Starting phenix.real_space_refine on Sat Aug 23 16:41:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p13_13154/08_2025/7p13_13154.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p13_13154/08_2025/7p13_13154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p13_13154/08_2025/7p13_13154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p13_13154/08_2025/7p13_13154.map" model { file = "/net/cci-nas-00/data/ceres_data/7p13_13154/08_2025/7p13_13154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p13_13154/08_2025/7p13_13154.cif" } resolution = 2.29 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= 0.268 sd= 0.983 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 S 49 5.16 5 C 8463 2.51 5 N 2408 2.21 5 O 2653 1.98 5 H 154 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13727 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1961 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 17, 'TRANS': 231} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.57, per 1000 atoms: 0.11 Number of scatterers: 13727 At special positions: 0 Unit cell: (115.092, 113.424, 102.582, 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 49 16.00 O 2653 8.00 N 2408 7.00 C 8463 6.00 H 154 1.00 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: 1.03 Conformation dependent library (CDL) restraints added in 503.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 71.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 79 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 179 through 223 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 242 through 268 Proline residue: A 248 - end of helix Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 79 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 146 through 166 Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 179 through 223 Processing helix chain 'B' and resid 225 through 235 Processing helix chain 'B' and resid 242 through 268 Proline residue: B 248 - end of helix Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 79 Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 146 through 166 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 179 through 223 Processing helix chain 'C' and resid 225 through 235 Processing helix chain 'C' and resid 242 through 268 Proline residue: C 248 - end of helix Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 79 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 146 through 166 Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 179 through 223 Processing helix chain 'D' and resid 225 through 235 Processing helix chain 'D' and resid 242 through 268 Proline residue: D 248 - end of helix Processing helix chain 'E' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 79 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 146 through 166 Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 179 through 223 Processing helix chain 'E' and resid 225 through 235 Processing helix chain 'E' and resid 242 through 268 Proline residue: E 248 - end of helix Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 79 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 130 through 142 Processing helix chain 'F' and resid 146 through 166 Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 179 through 223 Processing helix chain 'F' and resid 225 through 235 Processing helix chain 'F' and resid 242 through 268 Proline residue: F 248 - end of helix Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.636A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 79 Processing helix chain 'G' and resid 80 through 82 No H-bonds generated for 'chain 'G' and resid 80 through 82' Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 146 through 166 Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 179 through 223 Processing helix chain 'G' and resid 225 through 235 Processing helix chain 'G' and resid 242 through 268 Proline residue: G 248 - end of helix 987 hydrogen bonds defined for protein. 2919 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: 2.01 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 154 1.02 - 1.21: 49 1.21 - 1.41: 5677 1.41 - 1.60: 8043 1.60 - 1.80: 84 Bond restraints: 14007 Sorted by residual: bond pdb=" C LEU G 270 " pdb=" N GLU G 271 " ideal model delta sigma weight residual 1.329 1.272 0.056 1.60e-02 3.91e+03 1.24e+01 bond pdb=" C LEU E 270 " pdb=" N GLU E 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.23e+01 bond pdb=" C LEU F 270 " pdb=" N GLU F 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.22e+01 bond pdb=" C LEU C 270 " pdb=" N GLU C 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.21e+01 bond pdb=" C LEU B 270 " pdb=" N GLU B 271 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.60e-02 3.91e+03 1.21e+01 ... (remaining 14002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 18243 2.26 - 4.53: 818 4.53 - 6.79: 112 6.79 - 9.05: 14 9.05 - 11.31: 14 Bond angle restraints: 19201 Sorted by residual: angle pdb=" C GLU D 258 " pdb=" N LYS D 259 " pdb=" CA LYS D 259 " ideal model delta sigma weight residual 121.14 115.49 5.65 1.75e+00 3.27e-01 1.04e+01 angle pdb=" C GLU E 258 " pdb=" N LYS E 259 " pdb=" CA LYS E 259 " ideal model delta sigma weight residual 121.14 115.50 5.64 1.75e+00 3.27e-01 1.04e+01 angle pdb=" C GLU B 258 " pdb=" N LYS B 259 " pdb=" CA LYS B 259 " ideal model delta sigma weight residual 121.14 115.54 5.60 1.75e+00 3.27e-01 1.02e+01 angle pdb=" C GLU A 258 " pdb=" N LYS A 259 " pdb=" CA LYS A 259 " ideal model delta sigma weight residual 121.14 115.55 5.59 