Starting phenix.real_space_refine on Thu Jul 2 03:20:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8qg0_18386/07_2026/8qg0_18386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qg0_18386/07_2026/8qg0_18386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qg0_18386/07_2026/8qg0_18386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qg0_18386/07_2026/8qg0_18386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qg0_18386/07_2026/8qg0_18386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qg0_18386/07_2026/8qg0_18386.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8qg0_18386/07_2026/8qg0_18386.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8qg0_18386/07_2026/8qg0_18386.cif" } resolution = 3.43 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= 1.000 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 33 5.49 5 S 13 5.16 5 C 3811 2.51 5 N 1012 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6080 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3478 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 403} Chain: "B" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "Q" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 363 Classifications: {'RNA': 17} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 15} Time building chain proxies: 1.31, per 1000 atoms: 0.22 Number of scatterers: 6080 At special positions: 0 Unit cell: (67.1, 91.3, 104.5, 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 13 16.00 P 33 15.00 O 1211 8.00 N 1012 7.00 C 3811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 293.3 milliseconds 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 11 sheets defined 33.5% alpha, 13.7% beta 6 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 58 through 73 Processing helix chain 'A' and resid 92 through 107 removed outlier: 3.583A pdb=" N ASN A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.972A pdb=" N TYR A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 removed outlier: 3.808A pdb=" N ASN A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.948A pdb=" N ASN A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.534A pdb=" N VAL A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 359 through 376 removed outlier: 3.516A pdb=" N HIS A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 407 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.660A pdb=" N GLN A 421 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 removed outlier: 4.078A pdb=" N GLY B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.829A pdb=" N VAL B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 216 removed outlier: 3.531A pdb=" N PHE B 205 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 184 removed outlier: 6.841A pdb=" N ILE A 183 " --> pdb=" O HIS A 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.557A pdb=" N CYS A 197 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 195 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.874A pdb=" N GLU A 212 " --> pdb=" O MET A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 291 through 293 Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.608A pdb=" N ARG B 110 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.705A pdb=" N ASN B 30 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 234 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS B 223 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.716A pdb=" N SER B 38 " --> pdb=" O LEU B 61 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.73 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: 1447 1.33 - 1.45: 1410 1.45 - 1.57: 3348 1.57 - 1.69: 65 1.69 - 1.80: 25 Bond restraints: 6295 Sorted by residual: bond pdb=" C3' DC P 4 " pdb=" C2' DC P 4 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" N LEU A 249 " pdb=" CA LEU A 249 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.52e-02 4.33e+03 9.71e+00 bond pdb=" N ARG A 383 " pdb=" CA ARG A 383 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.21e-02 6.83e+03 9.59e+00 bond pdb=" N SER B 163 " pdb=" CA SER B 163 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.43e+00 bond pdb=" N ILE B 167 " pdb=" CA ILE B 167 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.26e+00 ... (remaining 6290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 8402 1.91 - 3.82: 245 3.82 - 5.72: 30 5.72 - 7.63: 5 7.63 - 9.54: 2 Bond angle restraints: 8684 Sorted by residual: angle pdb=" C LYS B 168 " pdb=" CA LYS B 168 " pdb=" CB LYS B 168 " ideal model delta sigma weight residual 116.54 110.28 6.26 1.15e+00 7.56e-01 2.97e+01 angle pdb=" N LEU A 249 " pdb=" CA LEU A 249 " pdb=" CB LEU A 249 " ideal model delta sigma weight residual 111.65 104.47 7.18 1.40e+00 5.10e-01 2.63e+01 angle pdb=" N3 DT P 17 " pdb=" C4 DT P 17 " pdb=" O4 DT P 17 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT P 3 " pdb=" C4 DT P 3 " pdb=" O4 DT P 3 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT P 12 " pdb=" C4 DT P 12 " pdb=" O4 DT P 12 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 