Starting phenix.real_space_refine on Tue Aug 4 14:09:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vj3_65102/08_2026/9vj3_65102_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vj3_65102/08_2026/9vj3_65102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vj3_65102/08_2026/9vj3_65102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vj3_65102/08_2026/9vj3_65102.map" model { file = "/net/cci-nas-00/data/ceres_data/9vj3_65102/08_2026/9vj3_65102_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vj3_65102/08_2026/9vj3_65102_neut.cif" } resolution = 3.4 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= 0.034 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 21 5.16 5 C 2536 2.51 5 N 538 2.21 5 O 606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 3702 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2259 Classifications: {'peptide': 280} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 259} Chain: "B" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1372 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'C14': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'46E': 1, 'C14': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.09, per 1000 atoms: 0.29 Number of scatterers: 3702 At special positions: 0 Unit cell: (75.48, 59.94, 89.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 1 15.00 O 606 8.00 N 538 7.00 C 2536 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: 0.36 Conformation dependent library (CDL) restraints added in 135.5 milliseconds 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 844 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 43 through 62 Processing helix chain 'A' and resid 65 through 82 removed outlier: 3.570A pdb=" N LYS A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 92 through 107 removed outlier: 3.848A pdb=" N TYR A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.611A pdb=" N ILE A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 161 through 171 Processing helix chain 'A' and resid 175 through 198 removed outlier: 3.927A pdb=" N GLY A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 removed outlier: 4.191A pdb=" N LYS A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 208 " --> pdb=" O TRP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.593A pdb=" N LEU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.662A pdb=" N CYS A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 291 removed outlier: 3.610A pdb=" N ALA A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 289 " --> pdb=" O TRP A 285 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 315 removed outlier: 3.947A pdb=" N TYR A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 43 removed outlier: 4.083A pdb=" N LEU B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 50 through 73 removed outlier: 4.085A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 110 Processing helix chain 'B' and resid 145 through 181 removed outlier: 3.513A pdb=" N HIS B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 221 242 hydrogen bonds defined for protein. 726 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: 0.57 Time building geometry restraints manager: 0.45 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: 603 1.33 - 1.45: 1139 1.45 - 1.57: 2058 1.57 - 1.69: 2 1.69 - 1.81: 32 Bond restraints: 3834 Sorted by residual: bond pdb=" C31 46E B 302 " pdb=" O31 46E B 302 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C21 46E B 302 " pdb=" O21 46E B 302 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" N TYR A 102 " pdb=" CA TYR A 102 " ideal model delta sigma weight residual 1.457 1.394 0.063 1.29e-02 6.01e+03 2.39e+01 bond pdb=" CB TYR A 102 " pdb=" CG TYR A 102 " ideal model delta sigma weight residual 1.512 1.433 0.079 2.20e-02 2.07e+03 1.29e+01 bond pdb=" C LEU A 101 " pdb=" N TYR A 102 " ideal model delta sigma weight residual 1.332 1.293 0.040 1.40e-02 5.10e+03 8.04e+00 ... (remaining 3829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 4946 1.84 - 3.69: 225 3.69 - 5.53: 33 5.53 - 7.37: 8 7.37 - 9.22: 6 Bond angle restraints: 5218 Sorted by residual: angle pdb=" N LYS A 314 " pdb=" CA LYS A 314 " pdb=" C LYS A 314 " ideal model delta sigma weight residual 111.82 117.50 -5.68 1.16e+00 7.43e-01 2.39e+01 angle pdb=" C PRO A 174 " pdb=" N THR A 175 " pdb=" CA THR A 175 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" N SER B 35 " pdb=" CA SER B 35 " pdb=" C SER B 35 " ideal model delta sigma weight residual 111.07 107.60 3.47 1.07e+00 8.73e-01 1.05e+01 angle pdb=" O11 46E B 302 " pdb=" P 46E B 302 " pdb=" O13 46E B 302 " ideal model delta sigma weight residual 93.37 102.59 -9.22 3.00e+00 1.11e-01 9.44e+00 angle pdb=" C LEU A 273 " pdb=" CA LEU A 273 " pdb=" CB LEU A 273 " ideal model delta sigma weight residual 112.12 107.57 4.55 1.50e+00 4.44e-01 9.19e+00 ... (remaining 5213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 