Starting phenix.real_space_refine on Sat May 2 09:20:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9np0_49625/05_2026/9np0_49625.cif Found real_map, /net/cci-nas-00/data/ceres_data/9np0_49625/05_2026/9np0_49625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9np0_49625/05_2026/9np0_49625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9np0_49625/05_2026/9np0_49625.map" model { file = "/net/cci-nas-00/data/ceres_data/9np0_49625/05_2026/9np0_49625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9np0_49625/05_2026/9np0_49625.cif" } resolution = 3.32 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= 0.000 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2625 2.51 5 N 720 2.21 5 O 815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4179 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2385 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 5, 'TRANS': 298} Chain: "B" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 960 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 834 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 1.22, per 1000 atoms: 0.29 Number of scatterers: 4179 At special positions: 0 Unit cell: (98.324, 67.99, 98.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 815 8.00 N 720 7.00 C 2625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 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: 0.38 Conformation dependent library (CDL) restraints added in 164.7 milliseconds 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 990 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 34.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.998A pdb=" N ALA A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 56 " --> pdb=" O HIS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.537A pdb=" N ASP A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 removed outlier: 4.138A pdb=" N GLN A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 88 " --> pdb=" O TYR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.824A pdb=" N LYS A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.663A pdb=" N VAL A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 126 removed outlier: 4.135A pdb=" N GLU A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 143 removed outlier: 3.522A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.815A pdb=" N ASN A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 179' Processing helix chain 'A' and resid 198 through 208 removed outlier: 4.046A pdb=" N ASP A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 206 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 removed outlier: 3.612A pdb=" N ASN A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.835A pdb=" N LEU A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 277 removed outlier: 3.748A pdb=" N PHE A 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 292 through 301 removed outlier: 3.763A pdb=" N LEU A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 4.042A pdb=" N LYS A 312 " --> pdb=" O MET A 308 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.559A pdb=" N ASP A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.564A pdb=" N LEU A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) 68 hydrogen bonds defined for protein. 198 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: 0.54 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1365 1.34 - 1.47: 990 1.47 - 1.59: 1862 1.59 - 1.71: 0 1.71 - 1.84: 30 Bond restraints: 4247 Sorted by residual: bond pdb=" CA VAL B 66 " pdb=" CB VAL B 66 " ideal model delta sigma weight residual 1.540 1.583 -0.043 1.36e-02 5.41e+03 1.00e+01 bond pdb=" CA VAL B 72 " pdb=" CB VAL B 72 " ideal model delta sigma weight residual 1.540 1.581 -0.041 1.36e-02 5.41e+03 9.10e+00 bond pdb=" CA VAL B 66 " pdb=" C VAL B 66 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.27e-02 6.20e+03 8.94e+00 bond pdb=" C LYS C 39 " pdb=" N PRO C 40 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 5.00e+00 bond pdb=" N LYS B 52 " pdb=" CA LYS B 52 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.58e+00 ... (remaining 4242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 