Starting phenix.real_space_refine on Wed Aug 5 08:50:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dzj_27801/08_2026/8dzj_27801.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzj_27801/08_2026/8dzj_27801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dzj_27801/08_2026/8dzj_27801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzj_27801/08_2026/8dzj_27801.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dzj_27801/08_2026/8dzj_27801.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dzj_27801/08_2026/8dzj_27801.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dzj_27801/08_2026/8dzj_27801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzj_27801/08_2026/8dzj_27801.map" } resolution = 2.9 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= -0.000 sd= 0.002 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 Zn 1 6.06 5 P 190 5.49 5 S 21 5.16 5 C 4988 2.51 5 N 1635 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s 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: 9030 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3369 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1622 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 560 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "E" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3272 Classifications: {'RNAv2': 153} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 75, 'rna3p_pyr': 62} Link IDs: {'rna2p': 16, 'rna3p': 136} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2994 SG CYS A 372 44.439 13.422 45.939 1.00 30.07 S ATOM 3015 SG CYS A 375 42.544 10.078 46.726 1.00 35.03 S ATOM 3132 SG CYS A 391 45.670 10.363 47.236 1.00 37.27 S ATOM 3154 SG CYS A 394 44.416 9.788 43.268 1.00 37.08 S Time building chain proxies: 1.94, per 1000 atoms: 0.21 Number of scatterers: 9030 At special positions: 0 Unit cell: (85.2, 116.085, 137.385, 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) Zn 1 29.99 S 21 16.00 P 190 15.00 O 2195 8.00 N 1635 7.00 C 4988 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: 0.89 Conformation dependent library (CDL) restraints added in 181.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 391 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 375 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 394 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 372 " Number of angles added : 6 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1148 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 5 sheets defined 50.6% alpha, 20.1% beta 69 base pairs and 112 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 16 through 57 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.736A pdb=" N TYR A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.517A pdb=" N TYR A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 170 through 182 Processing helix chain 'A' and resid 247 through 270 removed outlier: 3.814A pdb=" N LYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.141A pdb=" N HIS A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 316 Processing helix chain 'A' and resid 325 through 330 removed outlier: 4.120A pdb=" N ILE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 357 Processing helix chain 'A' and resid 400 through 410 Processing helix chain 'A' and resid 412 through 422 Processing helix chain 'B' and resid 16 through 46 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.525A pdb=" N TYR B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 111 removed outlier: 5.481A pdb=" N LYS B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 150 through 158 Processing helix chain 'B' and resid 171 through 183 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127 removed outlier: 4.550A pdb=" N SER A 206 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER A 190 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN A 204 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 192 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR A 202 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N HIS A 194 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS A 200 " --> pdb=" O HIS A 194 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TRP A 201 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 9 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 168 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 11 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER A 164 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR A 142 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245 removed outlier: 6.034A pdb=" N MET A 222 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU A 324 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ILE A 224 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 321 