1.75e+00 3.27e-01 1.02e+01 angle pdb=" C GLU G 258 " pdb=" N LYS G 259 " pdb=" CA LYS G 259 " ideal model delta sigma weight residual 121.14 115.56 5.58 1.75e+00 3.27e-01 1.02e+01 ... (remaining 19196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 7475 14.99 - 29.99: 881 29.99 - 44.98: 156 44.98 - 59.97: 21 59.97 - 74.97: 42 Dihedral angle restraints: 8575 sinusoidal: 3444 harmonic: 5131 Sorted by residual: dihedral pdb=" CA PRO C 286 " pdb=" C PRO C 286 " pdb=" N PRO C 287 " pdb=" CA PRO C 287 " ideal model delta harmonic sigma weight residual -180.00 -148.65 -31.35 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA PRO E 286 " pdb=" C PRO E 286 " pdb=" N PRO E 287 " pdb=" CA PRO E 287 " ideal model delta harmonic sigma weight residual -180.00 -148.70 -31.30 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA PRO D 286 " pdb=" C PRO D 286 " pdb=" N PRO D 287 " pdb=" CA PRO D 287 " ideal model delta harmonic sigma weight residual -180.00 -148.71 -31.29 0 5.00e+00 4.00e-02 3.92e+01 ... (remaining 8572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1238 0.055 - 0.110: 624 0.110 - 0.165: 161 0.165 - 0.221: 21 0.221 - 0.276: 7 Chirality restraints: 2051 Sorted by residual: chirality pdb=" CA GLU A 222 " pdb=" N GLU A 222 " pdb=" C GLU A 222 " pdb=" CB GLU A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU E 222 " pdb=" N GLU E 222 " pdb=" C GLU E 222 " pdb=" CB GLU E 222 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLU F 222 " pdb=" N GLU F 222 " pdb=" C GLU F 222 " pdb=" CB GLU F 222 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2048 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 286 " 0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO D 287 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 287 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 286 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.93e+00 pdb=" N PRO E 287 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 287 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 286 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO A 287 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.037 5.00e-02 4.00e+02 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.60: 422 2.60 - 3.10: 10723 3.10 - 3.60: 17626 3.60 - 4.10: 22963 4.10 - 4.60: 36459 Nonbonded interactions: 88193 Sorted by model distance: nonbonded pdb=" HB THR D 262 " pdb=" HG1 THR D 262 " model vdw 2.103 1.816 nonbonded pdb=" HB THR E 262 " pdb=" HG1 THR E 262 " model vdw 2.105 1.816 nonbonded pdb=" HB THR C 262 " pdb=" HG1 THR C 262 " model vdw 2.105 1.816 nonbonded pdb=" HB THR B 262 " pdb=" HG1 THR B 262 " model vdw 2.119 1.816 nonbonded pdb=" HB2 GLU F 258 " pdb=" HG3 GLU F 258 " model vdw 2.133 1.952 ... (remaining 88188 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.980 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: 0.130 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.320 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.016 0.075 13853 Z= 0.724 Angle : 1.063 11.313 18851 Z= 0.565 Chirality : 0.067 0.276 2051 Planarity : 0.008 0.075 2555 Dihedral : 14.069 74.966 5194 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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 aren not related in a simple way. whole: 2.06 (0.20), residues: 1715 helix: 1.67 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : 0.86 (0.30), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 256 TYR 0.029 0.006 TYR G 264 PHE 0.051 0.006 PHE F 130 TRP 0.016 0.004 TRP C 156 HIS 0.008 0.004 HIS D 216 Details of bonding type rmsd covalent geometry : bond 0.01588 (13853) covalent geometry : angle 1.06268 (18851) hydrogen bonds : bond 0.15423 ( 987) hydrogen bonds : angle 6.04757 ( 2919) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.362 Fit side-chains REVERT: B 221 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7619 (ttm170) REVERT: C 25 MET cc_start: 0.8513 (mtm) cc_final: 0.8097 (mtp) REVERT: C 130 PHE cc_start: 0.8261 (m-80) cc_final: 0.8049 (m-80) REVERT: D 245 GLN cc_start: 0.7345 (mm110) cc_final: 0.7037 (tp40) REVERT: F 11 GLN cc_start: 0.7993 (tt0) cc_final: 0.7760 (pm20) REVERT: G 205 MET cc_start: 0.8410 (ttp) cc_final: 0.8171 (ttp) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.7078 time to fit residues: 281.3937 Evaluate side-chains 251 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 ASN A 245 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 265 ASN C 11 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN E 254 GLN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN G 245 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.091561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082529 restraints weight = 22392.774| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.12 r_work: 0.3059 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13853 Z= 0.118 Angle : 0.504 7.345 18851 Z= 0.265 Chirality : 0.034 0.123 2051 Planarity : 0.005 0.063 2555 Dihedral : 3.988 14.977 1883 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.88 % Allowed : 10.89 % Favored : 87.23 % 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 aren not related in a simple way. whole: 4.28 (0.20), residues: 1715 helix: 3.62 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.94 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 234 TYR 0.016 0.002 TYR D 264 PHE 0.014 0.002 PHE C 152 TRP 0.016 0.001 TRP A 156 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00243 (13853) covalent geometry : angle 0.50440 (18851) hydrogen bonds : bond 0.04381 ( 987) hydrogen bonds : angle 3.89044 ( 2919) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 315 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: B 134 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8681 (ttpp) REVERT: D 134 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8721 (ttpp) REVERT: F 11 GLN cc_start: 0.8015 (tt0) cc_final: 0.7727 (pm20) REVERT: F 233 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: G 205 MET cc_start: 0.8880 (ttp) cc_final: 0.8636 (ttp) outliers start: 26 outliers final: 12 residues processed: 330 average time/residue: 0.5866 time to fit residues: 208.2726 Evaluate side-chains 291 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 276 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 233 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 134 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 128 optimal weight: 0.0010 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 104 optimal weight: 0.0970 chunk 45 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN A 265 ASN B 11 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN D 11 GLN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.093552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.084539 restraints weight = 22521.987| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.12 r_work: 0.3097 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13853 Z= 0.083 Angle : 0.420 6.290 18851 Z= 0.212 Chirality : 0.033 0.155 2051 Planarity : 0.004 0.047 2555 Dihedral : 3.395 11.801 1883 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.09 % Allowed : 12.19 % Favored : 85.71 % 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 aren not related in a simple way. whole: 5.00 (0.21), residues: 1715 helix: 4.16 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 1.03 (0.32), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 234 TYR 0.011 0.001 TYR G 236 PHE 0.013 0.002 PHE B 152 TRP 0.013 0.001 TRP B 156 HIS 0.002 0.000 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00166 (13853) covalent geometry : angle 0.42020 (18851) hydrogen bonds : bond 0.03397 ( 987) hydrogen bonds : angle 3.50710 ( 2919) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 305 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: B 134 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8705 (ttpp) REVERT: C 25 MET cc_start: 0.8735 (mtp) cc_final: 0.8490 (mtp) REVERT: F 11 GLN cc_start: 0.7995 (tt0) cc_final: 0.7720 (pm20) REVERT: G 205 MET cc_start: 0.8866 (ttp) cc_final: 0.8600 (ttp) outliers start: 29 outliers final: 8 residues processed: 319 average time/residue: 0.7702 time to fit residues: 264.2184 Evaluate side-chains 294 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 285 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 153 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 265 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.092416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083433 restraints weight = 22431.467| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.11 r_work: 0.3076 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13853 Z= 0.106 Angle : 0.421 5.108 18851 Z= 0.216 Chirality : 0.033 0.119 2051 Planarity : 0.004 0.041 2555 Dihedral : 3.303 10.952 1883 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.45 % Allowed : 13.06 % Favored : 84.49 % 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 aren not related in a simple way. whole: 5.16 (0.21), residues: 1715 helix: 4.25 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 1.16 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 234 TYR 0.012 0.001 TYR D 236 PHE 0.016 0.002 PHE C 152 TRP 0.012 0.001 TRP B 156 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00221 (13853) covalent geometry : angle 0.42108 (18851) hydrogen bonds : bond 0.03638 ( 987) hydrogen bonds : angle 3.48309 ( 2919) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 221 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7937 (ttm110) REVERT: B 134 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8735 (ttpp) REVERT: F 11 GLN cc_start: 0.8027 (tt0) cc_final: 0.7747 (pm20) REVERT: F 233 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: G 205 MET cc_start: 0.8875 (ttp) cc_final: 0.8614 (ttp) outliers start: 34 outliers final: 14 residues processed: 307 average time/residue: 0.7350 time to fit residues: 242.3250 Evaluate side-chains 300 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 283 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 9 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 265 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.083362 restraints weight = 22289.267| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.11 r_work: 0.3072 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 13853 Z= 0.111 Angle : 0.421 4.802 18851 Z= 0.217 Chirality : 0.033 0.121 2051 Planarity : 0.004 0.038 2555 Dihedral : 3.267 10.723 1883 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.17 % Allowed : 13.06 % Favored : 83.77 % 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 aren not related in a simple way. whole: 5.11 (0.21), residues: 1715 helix: 4.15 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : 1.21 (0.32), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 234 TYR 0.014 0.001 TYR G 236 PHE 0.017 0.002 PHE C 152 TRP 0.012 0.001 TRP D 156 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00232 (13853) covalent geometry : angle 0.42087 (18851) hydrogen