5251 2.12 - 4.25: 370 4.25 - 6.37: 86 6.37 - 8.49: 16 8.49 - 10.61: 5 Bond angle restraints: 5728 Sorted by residual: angle pdb=" N GLY A 193 " pdb=" CA GLY A 193 " pdb=" C GLY A 193 " ideal model delta sigma weight residual 112.65 119.19 -6.54 1.30e+00 5.92e-01 2.53e+01 angle pdb=" N THR A 145 " pdb=" CA THR A 145 " pdb=" C THR A 145 " ideal model delta sigma weight residual 110.80 100.19 10.61 2.13e+00 2.20e-01 2.48e+01 angle pdb=" N VAL B 66 " pdb=" CA VAL B 66 " pdb=" C VAL B 66 " ideal model delta sigma weight residual 109.34 119.20 -9.86 2.08e+00 2.31e-01 2.25e+01 angle pdb=" N HIS A 246 " pdb=" CA HIS A 246 " pdb=" C HIS A 246 " ideal model delta sigma weight residual 112.58 106.96 5.62 1.22e+00 6.72e-01 2.13e+01 angle pdb=" CA ILE B 71 " pdb=" C ILE B 71 " pdb=" N VAL B 72 " ideal model delta sigma weight residual 116.60 122.89 -6.29 1.45e+00 4.76e-01 1.88e+01 ... (remaining 5723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 2316 16.30 - 32.59: 201 32.59 - 48.88: 43 48.88 - 65.18: 9 65.18 - 81.47: 3 Dihedral angle restraints: 2572 sinusoidal: 1026 harmonic: 1546 Sorted by residual: dihedral pdb=" CA PHE B 70 " pdb=" C PHE B 70 " pdb=" N ILE B 71 " pdb=" CA ILE B 71 " ideal model delta harmonic sigma weight residual -180.00 -128.29 -51.71 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA THR B 59 " pdb=" C THR B 59 " pdb=" N THR B 60 " pdb=" CA THR B 60 " ideal model delta harmonic sigma weight residual 180.00 134.63 45.37 0 5.00e+00 4.00e-02 8.23e+01 dihedral pdb=" CA ILE B 71 " pdb=" C ILE B 71 " pdb=" N VAL B 72 " pdb=" CA VAL B 72 " ideal model delta harmonic sigma weight residual 180.00 134.69 45.31 0 5.00e+00 4.00e-02 8.21e+01 ... (remaining 2569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 458 0.056 - 0.112: 144 0.112 - 0.168: 35 0.168 - 0.224: 2 0.224 - 0.280: 2 Chirality restraints: 641 Sorted by residual: chirality pdb=" CG LEU A 141 " pdb=" CB LEU A 141 " pdb=" CD1 LEU A 141 " pdb=" CD2 LEU A 141 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CG LEU B 81 " pdb=" CB LEU B 81 " pdb=" CD1 LEU B 81 " pdb=" CD2 LEU B 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ASP B 104 " pdb=" N ASP B 104 " pdb=" C ASP B 104 " pdb=" CB ASP B 104 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 638 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 94 " 0.078 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO C 95 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 51 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C SER B 51 " -0.060 2.00e-02 2.50e+03 pdb=" O SER B 51 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS B 52 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 66 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.15e+00 pdb=" C VAL B 66 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL B 66 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS B 67 " 0.017 2.00e-02 2.50e+03 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 110 2.64 - 3.20: 4390 3.20 - 3.77: 5950 3.77 - 4.33: 8915 4.33 - 4.90: 13403 Nonbonded interactions: 32768 Sorted by model distance: nonbonded pdb=" OH TYR B 110 " pdb=" OE1 GLN C 89 " model vdw 2.074 3.040 nonbonded pdb=" OG1 THR A 216 " pdb=" OE1 GLU A 255 " model vdw 2.142 3.040 nonbonded pdb=" O LYS B 67 " pdb=" ND2 ASN B 86 " model vdw 2.173 3.120 nonbonded pdb=" NZ LYS A 242 " pdb=" O TYR B 62 " model vdw 2.193 3.120 nonbonded pdb=" O ASP A 175 " pdb=" ND2 ASN A 222 " model vdw 2.207 3.120 ... (remaining 32763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.220 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4104 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 4249 Z= 0.342 Angle : 1.311 10.614 5732 Z= 0.709 Chirality : 0.058 0.280 641 Planarity : 0.008 0.119 738 Dihedral : 13.212 69.683 1576 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 3.02 % Allowed : 31.57 % Favored : 65.41 % Rotamer: Outliers : 0.22 % Allowed : 7.57 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 16.67 % Twisted General : 3.46 % 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: -7.20 (0.23), residues: 529 helix: -4.68 (0.18), residues: 