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE A 363 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET A 323 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 391 Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 5.064A pdb=" N TRP B 201 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 11 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR B 142 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 295 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 174 hydrogen bonds 324 hydrogen bond angles 0 basepair planarities 69 basepair parallelities 112 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1711 1.33 - 1.45: 3255 1.45 - 1.57: 4226 1.57 - 1.69: 376 1.69 - 1.81: 37 Bond restraints: 9605 Sorted by residual: bond pdb=" C1' DT C 20 " pdb=" N1 DT C 20 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.24e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.21e-02 6.83e+03 9.61e+00 bond pdb=" C3' DA C 32 " pdb=" C2' DA C 32 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.32e+00 bond pdb=" N ILE A 329 " pdb=" CA ILE A 329 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.26e-02 6.30e+03 8.65e+00 bond pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 8.03e+00 ... (remaining 9600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 12812 1.41 - 2.81: 818 2.81 - 4.22: 193 4.22 - 5.63: 39 5.63 - 7.04: 2 Bond angle restraints: 13864 Sorted by residual: angle pdb=" O4' DC C 35 " pdb=" C4' DC C 35 " pdb=" C3' DC C 35 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" N3 DT C 20 " pdb=" C4 DT C 20 " pdb=" O4 DT C 20 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT C 22 " pdb=" C4 DT C 22 " pdb=" O4 DT C 22 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT C 16 " pdb=" C4 DT C 16 " pdb=" O4 DT C 16 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT D 10 " pdb=" C4 DT D 10 " pdb=" O4 DT D 10 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 13859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4366 17.98 - 35.95: 525 35.95 - 53.93: 296 53.93 - 71.90: 122 71.90 - 89.88: 16 Dihedral angle restraints: 5325 sinusoidal: 3530 harmonic: 1795 Sorted by residual: dihedral pdb=" C4' A E 105 " pdb=" C3' A E 105 " pdb=" C2' A E 105 " pdb=" C1' A E 105 " ideal model delta sinusoidal sigma weight residual 36.34 -36.84 73.19 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' A E 24 " pdb=" C3' A E 24 " pdb=" C2' A E 24 " pdb=" C1' A E 24 " ideal model delta sinusoidal sigma weight residual 36.34 -36.78 73.13 1 3.10e+00 1.04e-01 7.09e+02 dihedral pdb=" C4' A E 108 " pdb=" C3' A E 108 " pdb=" C2' A E 108 " pdb=" C1' A E 108 " ideal model delta sinusoidal sigma weight residual 36.34 -36.39 72.74 1 3.10e+00 1.04e-01 7.03e+02 ... (remaining 5322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1406 0.107 - 0.214: 62 0.214 - 0.321: 173 0.321 - 0.428: 0 0.428 - 0.535: 1 Chirality restraints: 1642 Sorted by residual: chirality pdb=" P G E 34 " pdb=" OP1 G E 34 " pdb=" OP2 G E 34 " pdb=" O5' G E 34 " both_signs ideal model delta sigma weight residual True 2.17 -2.71 -0.54 2.00e-01 2.50e+01 7.16e+00 chirality pdb=" P C E 67 " pdb=" OP1 C E 67 " pdb=" OP2 C E 67 " pdb=" O5' C E 67 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C2' G E 90 " pdb=" C3' G E 90 " pdb=" O2' G E 90 " pdb=" C1' G E 90 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1639 not shown) Planarity restraints: 1064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 233 " 0.015 2.00e-02 2.50e+03 1.53e-02 4.67e+00 pdb=" CG TYR A 233 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 233 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 233 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 233 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 233 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 233 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 233 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G E 31 " -0.026 2.00e-02 2.50e+03 1.20e-02 4.30e+00 pdb=" N9 G E 31 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G E 31 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G E 31 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G E 31 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G E 31 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G E 31 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G E 31 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G E 31 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G E 31 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G E 31 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G E 31 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A E 91 " 0.026 2.00e-02 2.50e+03 1.12e-02 3.48e+00 pdb=" N9 A E 91 " -0.024 2.00e-02 2.50e+03 pdb=" C8 A E 91 