2111 35.51 - 71.01: 48 71.01 - 106.51: 5 106.51 - 142.02: 3 142.02 - 177.52: 3 Dihedral angle restraints: 2170 sinusoidal: 856 harmonic: 1314 Sorted by residual: dihedral pdb=" CA PHE A 251 " pdb=" C PHE A 251 " pdb=" N PRO A 252 " pdb=" CA PRO A 252 " ideal model delta harmonic sigma weight residual 0.00 -26.31 26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ALA A 160 " pdb=" C ALA A 160 " pdb=" N PRO A 161 " pdb=" CA PRO A 161 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" C2 46E B 302 " pdb=" C21 46E B 302 " pdb=" O21 46E B 302 " pdb=" C22 46E B 302 " ideal model delta sinusoidal sigma weight residual 176.49 -1.03 177.52 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 2167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 493 0.064 - 0.129: 76 0.129 - 0.193: 3 0.193 - 0.257: 2 0.257 - 0.321: 1 Chirality restraints: 575 Sorted by residual: chirality pdb=" CA LYS A 314 " pdb=" N LYS A 314 " pdb=" C LYS A 314 " pdb=" CB LYS A 314 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA LYS A 274 " pdb=" N LYS A 274 " pdb=" C LYS A 274 " pdb=" CB LYS A 274 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C2 46E B 302 " pdb=" C1 46E B 302 " pdb=" C3 46E B 302 " pdb=" O21 46E B 302 " both_signs ideal model delta sigma weight residual False -2.34 -2.55 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 572 not shown) Planarity restraints: 617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 272 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C LYS A 272 " 0.051 2.00e-02 2.50e+03 pdb=" O LYS A 272 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU A 273 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 160 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO A 161 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 274 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.81e+00 pdb=" N PRO A 275 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 275 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 275 " -0.029 5.00e-02 4.00e+02 ... (remaining 614 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 355 2.74 - 3.28: 3769 3.28 - 3.82: 6071 3.82 - 4.36: 6459 4.36 - 4.90: 11499 Nonbonded interactions: 28153 Sorted by model distance: nonbonded pdb=" O TRP B 205 " pdb=" OG SER B 208 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 268 " pdb=" O PRO A 319 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR B 19 " pdb=" O ILE B 74 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASN A 235 " pdb=" N MET A 236 " model vdw 2.268 3.120 nonbonded pdb=" OH TYR A 205 " pdb=" O GLN A 212 " model vdw 2.273 3.040 ... (remaining 28148 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: 2.410 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.560 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 0.127 3834 Z= 0.285 Angle : 0.892 9.216 5218 Z= 0.489 Chirality : 0.045 0.321 575 Planarity : 0.007 0.065 617 Dihedral : 18.186 177.520 1326 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.41 % Favored : 93.14 % Rotamer: Outliers : 0.25 % Allowed : 1.78 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.32 (0.40), residues: 437 helix: 0.98 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -2.10 (0.62), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 164 TYR 0.015 0.001 TYR A 102 PHE 0.018 0.001 PHE A 144 TRP 0.019 0.001 TRP B 107 HIS 0.005 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.28 ( 3834) covalent geometry : angle 0.89244 / 0.49 ( 5218) hydrogen bonds : bond 0.13840 / 8.56 ( 242) hydrogen bonds : angle 5.76520 / 4.34 ( 726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.163 Fit side-chains REVERT: B 207 LYS cc_start: 0.6881 (tmtt) cc_final: 0.6659 (tptp) outliers start: 1 outliers final: 1 residues processed: 108 average time/residue: 0.0589 time to fit residues: 8.1766 Evaluate side-chains 89 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.0010 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 GLN A 219 HIS A 317 HIS B 168 ASN B 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.197050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151475 restraints weight = 4866.747| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.69 r_work: 0.3707 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3834 Z= 0.144 Angle : 0.626 6.392 5218 Z= 0.323 Chirality : 0.040 0.152 575 Planarity : 0.006 0.061 617 Dihedral : 18.029 160.716 543 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.95 % Favored : 93.82 % Rotamer: Outliers : 3.31 % Allowed : 10.94 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.72 (0.41), residues: 437 helix: 1.26 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -2.06 (0.64), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 113 TYR 0.010 0.001 TYR A 209 PHE 0.036 0.001 PHE A 266 TRP 0.008 0.001 TRP A 150 HIS 0.011 0.002 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 