146 sheet: None (None), residues: 0 loop : -5.30 (0.23), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 212 TYR 0.035 0.004 TYR C 91 PHE 0.023 0.004 PHE B 111 TRP 0.018 0.003 TRP C 35 HIS 0.005 0.002 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00731 ( 4247) covalent geometry : angle 1.30988 ( 5728) SS BOND : bond 0.00235 ( 2) SS BOND : angle 2.18931 ( 4) hydrogen bonds : bond 0.34386 ( 68) hydrogen bonds : angle 10.13223 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.3095 (tmt) cc_final: 0.2890 (tmt) REVERT: A 259 ASP cc_start: 0.6718 (p0) cc_final: 0.6511 (m-30) REVERT: A 286 MET cc_start: 0.0017 (tmm) cc_final: -0.1468 (mmp) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.1159 time to fit residues: 13.6360 Evaluate side-chains 71 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.0370 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.0050 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 overall best weight: 0.3472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 79 GLN A 86 GLN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN A 346 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5490 r_free = 0.5490 target = 0.317175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5270 r_free = 0.5270 target = 0.289311 restraints weight = 5939.920| |-----------------------------------------------------------------------------| r_work (start): 0.5231 rms_B_bonded: 3.32 r_work: 0.5112 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.5112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4454 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4249 Z= 0.191 Angle : 1.081 9.270 5732 Z= 0.556 Chirality : 0.054 0.212 641 Planarity : 0.007 0.088 738 Dihedral : 10.663 53.298 586 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 1.89 % Allowed : 28.36 % Favored : 69.75 % Rotamer: Outliers : 2.67 % Allowed : 16.70 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 2.50 % 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: -6.82 (0.24), residues: 529 helix: -3.77 (0.26), residues: 169 sheet: None (None), residues: 0 loop : -5.36 (0.23), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 77 TYR 0.021 0.002 TYR C 91 PHE 0.018 0.002 PHE B 70 TRP 0.010 0.002 TRP B 109 HIS 0.006 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4247) covalent geometry : angle 1.08075 ( 5728) SS BOND : bond 0.00828 ( 2) SS BOND : angle 1.50178 ( 4) hydrogen bonds : bond 0.05297 ( 68) hydrogen bonds : angle 6.96737 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 PRO cc_start: 0.7786 (Cg_exo) cc_final: 0.7574 (Cg_endo) REVERT: A 97 LYS cc_start: 0.7470 (pptt) cc_final: 0.6547 (tptp) REVERT: A 286 MET cc_start: 0.0388 (tmm) cc_final: -0.0917 (mmt) REVERT: B 113 VAL cc_start: 0.3344 (m) cc_final: 0.2900 (p) outliers start: 12 outliers final: 4 residues processed: 85 average time/residue: 0.0975 time to fit residues: 9.9492 Evaluate side-chains 69 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 81 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 153 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS B 84 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5476 r_free = 0.5476 target = 0.314506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5312 r_free = 0.5312 target = 0.295719 restraints weight = 6044.816| |-----------------------------------------------------------------------------| r_work (start): 0.5274 rms_B_bonded: 2.22 r_work: 0.5179 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.5179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4549 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4249 Z= 0.195 Angle : 1.053 9.341 5732 Z= 0.545 Chirality : 0.054 0.244 641 Planarity : 0.006 0.087 738 Dihedral : 10.225 54.118 586 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 2.08 % Allowed : 30.25 % Favored : 67.67 % Rotamer: Outliers : 5.35 % Allowed : 18.49 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 2.12 % 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: -6.31 (0.27), residues: 529 helix: -3.09 (0.31), residues: 167 sheet: None (None), residues: 0 loop : -5.18 (0.24), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 77 TYR 0.019 0.002 TYR A 240 PHE 0.020 0.003 PHE A 118 TRP 0.006 0.002 TRP B 36 HIS 0.006 0.002 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 4247) covalent geometry : angle 1.04738 ( 5728) SS BOND : bond 0.01034 ( 2) SS BOND : angle 4.23283 ( 4) hydrogen bonds : bond 0.05509 ( 68) hydrogen bonds : angle 6.56891 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.6806 (pptt) cc_final: 0.6085 (tptp) REVERT: A 146 ASN cc_start: 0.0071 (OUTLIER) cc_final: -0.0453 (m-40) REVERT: A 206 LEU cc_start: 0.7753 (mp) cc_final: 0.7495 (mp) REVERT: A 286 MET cc_start: 0.1027 (tmm) cc_final: -0.0831 (mmt) REVERT: B 67 LYS cc_start: 0.1925 (mppt) cc_final: 0.0509 (mttt) REVERT: C 3 VAL cc_start: 0.6572 (OUTLIER) cc_final: 0.6299 (m) REVERT: C 96 TYR cc_start: 0.5398 (OUTLIER) cc_final: 0.4456 (m-10) outliers start: 24 outliers final: 9 residues processed: 88 average time/residue: 0.0948 time to fit residues: 9.9330 Evaluate side-chains 75 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 96 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS B 84 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5511 r_free = 0.5511 target = 0.316254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5365 r_free = 0.5365 target = 0.298493 restraints weight = 5987.908| |-----------------------------------------------------------------------------| r_work (start): 0.5307 rms_B_bonded: 2.11 r_work: 0.5218 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.5218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4473 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4249 Z= 0.178 Angle : 1.009 8.849 5732 Z= 0.522 Chirality : 0.051 0.179 641 Planarity : 0.006 0.087 738 Dihedral : 9.780 51.984 586 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 1.51 % Allowed : 29.30 % Favored : 69.19 % Rotamer: Outliers : 5.57 % Allowed : 20.27 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 1.73 % 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: -6.12 (0.27), residues: 529 helix: -2.70 (0.33), residues: 171 sheet: None (None), residues: 0 loop : -5.21 (0.23), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 77 TYR 0.015 0.002 TYR A 240 PHE 0.014 0.002 PHE A 118 TRP 0.005 0.001 TRP B 36 HIS 0.006 0.002 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4247) covalent geometry : angle 1.00107 ( 5728) SS BOND : bond 0.00410 ( 2) SS BOND : angle 5.00295 ( 4) hydrogen bonds : bond 0.04372 ( 68) hydrogen bonds : angle 6.22885 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 146 ASN cc_start: 0.0125 (OUTLIER) cc_final: -0.0418 (m-40) REVERT: A 156 TYR cc_start: 0.5379 (OUTLIER) cc_final: 0.5158 (t80) REVERT: A 286 MET cc_start: 0.1043 (tmm) cc_final: -0.0765 (mmt) REVERT: B 67 LYS cc_start: 0.1932 (OUTLIER) cc_final: 0.1635 (mtpp) REVERT: C 3 VAL cc_start: 0.6542 (OUTLIER) cc_final: 0.6270 (m) outliers start: 25 outliers final: 12 residues processed: 88 average time/residue: 0.0946 time to fit residues: 10.0665 Evaluate side-chains 83 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN B 84 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5487 r_free = 0.5487 target = 0.313562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.294895 restraints weight = 5948.033| |-----------------------------------------------------------------------------| r_work (start): 0.5280 rms_B_bonded: 2.25 r_work: 0.5188 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.5188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4506 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4249 Z= 0.180 Angle : 1.010 10.131 5732 Z= 0.521 Chirality : 0.051 0.175 641 Planarity : 0.006 0.084 738 Dihedral : 9.563 51.530 586 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 1.32 % Allowed : 28.36 % Favored : 70.32 % Rotamer: Outliers : 7.57 % Allowed : 20.71 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 1.54 % 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: -5.99 (0.28), residues: 529 helix: -2.56 (0.33), residues: 179 sheet: None (None), residues: 0 loop : -5.18 (0.24), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 77 