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A E 91 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A E 91 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A E 91 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A E 91 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A E 91 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A E 91 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A E 91 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A E 91 " -0.005 2.00e-02 2.50e+03 ... (remaining 1061 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1068 2.75 - 3.29: 8440 3.29 - 3.82: 17829 3.82 - 4.36: 21444 4.36 - 4.90: 31208 Nonbonded interactions: 79989 Sorted by model distance: nonbonded pdb=" OE1 GLU A 288 " pdb=" NH2 ARG A 291 " model vdw 2.209 3.120 nonbonded pdb=" NH1 ARG A 291 " pdb=" OP1 DC C 21 " model vdw 2.211 3.120 nonbonded pdb=" O6 G E 36 " pdb=" O4 U E 62 " model vdw 2.229 2.432 nonbonded pdb=" O2' C E 174 " pdb=" O4' U E 175 " model vdw 2.235 3.040 nonbonded pdb=" O TYR B 84 " pdb=" OG SER B 150 " model vdw 2.255 3.040 ... (remaining 79984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.450 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:9.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.007 0.497 9609 Z= 0.340 Angle : 0.897 22.823 13870 Z= 0.472 Chirality : 0.090 0.535 1642 Planarity : 0.004 0.038 1064 Dihedral : 19.743 89.877 4177 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.38 % Allowed : 0.19 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.33), residues: 605 helix: 1.65 (0.30), residues: 298 sheet: 0.21 (0.43), residues: 130 loop : -0.75 (0.43), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 291 TYR 0.036 0.002 TYR A 233 PHE 0.008 0.001 PHE A 336 TRP 0.019 0.002 TRP B 43 HIS 0.012 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.29 ( 9605) covalent geometry : angle 0.81863 / 0.47 (13864) hydrogen bonds : bond 0.09213 / 5.64 ( 459) hydrogen bonds : angle 5.20261 / 3.68 ( 1170) metal coordination : bond 0.25011 / 16.65 ( 4) metal coordination : angle 17.63739 / 10.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 0.5647 time to fit residues: 53.4329 Evaluate side-chains 47 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.088637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.062609 restraints weight = 26971.769| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.34 r_work: 0.3199 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9609 Z= 0.334 Angle : 1.238 20.639 13870 Z= 0.529 Chirality : 0.118 1.445 1642 Planarity : 0.006 0.049 1064 Dihedral : 19.589 132.772 2925 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.88 % Allowed : 8.66 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.33), residues: 605 helix: 1.87 (0.29), residues: 303 sheet: -0.09 (0.41), residues: 134 loop : -0.93 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 242 TYR 0.026 0.002 TYR A 351 PHE 0.007 0.002 PHE A 33 TRP 0.015 0.002 TRP B 45 HIS 0.009 0.002 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.33 ( 9605) covalent geometry : angle 1.23211 / 0.53 (13864) hydrogen bonds : bond 0.05962 / 3.61 ( 459) hydrogen bonds : angle 4.51459 / 3.28 ( 1170) metal coordination : bond 0.02130 / 1.43 ( 4) metal coordination : angle 6.08823 / 4.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7814 (mt-10) REVERT: A 222 MET cc_start: 0.8521 (ttm) cc_final: 0.8115 (ttt) REVERT: A 323 MET cc_start: 0.8467 (ptt) cc_final: 0.8256 (ptt) REVERT: B 156 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8303 (tm-30) REVERT: B 177 MET cc_start: 0.8529 (mmm) cc_final: 0.8299 (mmm) outliers start: 10 outliers final: 7 residues processed: 50 average time/residue: 0.5061 time to fit residues: 27.3240 Evaluate side-chains 48 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 204 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 10.9990 chunk 59 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 GLN B 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.090094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.064202 restraints weight = 26863.521| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.29 r_work: 0.3244 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9609 Z= 0.195 Angle : 0.960 14.176 13870 Z= 0.418 Chirality : 0.082 0.827 1642 Planarity : 0.004 0.044 1064 Dihedral : 19.534 137.990 2923 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.32 % Allowed : 11.30 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.33), residues: 605 helix: 2.31 (0.29), residues: 301 sheet: -0.03 (0.40), residues: 134 loop : -0.85 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 242 TYR 0.022 0.001 TYR A 351 PHE 0.013 0.001 PHE A 253 TRP 0.010 0.001 TRP B 45 HIS 0.005 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 ( 9605) covalent geometry : angle 0.95531 / 0.42 (13864) hydrogen bonds : bond 0.05459 / 3.32 ( 459) hydrogen bonds : angle 4.31474 / 3.15 ( 1170) metal coordination : bond 0.00832 / 0.51 ( 4) metal coordination : angle 4.76288 / 3.