3834) covalent geometry : angle 0.62564 / 0.32 ( 5218) hydrogen bonds : bond 0.04708 / 3.01 ( 242) hydrogen bonds : angle 4.40192 / 3.14 ( 726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.134 Fit side-chains REVERT: A 108 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.5979 (m-80) REVERT: B 92 ASP cc_start: 0.8722 (t0) cc_final: 0.8186 (t0) REVERT: B 166 TYR cc_start: 0.7250 (t80) cc_final: 0.7000 (t80) REVERT: B 207 LYS cc_start: 0.6728 (tmtt) cc_final: 0.6434 (tptp) outliers start: 13 outliers final: 4 residues processed: 101 average time/residue: 0.0545 time to fit residues: 6.9902 Evaluate side-chains 96 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 214 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.194334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.149147 restraints weight = 4855.081| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.72 r_work: 0.3652 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3834 Z= 0.155 Angle : 0.613 6.487 5218 Z= 0.317 Chirality : 0.039 0.132 575 Planarity : 0.006 0.058 617 Dihedral : 17.197 159.476 539 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.86 % Favored : 92.91 % Rotamer: Outliers : 3.82 % Allowed : 14.50 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.82 (0.41), residues: 437 helix: 1.35 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -2.09 (0.63), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 203 TYR 0.015 0.001 TYR B 72 PHE 0.025 0.001 PHE A 171 TRP 0.008 0.001 TRP B 102 HIS 0.005 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 3834) covalent geometry : angle 0.61315 / 0.32 ( 5218) hydrogen bonds : bond 0.04799 / 3.08 ( 242) hydrogen bonds : angle 4.31615 / 3.06 ( 726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.135 Fit side-chains REVERT: A 108 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: A 144 PHE cc_start: 0.8730 (t80) cc_final: 0.8241 (m-80) REVERT: B 207 LYS cc_start: 0.6775 (tmtt) cc_final: 0.6474 (tptp) outliers start: 15 outliers final: 10 residues processed: 103 average time/residue: 0.0634 time to fit residues: 8.1870 Evaluate side-chains 101 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 215 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 GLN A 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.194518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149018 restraints weight = 4905.462| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.76 r_work: 0.3635 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3834 Z= 0.144 Angle : 0.596 7.172 5218 Z= 0.306 Chirality : 0.039 0.126 575 Planarity : 0.006 0.102 617 Dihedral : 16.609 175.850 539 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.18 % Favored : 93.59 % Rotamer: Outliers : 5.09 % Allowed : 16.03 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.81 (0.41), residues: 437 helix: 1.40 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -2.22 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.010 0.001 TYR A 209 PHE 0.021 0.001 PHE A 171 TRP 0.008 0.001 TRP B 102 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 3834) covalent geometry : angle 0.59576 / 0.31 ( 5218) hydrogen bonds : bond 0.04669 / 3.00 ( 242) hydrogen bonds : angle 4.25030 / 3.00 ( 726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 108 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.6113 (m-80) REVERT: A 270 PHE cc_start: 0.8574 (m-80) cc_final: 0.8358 (m-80) REVERT: B 207 LYS cc_start: 0.6731 (tmtt) cc_final: 0.6417 (tptp) outliers start: 20 outliers final: 10 residues processed: 107 average time/residue: 0.0567 time to fit residues: 7.7714 Evaluate side-chains 104 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 214 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.192490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146952 restraints weight = 4875.192| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.74 r_work: 0.3621 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3834 Z= 0.168 Angle : 0.659 9.315 5218 Z= 0.331 Chirality : 0.040 0.152 575 Planarity : 0.007 0.110 617 Dihedral : 15.397 150.334 539 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.41 % Favored : 93.36 % Rotamer: Outliers : 4.33 % Allowed : 18.83 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.73 (0.41), residues: 437 helix: 1.33 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -2.26 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.015 0.001 TYR B 72 PHE 0.023 0.001 PHE A 266 TRP 0.008 0.001 TRP B 102 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 3834) covalent geometry : angle 0.65920 / 0.33 ( 5218) hydrogen bonds : bond 0.04906 / 3.16 ( 242) hydrogen bonds : angle 4.32953 / 3.04 ( 726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 108 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.6147 (m-80) REVERT: A 144 PHE cc_start: 0.8798 (t80) cc_final: 0.8310 (m-80) REVERT: A 270 PHE