8679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3219 17.93 - 35.85: 360 35.85 - 53.78: 108 53.78 - 71.70: 38 71.70 - 89.63: 12 Dihedral angle restraints: 3737 sinusoidal: 1807 harmonic: 1930 Sorted by residual: dihedral pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CA LEU A 249 " pdb=" CB LEU A 249 " ideal model delta harmonic sigma weight residual 122.80 111.66 11.14 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" CA VAL A 300 " pdb=" C VAL A 300 " pdb=" N MET A 301 " pdb=" CA MET A 301 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA TYR B 22 " pdb=" C TYR B 22 " pdb=" N ILE B 23 " pdb=" CA ILE B 23 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 3734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 926 0.103 - 0.205: 44 0.205 - 0.308: 1 0.308 - 0.411: 0 0.411 - 0.514: 1 Chirality restraints: 972 Sorted by residual: chirality pdb=" CA LEU A 249 " pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CB LEU A 249 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CB ILE B 167 " pdb=" CA ILE B 167 " pdb=" CG1 ILE B 167 " pdb=" CG2 ILE B 167 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA TYR B 164 " pdb=" N TYR B 164 " pdb=" C TYR B 164 " pdb=" CB TYR B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 969 not shown) Planarity restraints: 974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 40 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO B 41 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 355 " 0.011 2.00e-02 2.50e+03 9.58e-03 2.29e+00 pdb=" CG TRP A 355 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 355 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 355 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 355 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 355 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 355 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 355 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 355 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 355 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 341 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO A 342 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 342 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 342 " 0.021 5.00e-02 4.00e+02 ... (remaining 971 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 543 2.74 - 3.28: 6374 3.28 - 3.82: 10696 3.82 - 4.36: 13200 4.36 - 4.90: 21656 Nonbonded interactions: 52469 Sorted by model distance: nonbonded pdb=" O6 DG P 11 " pdb=" N6 A Q 6 " model vdw 2.198 3.120 nonbonded pdb=" NE ARG A 257 " pdb=" O2' A Q 15 " model vdw 2.208 3.120 nonbonded pdb=" O2 DC P 8 " pdb=" N2 G Q 11 " model vdw 2.220 3.120 nonbonded pdb=" OG1 THR A 250 " pdb=" O ALA A 288 " model vdw 2.239 3.040 nonbonded pdb=" O ILE A 87 " pdb=" NE2 GLN A 99 " model vdw 2.246 3.120 ... (remaining 52464 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: 0.560 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: 0.020 Set scattering table: 0.020 Process input model: 7.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 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 0.052 6295 Z= 0.289 Angle : 0.747 9.538 8684 Z= 0.485 Chirality : 0.050 0.514 972 Planarity : 0.005 0.079 974 Dihedral : 17.660 89.630 2501 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.50 % Allowed : 0.50 % Favored : 99.00 % Cbeta Deviations : 0.32 % 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: -1.84 (0.33), residues: 652 helix: 0.39 (0.39), residues: 179 sheet: -2.31 (0.46), residues: 132 loop : -1.62 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 202 TYR 0.014 0.002 TYR A 323 PHE 0.018 0.002 PHE A 382 TRP 0.025 0.002 TRP A 355 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.29 ( 6295) covalent geometry : angle 0.74681 / 0.49 ( 8684) hydrogen bonds : bond 0.22439 / 14.70 ( 195) hydrogen bonds : angle 8.76424 / 5.94 ( 548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.197 Fit side-chains REVERT: B 21 LEU cc_start: 0.7830 (mp) cc_final: 0.7626 (mp) outliers start: 3 outliers final: 1 residues processed: 116 average time/residue: 0.0651 time to fit residues: 10.2371 Evaluate side-chains 99 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 378 ASN B 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.212713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.193023 restraints weight = 7702.029| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 2.15 r_work: 0.4394 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6295 Z= 0.191 Angle : 0.698 9.882 8684 Z= 0.370 Chirality : 0.049 0.211 972 Planarity : 0.005 0.070 974 Dihedral : 18.095 90.487 1155 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.99 % Allowed : 11.44 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.33), residues: 652 helix: 0.27 (0.37), residues: 189 sheet: -2.16 (0.46), residues: 138 loop : -1.69 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 383 TYR 0.018 0.002 TYR B 31 PHE 0.022 0.002 PHE B 80 TRP 0.009 0.002 TRP A 355 HIS 0.004 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 