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7775 (mt-10) REVERT: A 222 MET cc_start: 0.8442 (ttm) cc_final: 0.8077 (ttm) REVERT: A 270 TYR cc_start: 0.4545 (t80) cc_final: 0.4177 (m-80) REVERT: A 323 MET cc_start: 0.8422 (ptt) cc_final: 0.8200 (ptt) REVERT: B 156 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8556 (tm-30) REVERT: B 177 MET cc_start: 0.8526 (mmm) cc_final: 0.8290 (mmm) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.5043 time to fit residues: 26.0973 Evaluate side-chains 43 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.086890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.061016 restraints weight = 27702.464| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.35 r_work: 0.3163 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 9609 Z= 0.349 Angle : 1.048 12.515 13870 Z= 0.459 Chirality : 0.083 0.777 1642 Planarity : 0.005 0.057 1064 Dihedral : 19.560 137.744 2923 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.51 % Allowed : 13.56 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.33), residues: 605 helix: 1.91 (0.29), residues: 303 sheet: -0.24 (0.40), residues: 134 loop : -0.99 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 242 TYR 0.023 0.002 TYR A 351 PHE 0.015 0.002 PHE A 253 TRP 0.020 0.002 TRP B 43 HIS 0.007 0.002 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.35 ( 9605) covalent geometry : angle 1.04393 / 0.46 (13864) hydrogen bonds : bond 0.06422 / 3.87 ( 459) hydrogen bonds : angle 4.39073 / 3.21 ( 1170) metal coordination : bond 0.01262 / 0.75 ( 4) metal coordination : angle 4.69357 / 2.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7831 (mt-10) REVERT: A 222 MET cc_start: 0.8711 (ttm) cc_final: 0.8331 (ttm) REVERT: A 288 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8681 (mm-30) REVERT: A 292 ASP cc_start: 0.8809 (m-30) cc_final: 0.8534 (m-30) REVERT: B 156 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8489 (tm-30) REVERT: B 177 MET cc_start: 0.8626 (mmm) cc_final: 0.8371 (mmm) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.5911 time to fit residues: 30.4238 Evaluate side-chains 45 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.089172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.063417 restraints weight = 27043.286| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.34 r_work: 0.3227 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9609 Z= 0.173 Angle : 0.915 11.614 13870 Z= 0.399 Chirality : 0.073 0.682 1642 Planarity : 0.004 0.043 1064 Dihedral : 19.521 137.121 2923 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.51 % Allowed : 13.56 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.33), residues: 605 helix: 2.36 (0.29), residues: 303 sheet: -0.15 (0.40), residues: 132 loop : -0.83 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.019 0.001 TYR A 351 PHE 0.022 0.002 PHE A 253 TRP 0.008 0.001 TRP B 45 HIS 0.003 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 9605) covalent geometry : angle 0.91128 / 0.40 (13864) hydrogen bonds : bond 0.05512 / 3.38 ( 459) hydrogen bonds : angle 4.24400 / 3.11 ( 1170) metal coordination : bond 0.00723 / 0.42 ( 4) metal coordination : angle 4.03893 / 2.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7789 (mt-10) REVERT: A 157 MET cc_start: 0.8702 (mmm) cc_final: 0.8482 (tpp) REVERT: A 222 MET cc_start: 0.8446 (ttm) cc_final: 0.8063 (ttm) REVERT: A 244 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8674 (pttp) REVERT: A 288 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8119 (mm-30) REVERT: A 292 ASP cc_start: 0.8766 (m-30) cc_final: 0.8268 (m-30) REVERT: B 26 GLN cc_start: 0.8017 (mm110) cc_final: 0.7620 (mm-40) REVERT: B 156 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8454 (tm-30) REVERT: B 177 MET cc_start: 0.8637 (mmm) cc_final: 0.8433 (mmm) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.5870 time to fit residues: 32.7284 Evaluate side-chains 49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.087497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.061675 restraints weight = 27254.962| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.33 r_work: 0.3185 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 9609 Z= 0.274 Angle : 0.956 11.626 13870 Z= 0.420 Chirality : 0.075 0.670 1642 Planarity : 0.005 0.049 1064 Dihedral : 19.517 137.324 2923 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.32 % Allowed : 14.69 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.33), residues: 605 helix: 2.24 (0.29), residues: 303 sheet: -0.24 (0.39), residues: 132 loop : -0.94 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.022 0.002 TYR A 351 PHE 0.022 0.002 PHE A 253 TRP 0.016 0.002 TRP B 43 HIS 0.005 0.002 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.27 ( 9605) covalent geometry : angle 0.95305 / 0.42 (13864) hydrogen bonds : bond 0.05972 / 3.64 ( 459) hydrogen bonds : angle 4.26709 / 3.13 ( 1170) metal coordination : bond 0.00992 / 0.57 ( 4) metal coordination : angle 3.92307 / 2.