (m-10) REVERT: B 71 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.5561 (mmp-170) REVERT: B 170 PHE cc_start: 0.6112 (OUTLIER) cc_final: 0.5785 (t80) REVERT: B 238 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6582 (mtm-85) REVERT: B 387 TRP cc_start: 0.4961 (OUTLIER) cc_final: 0.3754 (t60) REVERT: B 393 PHE cc_start: 0.6731 (m-10) cc_final: 0.6268 (m-10) outliers start: 25 outliers final: 12 residues processed: 108 average time/residue: 0.1054 time to fit residues: 14.6535 Evaluate side-chains 108 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 172 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.161698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.121529 restraints weight = 7024.036| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.68 r_work: 0.3158 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7288 Z= 0.107 Angle : 0.483 6.847 9796 Z= 0.234 Chirality : 0.039 0.144 1004 Planarity : 0.003 0.033 1128 Dihedral : 21.333 167.229 1408 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.09 % Allowed : 21.47 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.45 (0.31), residues: 746 helix: 1.50 (0.23), residues: 548 sheet: None (None), residues: 0 loop : -0.44 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 184 TYR 0.007 0.001 TYR B 291 PHE 0.009 0.001 PHE A 79 TRP 0.017 0.001 TRP B 321 HIS 0.002 0.000 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 7288) covalent geometry : angle 0.48282 / 0.23 ( 9796) hydrogen bonds : bond 0.03536 / 2.35 ( 393) hydrogen bonds : angle 4.11305 / 2.93 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.246 Fit side-chains REVERT: A 19 MET cc_start: 0.7632 (ttt) cc_final: 0.7412 (ttt) REVERT: A 71 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.5630 (mmp-170) REVERT: A 88 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8460 (m-10) REVERT: A 170 PHE cc_start: 0.5904 (OUTLIER) cc_final: 0.4386 (m-80) REVERT: A 298 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: A 387 TRP cc_start: 0.4984 (OUTLIER) cc_final: 0.3645 (t60) REVERT: A 393 PHE cc_start: 0.6701 (m-10) cc_final: 0.6290 (m-10) REVERT: B 71 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.5549 (mmp-170) REVERT: B 170 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.4420 (m-80) REVERT: B 238 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6540 (mtm-85) REVERT: B 387 TRP cc_start: 0.4918 (OUTLIER) cc_final: 0.3755 (t60) REVERT: B 393 PHE cc_start: 0.6638 (m-10) cc_final: 0.6187 (m-10) outliers start: 21 outliers final: 10 residues processed: 109 average time/residue: 0.1201 time to fit residues: 16.6379 Evaluate side-chains 108 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 0.0170 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.163471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123379 restraints weight = 6972.957| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.68 r_work: 0.3195 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7288 Z= 0.099 Angle : 0.473 6.629 9796 Z= 0.228 Chirality : 0.039 0.144 1004 Planarity : 0.003 0.032 1128 Dihedral : 19.941 166.487 1408 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.09 % Allowed : 21.91 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.71 (0.31), residues: 746 helix: 1.69 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.38 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 184 TYR 0.007 0.001 TYR A 291 PHE 0.009 0.001 PHE A 21 TRP 0.018 0.001 TRP B 321 HIS 0.002 0.000 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 7288) covalent geometry : angle 0.47266 / 0.23 ( 9796) hydrogen bonds : bond 0.03327 / 2.20 ( 393) hydrogen bonds : angle 3.97581 / 2.83 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.247 Fit side-chains REVERT: A 71 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.5672 (mmp-170) REVERT: A 88 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8121 (m-10) REVERT: A 170 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.4567 (m-10) REVERT: A 298 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: A 387 TRP cc_start: 0.4950 (OUTLIER) cc_final: 0.3673 (t60) REVERT: A 393 PHE cc_start: 0.6644 (m-10) cc_final: 0.6237 (m-10) REVERT: B 71 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.5657 (mmp-170) REVERT: B 88 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8017 (m-10) REVERT: B 170 PHE cc_start: 0.5958 (OUTLIER) cc_final: 0.4567 (m-10) REVERT: B 387 TRP cc_start: 0.4890 (OUTLIER) cc_final: 0.3790 (t60) REVERT: B 393 PHE cc_start: 0.6667 (m-10) cc_final: 0.6212 (m-10) outliers start: 21 outliers final: 11 residues processed: 103 average time/residue: 0.1284 time to fit residues: 16.4908 Evaluate side-chains 103 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.162990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122778 restraints weight = 7071.955| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.70 r_work: 0.3178 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7288 Z= 0.106 Angle : 0.473 6.418 9796 Z= 0.230 Chirality : 0.039 0.146 1004 Planarity : 0.003 0.032 1128 Dihedral : 19.766 165.352 1408 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.53 % Allowed : 20.88 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.76 (0.31), residues: 746 helix: 1.73 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.38 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 60 TYR 0.007 0.001 TYR B 186 PHE 0.010 0.001 PHE A 79 TRP 0.016 0.001 TRP B 321 HIS 0.002 0.000 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 7288) covalent geometry : angle 0.47307 / 0.23 ( 9796) hydrogen bonds : bond 0.03396 / 2.25 ( 393) hydrogen bonds : angle 3.96645 / 2.82 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.177 Fit side-chains REVERT: A 19 MET cc_start: 0.7665 (ttt) cc_final: 0.7313 (ttt) REVERT: A 71 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.5627 (mmp-170) REVERT: A 88 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8126 (m-10) REVERT: A 170 PHE cc_start: 0.5914 (OUTLIER) cc_final: 0.4510 (m-10) REVERT: A 298 