6295) covalent geometry : angle 0.69849 / 0.37 ( 8684) hydrogen bonds : bond 0.06274 / 4.13 ( 195) hydrogen bonds : angle 6.28868 / 4.29 ( 548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.202 Fit side-chains REVERT: A 355 TRP cc_start: 0.7028 (m-10) cc_final: 0.6434 (m-90) REVERT: B 110 ARG cc_start: 0.5833 (mmm160) cc_final: 0.5141 (mmm160) outliers start: 12 outliers final: 10 residues processed: 102 average time/residue: 0.0632 time to fit residues: 8.8425 Evaluate side-chains 102 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 54 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 354 ASN A 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.225266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.206639 restraints weight = 7942.608| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 2.13 r_work: 0.4443 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6295 Z= 0.144 Angle : 0.630 8.670 8684 Z= 0.334 Chirality : 0.047 0.220 972 Planarity : 0.005 0.060 974 Dihedral : 18.021 90.832 1155 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.65 % Allowed : 13.60 % Favored : 83.75 % 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: -1.76 (0.33), residues: 652 helix: 0.22 (0.37), residues: 199 sheet: -2.08 (0.49), residues: 132 loop : -1.63 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.011 0.001 TYR B 62 PHE 0.008 0.001 PHE B 205 TRP 0.009 0.001 TRP A 76 HIS 0.004 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6295) covalent geometry : angle 0.63016 / 0.33 ( 8684) hydrogen bonds : bond 0.05030 / 3.31 ( 195) hydrogen bonds : angle 5.69797 / 3.87 ( 548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.209 Fit side-chains REVERT: A 355 TRP cc_start: 0.6984 (m-10) cc_final: 0.6510 (m-10) outliers start: 16 outliers final: 11 residues processed: 103 average time/residue: 0.0666 time to fit residues: 9.6309 Evaluate side-chains 100 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 10 optimal weight: 0.0270 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN A 378 ASN A 417 ASN B 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.219789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.199436 restraints weight = 8034.964| |-----------------------------------------------------------------------------| r_work (start): 0.4578 rms_B_bonded: 2.31 r_work: 0.4396 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6295 Z= 0.169 Angle : 0.634 9.332 8684 Z= 0.337 Chirality : 0.047 0.206 972 Planarity : 0.005 0.082 974 Dihedral : 18.010 91.340 1155 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.65 % Allowed : 15.75 % Favored : 81.59 % 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: -1.74 (0.33), residues: 652 helix: 0.22 (0.37), residues: 199 sheet: -1.99 (0.49), residues: 130 loop : -1.64 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 383 TYR 0.011 0.001 TYR B 64 PHE 0.009 0.001 PHE B 205 TRP 0.011 0.001 TRP A 76 HIS 0.004 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 6295) covalent geometry : angle 0.63447 / 0.34 ( 8684) hydrogen bonds : bond 0.04807 / 3.17 ( 195) hydrogen bonds : angle 5.45395 / 3.72 ( 548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.202 Fit side-chains REVERT: A 112 MET cc_start: 0.6747 (mtp) cc_final: 0.6531 (mtm) REVERT: A 355 TRP cc_start: 0.7057 (m-10) cc_final: 0.6602 (m-10) REVERT: A 363 ASN cc_start: 0.6682 (OUTLIER) cc_final: 0.6161 (t0) outliers start: 16 outliers final: 15 residues processed: 101 average time/residue: 0.0730 time to fit residues: 10.0715 Evaluate side-chains 108 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 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 = 0.4788 r_free = 0.4788 target = 0.221551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.200341 restraints weight = 8137.909| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 2.44 r_work: 0.4405 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6295 Z= 0.161 Angle : 0.619 8.635 8684 Z= 0.330 Chirality : 0.046 0.197 972 Planarity : 0.005 0.071 974 Dihedral : 18.034 91.923 1155 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.82 % Allowed : 16.58 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.33), residues: 652 helix: 0.25 (0.37), residues: 199 sheet: -1.93 (0.49), residues: 129 loop : -1.60 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 147 TYR 0.010 0.001 TYR B 87 PHE 0.008 0.001 PHE B 205 TRP 0.011 0.001 TRP A 76 HIS 0.004 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 6295) covalent geometry : angle 0.61853 / 0.33 ( 8684) hydrogen bonds : bond 0.04633 / 3.06 ( 195) hydrogen bonds : angle 5.33043 / 3.65 ( 548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.171 Fit side-chains REVERT: A 355 TRP cc_start: 0.7038 (m-10) cc_final: 0.6588 (m-10) REVERT: A 363 ASN cc_start: 0.6718 (OUTLIER) cc_final: 0.6196 (t0) REVERT: B 170 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.6186 (pttt) outliers start: 17 outliers final: 14 residues processed: 102 average time/residue: 0.0639 time to fit residues: 8.8940 