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7842 (mt-10) REVERT: A 114 MET cc_start: 0.7824 (ptp) cc_final: 0.7521 (ptm) REVERT: A 222 MET cc_start: 0.8613 (ttm) cc_final: 0.8268 (ttm) REVERT: A 288 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8094 (mm-30) REVERT: A 292 ASP cc_start: 0.8768 (m-30) cc_final: 0.8260 (m-30) REVERT: B 26 GLN cc_start: 0.8082 (mm110) cc_final: 0.7803 (mm-40) REVERT: B 156 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8449 (tm-30) REVERT: B 177 MET cc_start: 0.8646 (mmm) cc_final: 0.8386 (mmm) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.5229 time to fit residues: 27.6021 Evaluate side-chains 47 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.090068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.064545 restraints weight = 26872.457| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.28 r_work: 0.3261 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9609 Z= 0.151 Angle : 0.872 10.945 13870 Z= 0.381 Chirality : 0.069 0.619 1642 Planarity : 0.004 0.043 1064 Dihedral : 19.456 136.612 2923 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.88 % Allowed : 14.50 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.34), residues: 605 helix: 2.50 (0.29), residues: 303 sheet: -0.10 (0.40), residues: 132 loop : -0.71 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 242 TYR 0.017 0.001 TYR A 351 PHE 0.033 0.002 PHE A 253 TRP 0.007 0.001 TRP B 45 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 9605) covalent geometry : angle 0.86934 / 0.38 (13864) hydrogen bonds : bond 0.05414 / 3.38 ( 459) hydrogen bonds : angle 4.13249 / 3.03 ( 1170) metal coordination : bond 0.00521 / 0.30 ( 4) metal coordination : angle 3.36911 / 1.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7821 (mt-10) REVERT: A 114 MET cc_start: 0.7742 (ptp) cc_final: 0.7485 (ptm) REVERT: A 157 MET cc_start: 0.8724 (mmm) cc_final: 0.8464 (tpp) REVERT: A 222 MET cc_start: 0.8308 (ttm) cc_final: 0.7981 (ttm) REVERT: A 253 PHE cc_start: 0.8893 (t80) cc_final: 0.8527 (t80) REVERT: A 288 GLU cc_start: 0.9012 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 292 ASP cc_start: 0.8730 (m-30) cc_final: 0.8179 (m-30) REVERT: B 26 GLN cc_start: 0.8091 (mm110) cc_final: 0.7666 (mm-40) REVERT: B 137 MET cc_start: 0.7434 (mpp) cc_final: 0.7069 (pmm) REVERT: B 156 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8445 (tm-30) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.5994 time to fit residues: 34.0603 Evaluate side-chains 52 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.085988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.060324 restraints weight = 27478.081| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.29 r_work: 0.3154 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 9609 Z= 0.383 Angle : 1.048 14.011 13870 Z= 0.460 Chirality : 0.078 0.723 1642 Planarity : 0.005 0.060 1064 Dihedral : 19.535 137.066 2923 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.51 % Allowed : 14.69 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.99 (0.33), residues: 605 helix: 2.03 (0.29), residues: 303 sheet: -0.40 (0.40), residues: 131 loop : -0.94 (0.43), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 280 TYR 0.022 0.002 TYR A 351 PHE 0.020 0.003 PHE A 253 TRP 0.022 0.003 TRP B 43 HIS 0.006 0.002 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.38 ( 9605) covalent geometry : angle 1.04505 / 0.46 (13864) hydrogen bonds : bond 0.06610 / 4.07 ( 459) hydrogen bonds : angle 4.34036 / 3.18 ( 1170) metal coordination : bond 0.01251 / 0.72 ( 4) metal coordination : angle 4.08887 / 2.