cc_start: 0.8572 (m-80) cc_final: 0.8363 (m-80) REVERT: B 207 LYS cc_start: 0.6747 (tmtt) cc_final: 0.6434 (tptp) outliers start: 17 outliers final: 13 residues processed: 105 average time/residue: 0.0619 time to fit residues: 8.1015 Evaluate side-chains 107 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 209 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.194066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.147656 restraints weight = 5057.208| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.88 r_work: 0.3644 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3834 Z= 0.139 Angle : 0.623 8.522 5218 Z= 0.316 Chirality : 0.039 0.146 575 Planarity : 0.007 0.110 617 Dihedral : 14.407 147.120 539 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.95 % Favored : 93.82 % Rotamer: Outliers : 5.85 % Allowed : 19.08 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.85 (0.41), residues: 437 helix: 1.45 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -2.36 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 113 TYR 0.019 0.001 TYR B 72 PHE 0.022 0.001 PHE A 171 TRP 0.007 0.001 TRP B 102 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 3834) covalent geometry : angle 0.62303 / 0.32 ( 5218) hydrogen bonds : bond 0.04511 / 2.89 ( 242) hydrogen bonds : angle 4.14868 / 2.93 ( 726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 108 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: A 144 PHE cc_start: 0.8762 (t80) cc_final: 0.8332 (m-80) REVERT: A 212 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6813 (pm20) REVERT: A 261 MET cc_start: 0.8265 (tpp) cc_final: 0.7511 (tpp) REVERT: B 149 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: B 207 LYS cc_start: 0.6708 (tmtt) cc_final: 0.6409 (tptp) outliers start: 23 outliers final: 14 residues processed: 104 average time/residue: 0.0551 time to fit residues: 7.3640 Evaluate side-chains 111 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 215 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.189247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.142502 restraints weight = 4967.329| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.81 r_work: 0.3581 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3834 Z= 0.215 Angle : 0.692 9.687 5218 Z= 0.353 Chirality : 0.042 0.142 575 Planarity : 0.007 0.113 617 Dihedral : 14.291 142.344 539 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.41 % Favored : 93.36 % Rotamer: Outliers : 6.36 % Allowed : 18.83 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.59 (0.40), residues: 437 helix: 1.24 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -2.31 (0.59), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.010 0.001 TYR A 209 PHE 0.018 0.001 PHE A 50 TRP 0.012 0.001 TRP A 285 HIS 0.006 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 ( 3834) covalent geometry : angle 0.69198 / 0.35 ( 5218) hydrogen bonds : bond 0.05321 / 3.43 ( 242) hydrogen bonds : angle 4.37624 / 3.07 ( 726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 108 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.6125 (m-80) REVERT: A 186 TYR cc_start: 0.8471 (m-80) cc_final: 0.7830 (m-80) REVERT: B 207 LYS cc_start: 0.6713 (tmtt) cc_final: 0.6404 (tptp) outliers start: 25 outliers final: 14 residues processed: 111 average time/residue: 0.0459 time to fit residues: 6.6184 Evaluate side-chains 111 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 209 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** B 176 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 = 0.4269 r_free = 0.4269 target = 0.193813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.148731 restraints weight = 4845.836| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.74 r_work: 0.3645 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3834 Z= 0.146 Angle : 0.673 10.377 5218 Z= 0.336 Chirality : 0.040 0.142 575 Planarity : 0.007 0.119 617 Dihedral : 13.924 142.091 539 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.49 % Favored : 94.28 % Rotamer: Outliers : 4.83 % Allowed : 22.39 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.83 (0.41), residues: 437 helix: 1.39 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -2.20 (0.62), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.007 0.001 TYR A 129 PHE 0.024 0.001 PHE A 171 TRP 0.008 0.001 TRP B 102 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 3834) covalent geometry : angle 0.67258 / 0.34 ( 5218) hydrogen bonds : bond 0.04704 / 3.01 ( 242) hydrogen bonds : angle 4.22019 / 2.98 ( 726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 108 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.6205 (m-80) REVERT: B 149 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: B 170 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7199 (mm) REVERT: B 207 LYS cc_start: 0.6675 (tmtt) cc_final: 0.6365 (tptp) outliers start: 19 outliers