TYR 0.014 0.002 TYR A 240 PHE 0.017 0.002 PHE C 87 TRP 0.004 0.001 TRP B 36 HIS 0.007 0.002 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4247) covalent geometry : angle 1.00231 ( 5728) SS BOND : bond 0.00070 ( 2) SS BOND : angle 4.93465 ( 4) hydrogen bonds : bond 0.04246 ( 68) hydrogen bonds : angle 6.11936 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 146 ASN cc_start: 0.0156 (OUTLIER) cc_final: -0.0602 (m-40) REVERT: A 262 LYS cc_start: 0.5947 (mmtm) cc_final: 0.4931 (tppt) REVERT: A 286 MET cc_start: 0.1135 (tmm) cc_final: -0.0682 (mmt) REVERT: B 67 LYS cc_start: 0.2582 (OUTLIER) cc_final: 0.1640 (mtpp) REVERT: C 3 VAL cc_start: 0.6512 (OUTLIER) cc_final: 0.6264 (m) outliers start: 34 outliers final: 21 residues processed: 93 average time/residue: 0.0969 time to fit residues: 10.7919 Evaluate side-chains 85 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.0470 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** C 37 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 = 0.5490 r_free = 0.5490 target = 0.313795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5344 r_free = 0.5344 target = 0.296282 restraints weight = 6139.980| |-----------------------------------------------------------------------------| r_work (start): 0.5289 rms_B_bonded: 2.16 r_work: 0.5203 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.5203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4487 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4249 Z= 0.178 Angle : 1.002 9.361 5732 Z= 0.521 Chirality : 0.050 0.173 641 Planarity : 0.006 0.086 738 Dihedral : 9.477 50.676 586 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 1.13 % Allowed : 28.54 % Favored : 70.32 % Rotamer: Outliers : 6.90 % Allowed : 22.49 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 1.35 % 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: -5.92 (0.28), residues: 529 helix: -2.38 (0.34), residues: 178 sheet: None (None), residues: 0 loop : -5.21 (0.23), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 77 TYR 0.014 0.002 TYR A 240 PHE 0.016 0.002 PHE C 87 TRP 0.005 0.001 TRP C 35 HIS 0.008 0.002 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4247) covalent geometry : angle 0.99589 ( 5728) SS BOND : bond 0.00469 ( 2) SS BOND : angle 4.42666 ( 4) hydrogen bonds : bond 0.04329 ( 68) hydrogen bonds : angle 6.28149 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 262 LYS cc_start: 0.5725 (mmtm) cc_final: 0.4944 (tppt) REVERT: A 286 MET cc_start: 0.1368 (tmm) cc_final: -0.0738 (mmt) REVERT: C 3 VAL cc_start: 0.6547 (OUTLIER) cc_final: 0.6328 (m) outliers start: 31 outliers final: 17 residues processed: 87 average time/residue: 0.0887 time to fit residues: 9.2900 Evaluate side-chains 79 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 29 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN C 8 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5372 r_free = 0.5372 target = 0.293048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5177 r_free = 0.5177 target = 0.266825 restraints weight = 5992.752| |-----------------------------------------------------------------------------| r_work (start): 0.5170 rms_B_bonded: 3.29 r_work: 0.5035 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.5035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4768 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4249 Z= 0.198 Angle : 1.049 11.243 5732 Z= 0.543 Chirality : 0.053 0.200 641 Planarity : 0.007 0.085 738 Dihedral : 9.548 50.138 586 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 1.32 % Allowed : 29.68 % Favored : 69.00 % Rotamer: Outliers : 7.13 % Allowed : 22.05 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 1.73 % 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: -5.77 (0.29), residues: 529 helix: -2.26 (0.35), residues: 174 sheet: None (None), residues: 0 loop : -5.09 (0.24), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 77 TYR 0.016 0.002 TYR A 240 PHE 0.021 0.002 PHE A 118 TRP 0.011 0.002 TRP B 47 HIS 0.008 0.002 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 4247) covalent geometry : angle 1.04284 ( 5728) SS BOND : bond 0.00862 ( 2) SS BOND : angle 4.35404 ( 4) hydrogen bonds : bond 0.04060 ( 68) hydrogen bonds : angle 6.36748 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 VAL cc_start: 0.6864 (OUTLIER) cc_final: 0.6598 (t) REVERT: A 146 ASN cc_start: 0.0355 (OUTLIER) cc_final: -0.0410 (m-40) REVERT: A 262 LYS cc_start: 0.5860 (mmtm) cc_final: 0.5253 (tppt) REVERT: B 85 MET cc_start: 0.5689 (OUTLIER) cc_final: 0.5400 (mmt) REVERT: C 3 VAL cc_start: 0.6808 (OUTLIER) cc_final: 0.6588 (m) outliers start: 32 outliers final: 16 residues processed: 92 average time/residue: 0.0811 time to fit residues: 9.0692 Evaluate side-chains 77 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.0170 chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 22 optimal weight: 0.0980 chunk 1 optimal weight: 0.0970 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN A 293 HIS B 84 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5479 r_free = 0.5479 target = 0.312658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5336 r_free = 0.5336 target = 0.295507 restraints weight = 6107.800| |-----------------------------------------------------------------------------| r_work (start): 0.5286 rms_B_bonded: 2.15 r_work: 0.5198 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.5198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4461 moved from start: 0.6462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4249 Z= 0.172 Angle : 1.029 10.921 5732 Z= 0.534 Chirality : 0.052 0.194 641 Planarity : 0.007 0.087 738 Dihedral : 9.390 53.574 586 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.95 % Allowed : 28.36 % Favored : 70.70 % Rotamer: Outliers : 5.12 % Allowed : 25.39 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 1.35 % 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: -5.75 (0.29), residues: 529 helix: -2.22 (0.35), residues: 175 sheet: None (None), residues: 0 loop : -5.10 (0.24), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 77 TYR 0.011 0.002 TYR A 240 PHE 0.036 0.002 PHE B 70 TRP 0.010 0.001 TRP B 114 HIS 0.007 0.002 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4247) covalent geometry : angle 1.02054 ( 5728) SS BOND : bond 0.00647 ( 2) SS BOND : angle 5.21231 ( 4) hydrogen bonds : bond 0.03962 ( 68) hydrogen bonds : angle 6.32595 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 HIS cc_start: 0.5330 (OUTLIER) cc_final: 0.4734 (p-80) REVERT: A 259 ASP cc_start: 0.6672 (p0) cc_final: 0.6466 (p0) REVERT: A 262 LYS cc_start: 0.5627 (mmtm) cc_final: 0.5180 (tppt) REVERT: A 286 MET cc_start: 0.2769 (ppp) cc_final: -0.1182 (mmt) REVERT: C 3 VAL cc_start: 0.6572 (OUTLIER) cc_final: 0.6353 (m) outliers start: 23 outliers final: 15 residues processed: 80 average time/residue: 0.0897 time to fit residues: 8.6297 Evaluate side-chains 78 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 0.4980 chunk 21 optimal weight: 0.0030 chunk 43 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 249 ASN B 84 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5465 r_free = 0.5465 target = 0.310710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.293103 restraints weight = 6125.837| |-----------------------------------------------------------------------------| r_work (start): 0.5264 rms_B_bonded: 2.16 r_work: 0.5174 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.5174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4530 moved from start: 0.6661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4249 Z= 0.178 Angle : 1.039 11.251 5732 Z= 0.534 Chirality : 0.051 0.181 641 Planarity : 0.007 0.085 738 Dihedral : 9.259 52.467 586 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 1.13 % Allowed : 28.92 % Favored : 69.94 % Rotamer: Outliers : 4.68 % Allowed : 24.72 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 1.35 % 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: -5.73 (0.29), residues: 529 helix: -2.11 (0.36), residues: 178 sheet: None (None), residues: 0 loop : -5.17 (0.23), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 77 TYR 0.015 0.002 TYR A 240 PHE 0.034 0.002 PHE B 70 TRP 0.009 0.002 TRP B 47 HIS 0.006 0.002 