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7856 (mt-10) REVERT: A 222 MET cc_start: 0.8687 (ttm) cc_final: 0.8354 (ttm) REVERT: A 288 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8057 (mm-30) REVERT: A 292 ASP cc_start: 0.8780 (m-30) cc_final: 0.8281 (m-30) REVERT: B 26 GLN cc_start: 0.8180 (mm110) cc_final: 0.7847 (mm-40) REVERT: B 137 MET cc_start: 0.7509 (mpp) cc_final: 0.7099 (pmm) REVERT: B 156 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8497 (tm-30) outliers start: 8 outliers final: 7 residues processed: 46 average time/residue: 0.5697 time to fit residues: 28.2163 Evaluate side-chains 45 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.089482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.064131 restraints weight = 26956.439| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.26 r_work: 0.3248 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9609 Z= 0.155 Angle : 0.889 13.009 13870 Z= 0.390 Chirality : 0.069 0.551 1642 Planarity : 0.004 0.046 1064 Dihedral : 19.522 137.283 2923 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.88 % Allowed : 14.88 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.34), residues: 605 helix: 2.44 (0.29), residues: 302 sheet: -0.29 (0.40), residues: 132 loop : -0.69 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 242 TYR 0.016 0.001 TYR A 351 PHE 0.039 0.002 PHE A 253 TRP 0.008 0.001 TRP B 45 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 ( 9605) covalent geometry : angle 0.88622 / 0.39 (13864) hydrogen bonds : bond 0.05480 / 3.43 ( 459) hydrogen bonds : angle 4.14156 / 3.03 ( 1170) metal coordination : bond 0.00503 / 0.28 ( 4) metal coordination : angle 3.59327 / 2.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7831 (mt-10) REVERT: A 222 MET cc_start: 0.8379 (ttm) cc_final: 0.8072 (ttm) REVERT: A 288 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 292 ASP cc_start: 0.8750 (m-30) cc_final: 0.8225 (m-30) REVERT: B 26 GLN cc_start: 0.8162 (mm110) cc_final: 0.7480 (mm-40) REVERT: B 30 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7861 (mp0) REVERT: B 137 MET cc_start: 0.7491 (mpp) cc_final: 0.7121 (pmm) REVERT: B 156 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8414 (tm-30) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 0.5498 time to fit residues: 27.7918 Evaluate side-chains 49 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 69 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 0.0050 chunk 49 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.089985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.064475 restraints weight = 26875.946| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.31 r_work: 0.3261 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9609 Z= 0.154 Angle : 0.853 11.810 13870 Z= 0.378 Chirality : 0.066 0.495 1642 Planarity : 0.004 0.044 1064 Dihedral : 19.372 137.590 2923 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.13 % Allowed : 15.44 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.34), residues: 605 helix: 2.50 (0.29), residues: 302 sheet: -0.19 (0.40), residues: 132 loop : -0.70 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 242 TYR 0.020 0.001 TYR A 351 PHE 0.046 0.003 PHE A 253 TRP 0.007 0.001 TRP B 45 HIS 0.002 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 9605) covalent geometry : angle 0.85118 / 0.38 (13864) hydrogen bonds : bond 0.05473 / 3.42 ( 459) hydrogen bonds : angle 4.10316 / 2.99 ( 1170) metal coordination : bond 0.00461 / 0.27 ( 4) metal coordination : angle 3.05435 / 1.84 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7822 (mt-10) REVERT: A 222 MET cc_start: 0.8263 (ttm) cc_final: 0.7975 (ttm) REVERT: A 288 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8002 (mm-30) REVERT: A 292 ASP cc_start: 0.8754 (m-30) cc_final: 0.8234 (m-30) REVERT: B 26 GLN cc_start: 0.8138 (mm110) cc_final: 0.7462 (mm-40) REVERT: B 30 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7829 (mp0) REVERT: B 137 MET cc_start: 0.7541 (mpp) cc_final: 0.7267 (pmm) REVERT: B 156 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8342 (tm-30) outliers start: 6 outliers final: 6 residues processed: 49 average time/residue: 0.6077 time to fit residues: 31.9154 Evaluate side-chains 50 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.088223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.062474 restraints weight = 26835.116| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.33 r_work: 0.3213 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9609 Z= 0.233 Angle : 0.907 13.032 13870 Z= 0.402 Chirality : 0.068 0.546 1642 Planarity : 0.005 0.051 1064 Dihedral : 19.408 138.093 2923 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.13 % Allowed : 16.01 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.34), residues: 605 helix: 2.46 (0.30), residues: 302 sheet: -0.26 (0.40), residues: 131 loop : -0.73 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.022 0.002 TYR A 270 PHE 0.058 0.003 PHE A 253 TRP 0.014 0.002 TRP B 43 HIS 0.004 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 ( 9605) covalent geometry : angle 0.90463 / 0.40 (13864) hydrogen bonds : bond 0.05830 / 3.62 ( 459) hydrogen bonds : angle 4.15454 / 3.04 ( 1170) metal coordination : bond 0.00773 / 0.44 ( 4) metal coordination : angle 3.42422 / 2.10 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3375.48 seconds wall clock time: 58 minutes 12.99 seconds (3492.99 seconds total)