final: 13 residues processed: 103 average time/residue: 0.0518 time to fit residues: 6.8552 Evaluate side-chains 110 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 209 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.194173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.148848 restraints weight = 4819.887| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.75 r_work: 0.3660 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3834 Z= 0.145 Angle : 0.668 11.590 5218 Z= 0.334 Chirality : 0.040 0.137 575 Planarity : 0.007 0.117 617 Dihedral : 13.600 139.498 539 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.72 % Favored : 94.05 % Rotamer: Outliers : 3.82 % Allowed : 23.41 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.41), residues: 437 helix: 1.46 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -2.08 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.010 0.001 TYR A 205 PHE 0.023 0.001 PHE A 50 TRP 0.007 0.001 TRP B 102 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 3834) covalent geometry : angle 0.66834 / 0.33 ( 5218) hydrogen bonds : bond 0.04559 / 2.91 ( 242) hydrogen bonds : angle 4.17043 / 2.96 ( 726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 108 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.6196 (m-80) REVERT: A 212 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6800 (pm20) REVERT: A 261 MET cc_start: 0.8198 (tpp) cc_final: 0.7476 (tpp) REVERT: B 149 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: B 170 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7183 (mm) REVERT: B 207 LYS cc_start: 0.6673 (tmtt) cc_final: 0.6386 (tptp) outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.0351 time to fit residues: 4.6304 Evaluate side-chains 107 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 214 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.193920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148331 restraints weight = 4896.470| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.79 r_work: 0.3655 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 3834 Z= 0.215 Angle : 1.244 59.176 5218 Z= 0.721 Chirality : 0.041 0.136 575 Planarity : 0.007 0.122 617 Dihedral : 13.600 139.446 539 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.95 % Favored : 93.82 % Rotamer: Outliers : 4.07 % Allowed : 23.41 % Favored : 72.52 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 4.17 % 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: 0.92 (0.41), residues: 437 helix: 1.45 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -2.06 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.008 0.001 TYR A 205 PHE 0.020 0.001 PHE A 50 TRP 0.007 0.001 TRP B 102 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 ( 3834) covalent geometry : angle 1.24381 / 0.72 ( 5218) hydrogen bonds : bond 0.04567 / 2.91 ( 242) hydrogen bonds : angle 4.16951 / 2.96 ( 726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: A 108 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.6196 (m-80) REVERT: A 261 MET cc_start: 0.8213 (tpp) cc_final: 0.7478 (tpp) REVERT: B 149 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: B 170 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.7201 (mm) REVERT: B 207 LYS cc_start: 0.6682 (tmtt) cc_final: 0.6393 (tptp) outliers start: 16 outliers final: 12 residues processed: 98 average time/residue: 0.0350 time to fit residues: 4.4610 Evaluate side-chains 106 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 HIS Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 214 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.0010 chunk 19 optimal weight: 7.9990 chunk 27 optimal weight: 0.0050 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.194278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148685 restraints weight = 4803.702| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.75 r_work: 0.3653 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.280 3834 Z= 0.281 Angle : 1.156 45.350 5218 Z= 0.807 Chirality : 0.041 0.136 575 Planarity : 0.008 0.124 617 Dihedral : 13.600 139.446 539 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.95 % Favored : 93.82 % Rotamer: Outliers : 3.82 % Allowed : 23.66 % Favored : 72.52 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 4.17 % 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: 0.92 (0.41), residues: 437 helix: 1.45 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -2.06 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.008 0.001 TYR A 205 PHE 0.020 0.001 PHE A 50 TRP 0.007 0.001 TRP B 102 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.28 ( 3834) covalent geometry : angle 1.15570 / 0.81 ( 5218) hydrogen bonds : bond 0.04567 / 2.91 ( 242) hydrogen bonds : angle 4.16952 / 2.96 ( 726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 958.08 seconds wall clock time: 17 minutes 5.93 seconds (1025.93 seconds total)