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: A 387 TRP cc_start: 0.4982 (OUTLIER) cc_final: 0.3700 (t60) REVERT: A 393 PHE cc_start: 0.6610 (m-10) cc_final: 0.6231 (m-10) REVERT: B 71 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.5616 (mmp-170) REVERT: B 88 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8107 (m-10) REVERT: B 170 PHE cc_start: 0.5997 (OUTLIER) cc_final: 0.4624 (m-10) REVERT: B 387 TRP cc_start: 0.4903 (OUTLIER) cc_final: 0.3777 (t60) REVERT: B 393 PHE cc_start: 0.6620 (m-10) cc_final: 0.6193 (m-10) outliers start: 24 outliers final: 13 residues processed: 106 average time/residue: 0.1110 time to fit residues: 14.9440 Evaluate side-chains 110 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 0.0980 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 0.0020 chunk 71 optimal weight: 0.0070 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 0.3006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.163859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123619 restraints weight = 6991.282| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.69 r_work: 0.3166 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7288 Z= 0.087 Angle : 0.458 6.360 9796 Z= 0.223 Chirality : 0.038 0.140 1004 Planarity : 0.003 0.030 1128 Dihedral : 19.421 164.822 1408 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.53 % Allowed : 20.88 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.87 (0.30), residues: 746 helix: 1.83 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 184 TYR 0.008 0.001 TYR B 186 PHE 0.009 0.001 PHE A 79 TRP 0.017 0.001 TRP B 321 HIS 0.003 0.000 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 ( 7288) covalent geometry : angle 0.45850 / 0.22 ( 9796) hydrogen bonds : bond 0.03145 / 2.09 ( 393) hydrogen bonds : angle 3.87507 / 2.75 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 19 MET cc_start: 0.7458 (ttt) cc_final: 0.7084 (ttt) REVERT: A 22 ARG cc_start: 0.7626 (mtp-110) cc_final: 0.7385 (mtp85) REVERT: A 71 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.5501 (mmp-170) REVERT: A 88 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8092 (m-10) REVERT: A 170 PHE cc_start: 0.5824 (OUTLIER) cc_final: 0.4459 (m-10) REVERT: A 393 PHE cc_start: 0.6483 (m-10) cc_final: 0.6106 (m-10) REVERT: B 71 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6484 (mmm-85) REVERT: B 88 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8026 (m-10) REVERT: B 170 PHE cc_start: 0.5842 (OUTLIER) cc_final: 0.4484 (m-10) REVERT: B 387 TRP cc_start: 0.4826 (OUTLIER) cc_final: 0.3800 (t60) REVERT: B 393 PHE cc_start: 0.6480 (m-10) cc_final: 0.6061 (m-10) outliers start: 24 outliers final: 16 residues processed: 103 average time/residue: 0.1080 time to fit residues: 14.1273 Evaluate side-chains 109 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 50 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.162682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121920 restraints weight = 6952.971| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.71 r_work: 0.3387 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7288 Z= 0.110 Angle : 0.475 6.264 9796 Z= 0.230 Chirality : 0.039 0.146 1004 Planarity : 0.003 0.032 1128 Dihedral : 19.493 164.469 1408 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.38 % Allowed : 21.47 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.83 (0.30), residues: 746 helix: 1.79 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.38 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 184 TYR 0.008 0.001 TYR B 186 PHE 0.010 0.001 PHE A 79 TRP 0.016 0.001 TRP B 321 HIS 0.003 0.000 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 7288) covalent geometry : angle 0.47502 / 0.23 ( 9796) hydrogen bonds : bond 0.03350 / 2.22 ( 393) hydrogen bonds : angle 3.92510 / 2.79 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.190 Fit side-chains REVERT: A 19 MET cc_start: 0.7695 (ttt) cc_final: 0.7340 (ttt) REVERT: A 22 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.7527 (mtp85) REVERT: A 71 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.5891 (mmp-170) REVERT: A 88 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8272 (m-10) REVERT: A 170 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.4742 (m-10) REVERT: A 387 TRP cc_start: 0.5161 (OUTLIER) cc_final: 0.4069 (t60) REVERT: A 393 PHE cc_start: 0.6724 (m-10) cc_final: 0.6344 (m-10) REVERT: B 71 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.7028 (mmm160) REVERT: B 88 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8154 (m-10) REVERT: B 170 PHE cc_start: 0.6112 (OUTLIER) cc_final: 0.4750 (m-10) REVERT: B 387 TRP cc_start: 0.4977 (OUTLIER) cc_final: 0.3894 (t60) REVERT: B 393 PHE cc_start: 0.6951 (m-10) cc_final: 0.6532 (m-10) outliers start: 23 outliers final: 13 residues processed: 102 average time/residue: 0.1059 time to fit residues: 13.8574 Evaluate side-chains 108 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 394 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.162462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120913 restraints weight = 6971.632| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.78 r_work: 0.3375 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7288 Z= 0.109 Angle : 0.474 6.256 9796 Z= 0.230 Chirality : 0.039 0.147 1004 Planarity : 0.003 0.031 1128 Dihedral : 19.501 164.335 1408 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.24 % Allowed : 21.47 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.84 (0.30), residues: 746 helix: 1.79 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.37 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 184 TYR 0.008 0.001 TYR B 186 PHE 0.019 0.001 PHE B 36 TRP 0.016 0.001 TRP B 321 HIS 0.002 0.000 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 7288) covalent geometry : angle 0.47431 / 0.23 ( 9796) hydrogen bonds : bond 0.03358 / 2.23 ( 393) hydrogen bonds : angle 3.92576 / 2.79 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1976.07 seconds wall clock time: 34 minutes 29.89 seconds (2069.89 seconds total)