bonds : bond 0.03701 ( 987) hydrogen bonds : angle 3.46642 ( 2919) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.430 Fit side-chains REVERT: A 134 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8678 (ttpp) REVERT: C 245 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: F 11 GLN cc_start: 0.8042 (tt0) cc_final: 0.7735 (pm20) REVERT: F 233 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: G 134 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8695 (ttpp) REVERT: G 205 MET cc_start: 0.8875 (ttp) cc_final: 0.8615 (ttp) outliers start: 44 outliers final: 19 residues processed: 300 average time/residue: 0.7154 time to fit residues: 230.8567 Evaluate side-chains 293 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 54 optimal weight: 0.8980 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 254 GLN B 265 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082998 restraints weight = 22261.738| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.11 r_work: 0.3066 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13853 Z= 0.121 Angle : 0.435 4.623 18851 Z= 0.224 Chirality : 0.034 0.121 2051 Planarity : 0.004 0.041 2555 Dihedral : 3.282 10.679 1883 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.10 % Allowed : 14.14 % Favored : 82.76 % 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 aren not related in a simple way. whole: 5.10 (0.21), residues: 1715 helix: 4.14 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : 1.24 (0.32), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 234 TYR 0.014 0.002 TYR G 236 PHE 0.017 0.002 PHE B 152 TRP 0.012 0.001 TRP E 156 HIS 0.005 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00256 (13853) covalent geometry : angle 0.43481 (18851) hydrogen bonds : bond 0.03813 ( 987) hydrogen bonds : angle 3.49302 ( 2919) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8686 (ttpp) REVERT: F 11 GLN cc_start: 0.8043 (tt0) cc_final: 0.7735 (pm20) REVERT: F 233 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: G 134 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8724 (ttpp) REVERT: G 205 MET cc_start: 0.8865 (ttp) cc_final: 0.8610 (ttp) outliers start: 43 outliers final: 20 residues processed: 287 average time/residue: 0.6988 time to fit residues: 215.0585 Evaluate side-chains 287 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 127 optimal weight: 0.0770 chunk 32 optimal weight: 0.0050 chunk 73 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 265 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082826 restraints weight = 22374.070| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.12 r_work: 0.3063 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13853 Z= 0.124 Angle : 0.435 4.938 18851 Z= 0.225 Chirality : 0.034 0.121 2051 Planarity : 0.004 0.041 2555 Dihedral : 3.282 12.051 1883 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.74 % Allowed : 14.86 % Favored : 82.40 % 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 aren not related in a simple way. whole: 5.13 (0.21), residues: 1715 helix: 4.19 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 1.27 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 234 TYR 0.017 0.002 TYR G 236 PHE 0.018 0.002 PHE B 152 TRP 0.013 0.001 TRP D 156 HIS 0.005 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00263 (13853) covalent geometry : angle 0.43514 (18851) hydrogen bonds : bond 0.03868 ( 987) hydrogen bonds : angle 3.50696 ( 2919) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.486 Fit side-chains REVERT: A 134 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8693 (ttpp) REVERT: E 233 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7538 (tt0) REVERT: F 11 GLN cc_start: 0.8041 (tt0) cc_final: 0.7735 (pm20) REVERT: F 233 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: G 134 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8705 (ttpp) REVERT: G 205 MET cc_start: 0.8869 (ttp) cc_final: 0.8616 (ttp) outliers start: 38 outliers final: 19 residues processed: 285 average time/residue: 0.6468 time to fit residues: 198.0884 Evaluate side-chains 295 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 272 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 139 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 155 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 265 ASN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.084035 restraints weight = 22117.717| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.11 r_work: 0.3085 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 13853 Z= 0.090 Angle : 0.402 4.544 18851 Z= 0.206 Chirality : 0.032 0.122 2051 Planarity : 0.003 0.035 2555 Dihedral : 3.137 10.654 1883 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.38 % Allowed : 15.37 % Favored : 82.25 % 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 aren not related in a simple way. whole: 5.34 (0.21), residues: 1715 helix: 4.35 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 1.31 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 234 TYR 0.016 0.001 TYR G 236 PHE 0.015 0.001 PHE B 152 TRP 0.012 0.001 TRP D 156 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00183 (13853) covalent geometry : angle 0.40235 (18851) hydrogen bonds : bond 0.03433 ( 987) hydrogen bonds : angle 3.37986 ( 2919) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: E 233 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: F 11 GLN cc_start: 0.8022 (tt0) cc_final: 0.7719 (pm20) REVERT: F 233 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: G 134 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8688 (ttpp) REVERT: G 205 MET cc_start: 0.8846 (ttp) cc_final: 0.8596 (ttp) outliers start: 33 outliers final: 18 residues processed: 300 average time/residue: 0.6817 time to fit residues: 219.7331 Evaluate side-chains 296 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 275 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 134 LYS Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 202 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 10 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 GLN F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.093302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.084262 restraints weight = 22429.886| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.11 r_work: 0.3100 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 13853 Z= 0.088 Angle : 0.399 4.626 18851 Z= 0.203 Chirality : 0.032 0.121 2051 Planarity : 0.003 0.032 2555 Dihedral : 3.068 10.702 1883 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.95 % Allowed : 16.16 % Favored : 81.89 % 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 aren not related in a simple way. whole: 5.42 (0.21), residues: 1715 helix: 4.42 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 1.33 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 234 TYR 0.017 0.001 TYR G 236 PHE 0.015 0.002 PHE B 152 TRP 0.012 0.001 TRP A 156 HIS 0.003 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00179 (13853) covalent geometry : angle 0.39901 (18851) hydrogen bonds : bond 0.03337 ( 987) hydrogen bonds : angle 3.31727 ( 2919) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 0.432 Fit side-chains REVERT: E 233 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: F 11 GLN cc_start: 0.8061 (tt0) cc_final: 0.7702 (pm20) REVERT: F 233 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: G 134 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8640 (ttpp) REVERT: G 205 MET cc_start: 0.8829 (ttp) cc_final: 0.8581 (ttp) outliers start: 27 outliers final: 14 residues processed: 289 average time/residue: 0.7095 time to fit residues: 219.6411 Evaluate side-chains 294 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 277 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 134 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 68 optimal weight: 0.0770 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.092064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.083017 restraints weight = 22290.573| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.11 r_work: 0.3066 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13853 Z= 0.127 Angle : 0.435 4.860 18851 Z= 0.224 Chirality : 0.034 0.120 2051 Planarity : 0.004 0.047 2555 Dihedral : 3.204 10.877 1883 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.52 % Allowed : 16.88 % Favored : 81.60 % 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 aren not related in a simple way. whole: 5.20 (0.21), residues: 1715 helix: 4.23 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 1.31 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 234 TYR 0.018 0.002 TYR G 236 PHE 0.018 0.002 PHE B 152 TRP 0.013 0.001 TRP D 156 HIS 0.005 0.002 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00270 (13853) covalent geometry : angle 0.43506 (18851) hydrogen bonds : bond 0.03859 ( 987) hydrogen bonds : angle 3.47382 ( 2919) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 270 time to evaluate : 0.561 Fit side-chains REVERT: A 134 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8674 (ttpp) REVERT: E 233 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: F 11 GLN cc_start: 0.8056 (tt0) cc_final: 0.7745 (pm20) REVERT: F 233 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: G 134 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8702 (ttpp) REVERT: G 205 MET cc_start: 0.8856 (ttp) cc_final: 0.8608 (ttp) outliers start: 21 outliers final: 12 residues processed: 278 average time/residue: 0.7526 time to fit residues: 223.9952 Evaluate side-chains 288 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 134 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 62 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN A 265 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 265 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 265 ASN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.092484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083416 restraints weight = 22267.858| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.11 r_work: 0.3075 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13853 Z= 0.110 Angle : 0.418 4.755 18851 Z= 0.215 Chirality : 0.033 0.122 2051 Planarity : 0.004 0.043 2555 Dihedral : 3.167 10.806 1883 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.73 % Allowed : 17.10 % Favored : 81.17 % 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 aren not related in a simple way. whole: 5.26 (0.21), residues: 1715 helix: 4.29 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 1.31 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 234 TYR 0.016 0.001 TYR G 236 PHE 0.017 0.002 PHE C 152 TRP 0.013 0.001 TRP D 156 HIS 0.004 0.001 HIS F 216 Details of bonding type rmsd covalent geometry : bond 0.00231 (13853) covalent geometry : angle 0.41795 (18851) hydrogen bonds : bond 0.03677 ( 987) hydrogen bonds : angle 3.43115 ( 2919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5596.20 seconds wall clock time: 95 minutes 46.55 seconds (5746.55 seconds total)