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 4247) covalent geometry : angle 1.03103 ( 5728) SS BOND : bond 0.00470 ( 2) SS BOND : angle 5.05872 ( 4) hydrogen bonds : bond 0.03800 ( 68) hydrogen bonds : angle 6.38292 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 103 HIS cc_start: 0.5582 (OUTLIER) cc_final: 0.4986 (p-80) REVERT: A 262 LYS cc_start: 0.5507 (OUTLIER) cc_final: 0.5235 (tppt) REVERT: A 286 MET cc_start: 0.2674 (ppp) cc_final: -0.1281 (mmt) REVERT: C 3 VAL cc_start: 0.6448 (OUTLIER) cc_final: 0.6236 (m) outliers start: 21 outliers final: 16 residues processed: 81 average time/residue: 0.0796 time to fit residues: 7.9054 Evaluate side-chains 84 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 249 ASN B 84 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5458 r_free = 0.5458 target = 0.309788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5312 r_free = 0.5312 target = 0.292388 restraints weight = 5986.001| |-----------------------------------------------------------------------------| r_work (start): 0.5258 rms_B_bonded: 2.11 r_work: 0.5167 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.5167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4553 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4249 Z= 0.182 Angle : 1.052 11.732 5732 Z= 0.540 Chirality : 0.052 0.177 641 Planarity : 0.007 0.087 738 Dihedral : 9.243 51.888 586 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.95 % Allowed : 29.30 % Favored : 69.75 % Rotamer: Outliers : 4.45 % Allowed : 25.84 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 1.54 % 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: -5.71 (0.29), residues: 529 helix: -2.08 (0.36), residues: 178 sheet: None (None), residues: 0 loop : -5.16 (0.23), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 77 TYR 0.015 0.002 TYR A 240 PHE 0.033 0.003 PHE B 70 TRP 0.011 0.002 TRP C 35 HIS 0.006 0.002 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4247) covalent geometry : angle 1.04351 ( 5728) SS BOND : bond 0.00527 ( 2) SS BOND : angle 5.08673 ( 4) hydrogen bonds : bond 0.03908 ( 68) hydrogen bonds : angle 6.46241 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 103 HIS cc_start: 0.5538 (OUTLIER) cc_final: 0.4898 (p-80) REVERT: A 286 MET cc_start: 0.2567 (ppp) cc_final: -0.1130 (mmt) REVERT: C 3 VAL cc_start: 0.6567 (OUTLIER) cc_final: 0.6308 (m) outliers start: 20 outliers final: 15 residues processed: 81 average time/residue: 0.0785 time to fit residues: 7.7853 Evaluate side-chains 79 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 0.0270 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN A 325 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5461 r_free = 0.5461 target = 0.310384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.293161 restraints weight = 6050.267| |-----------------------------------------------------------------------------| r_work (start): 0.5263 rms_B_bonded: 2.12 r_work: 0.5174 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.5174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4526 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4249 Z= 0.180 Angle : 1.063 14.836 5732 Z= 0.541 Chirality : 0.051 0.172 641 Planarity : 0.007 0.086 738 Dihedral : 9.128 51.579 586 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.76 % Allowed : 29.49 % Favored : 69.75 % Rotamer: Outliers : 4.23 % Allowed : 25.39 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.96 % 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: -5.63 (0.29), residues: 529 helix: -2.06 (0.36), residues: 172 sheet: None (None), residues: 0 loop : -5.05 (0.23), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 77 TYR 0.014 0.002 TYR A 240 PHE 0.031 0.003 PHE B 70 TRP 0.013 0.002 TRP C 35 HIS 0.006 0.002 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4247) covalent geometry : angle 1.05629 ( 5728) SS BOND : bond 0.00467 ( 2) SS BOND : angle 4.78659 ( 4) hydrogen bonds : bond 0.03781 ( 68) hydrogen bonds : angle 6.33814 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1276.02 seconds wall clock time: 22 minutes 33.48 seconds (1353.48 seconds total)