Evaluate side-chains 105 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.222430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.201513 restraints weight = 7995.997| |-----------------------------------------------------------------------------| r_work (start): 0.4615 rms_B_bonded: 2.40 r_work: 0.4436 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6295 Z= 0.143 Angle : 0.608 9.477 8684 Z= 0.323 Chirality : 0.046 0.196 972 Planarity : 0.005 0.065 974 Dihedral : 18.033 92.390 1155 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.15 % Allowed : 16.42 % Favored : 79.44 % 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: -1.58 (0.33), residues: 652 helix: 0.32 (0.37), residues: 199 sheet: -1.85 (0.49), residues: 127 loop : -1.55 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 202 TYR 0.013 0.001 TYR B 164 PHE 0.009 0.001 PHE B 205 TRP 0.011 0.001 TRP A 76 HIS 0.003 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6295) covalent geometry : angle 0.60837 / 0.32 ( 8684) hydrogen bonds : bond 0.04420 / 2.90 ( 195) hydrogen bonds : angle 5.18591 / 3.57 ( 548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.212 Fit side-chains REVERT: A 355 TRP cc_start: 0.6983 (m-10) cc_final: 0.6623 (m-10) REVERT: A 363 ASN cc_start: 0.6826 (OUTLIER) cc_final: 0.6283 (t0) REVERT: B 77 ASN cc_start: 0.7637 (t0) cc_final: 0.7383 (t0) REVERT: B 145 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6795 (tt) REVERT: B 164 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6936 (m-80) REVERT: B 170 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.6187 (pttt) REVERT: B 187 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.6305 (t70) outliers start: 25 outliers final: 15 residues processed: 113 average time/residue: 0.0693 time to fit residues: 10.7392 Evaluate side-chains 111 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.224471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.204222 restraints weight = 8001.600| |-----------------------------------------------------------------------------| r_work (start): 0.4636 rms_B_bonded: 2.29 r_work: 0.4462 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6295 Z= 0.132 Angle : 0.625 11.045 8684 Z= 0.326 Chirality : 0.045 0.186 972 Planarity : 0.005 0.061 974 Dihedral : 18.047 92.377 1155 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.81 % Allowed : 17.91 % Favored : 78.28 % 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: -1.46 (0.33), residues: 652 helix: 0.40 (0.38), residues: 199 sheet: -1.78 (0.48), residues: 129 loop : -1.47 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 188 TYR 0.010 0.001 TYR B 164 PHE 0.007 0.001 PHE B 186 TRP 0.012 0.001 TRP A 76 HIS 0.014 0.002 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6295) covalent geometry : angle 0.62475 / 0.33 ( 8684) hydrogen bonds : bond 0.04311 / 2.82 ( 195) hydrogen bonds : angle 5.00404 / 3.44 ( 548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.135 Fit side-chains REVERT: A 355 TRP cc_start: 0.6975 (m-10) cc_final: 0.6580 (m-10) REVERT: A 363 ASN cc_start: 0.6706 (OUTLIER) cc_final: 0.6203 (t0) REVERT: A 377 MET cc_start: 0.6409 (tpp) cc_final: 0.6195 (tpp) REVERT: B 77 ASN cc_start: 0.7638 (t0) cc_final: 0.7400 (t0) REVERT: B 145 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6811 (tt) REVERT: B 170 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6267 (pttt) REVERT: B 187 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6196 (t70) outliers start: 23 outliers final: 16 residues processed: 116 average time/residue: 0.0733 time to fit residues: 11.5932 Evaluate side-chains 113 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.0070 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.218324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.197711 restraints weight = 8071.224| |-----------------------------------------------------------------------------| r_work (start): 0.4576 rms_B_bonded: 2.31 r_work: 0.4395 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6295 Z= 0.216 Angle : 0.690 10.875 8684 Z= 0.361 Chirality : 0.048 0.183 972 Planarity : 0.005 0.065 974 Dihedral : 18.120 93.592 1155 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.15 % Allowed : 17.91 % Favored : 77.94 % 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: -1.67 (0.33), residues: 652 helix: 0.20 (0.37), residues: 200 sheet: -1.80 (0.48), residues: 129 loop : -1.63 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 188 TYR 0.013 0.002 TYR A 360 PHE 0.015 0.002 PHE A 202 TRP 0.013 0.002 TRP A 76 HIS 0.016 0.002 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.22 ( 6295) covalent geometry : angle 0.69019 / 0.36 ( 8684) hydrogen bonds : bond 0.04734 / 3.11 ( 195) hydrogen bonds : angle 5.09957 / 3.51 ( 548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.186 Fit side-chains REVERT: A 355 TRP cc_start: 0.7098 (m-10) cc_final: 0.6685 (m-10) REVERT: A 363 ASN cc_start: 0.6826 (OUTLIER) cc_final: 0.6279 (t0) REVERT: B 145 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6706 (tt) REVERT: B 187 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.6439 (t70) outliers start: 25 outliers final: 19 residues processed: 108 average time/residue: 0.0656 time to fit residues: 9.8419 Evaluate side-chains 114 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.0070 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.222879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.202508 restraints weight = 8077.618| |-----------------------------------------------------------------------------| r_work (start): 0.4622 rms_B_bonded: 2.31 r_work: 0.4441 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6295 Z= 0.142 Angle : 0.653 11.908 8684 Z= 0.340 Chirality : 0.046 0.179 972 Planarity : 0.005 0.062 974 Dihedral : 18.118 94.029 1155 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.81 % Allowed : 18.57 % Favored : 77.61 % 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: -1.54 (0.33), residues: 652 helix: 0.35 (0.37), residues: 200 sheet: -1.77 (0.49), residues: 129 loop : -1.55 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 147 TYR 0.020 0.001 TYR A 323 PHE 0.010 0.001 PHE A 202 TRP 0.011 0.001 TRP A 76 HIS 0.017 0.002 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 6295) covalent geometry : angle 0.65250 / 0.34 ( 8684) hydrogen bonds : bond 0.04409 / 2.88 ( 195) hydrogen bonds : angle 4.98168 / 3.43 ( 548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.213 Fit side-chains REVERT: A 355 TRP cc_start: 0.7028 (m-10) cc_final: 0.6615 (m-10) REVERT: A 363 ASN cc_start: 0.6754 (OUTLIER) cc_final: 0.6248 (t0) REVERT: B 145 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6665 (tt) REVERT: B 170 LYS cc_start: 0.6682 (OUTLIER) cc_final: 0.6168 (pttt) REVERT: B 187 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.5452 (t-170) outliers start: 23 outliers final: 17 residues processed: 107 average time/residue: 0.0682 time to fit residues: 10.1786 Evaluate side-chains 112 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 65 optimal weight: 5.9990 chunk 41 optimal weight: 0.0670 chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.222054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.200958 restraints weight = 8006.870| |-----------------------------------------------------------------------------| r_work (start): 0.4602 rms_B_bonded: 2.42 r_work: 0.4422 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6295 Z= 0.159 Angle : 0.663 13.409 8684 Z= 0.345 Chirality : 0.046 0.177 972 Planarity : 0.005 0.063 974 Dihedral : 18.134 94.367 1155 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.32 % Allowed : 19.40 % Favored : 77.28 % 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 (0.33), residues: 652 helix: 0.34 (0.37), residues: 200 sheet: -1.78 (0.48), residues: 131 loop : -1.51 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 147 TYR 0.015 0.001 TYR A 323 PHE 0.010 0.001 PHE A 202 TRP 0.012 0.001 TRP A 76 HIS 0.014 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 6295) covalent geometry : angle 0.66339 / 0.35 ( 8684) hydrogen bonds : bond 0.04425 / 2.91 ( 195) hydrogen bonds : angle 4.96503 / 3.42 ( 548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.211 Fit side-chains REVERT: A 355 TRP cc_start: 0.7025 (m-10) cc_final: 0.6618 (m-10) REVERT: A 363 ASN cc_start: 0.6776 (OUTLIER) cc_final: 0.6254 (t0) REVERT: B 31 TYR cc_start: 0.6979 (p90) cc_final: 0.6685 (p90) REVERT: B 145 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6718 (tt) REVERT: B 170 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6178 (pttt) REVERT: B 187 HIS cc_start: 0.7044 (OUTLIER) cc_final: 0.6354 (t70) outliers start: 20 outliers final: 16 residues processed: 106 average time/residue: 0.0705 time to fit residues: 10.3033 Evaluate side-chains 112 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 24 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.218973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.198645 restraints weight = 8097.781| |-----------------------------------------------------------------------------| r_work (start): 0.4571 rms_B_bonded: 2.29 r_work: 0.4395 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6295 Z= 0.142 Angle : 0.652 13.506 8684 Z= 0.338 Chirality : 0.046 0.173 972 Planarity : 0.005 0.062 974 Dihedral : 18.144 94.470 1155 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.32 % Allowed : 19.40 % Favored : 77.28 % 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: -1.44 (0.33), residues: 652 helix: 0.47 (0.37), residues: 197 sheet: -1.74 (0.49), residues: 129 loop : -1.50 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 147 TYR 0.015 0.001 TYR A 323 PHE 0.010 0.001 PHE B 186 TRP 0.012 0.001 TRP A 76 HIS 0.015 0.002 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6295) covalent geometry : angle 0.65196 / 0.34 ( 8684) hydrogen bonds : bond 0.04333 / 2.84 ( 195) hydrogen bonds : angle 4.90947 / 3.38 ( 548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1341.06 seconds wall clock time: 23 minutes 57.13 seconds (1437.13 seconds total)