Starting phenix.real_space_refine on Wed Sep 17 04:27:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n3c_0334/09_2025/6n3c_0334.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n3c_0334/09_2025/6n3c_0334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6n3c_0334/09_2025/6n3c_0334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n3c_0334/09_2025/6n3c_0334.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n3c_0334/09_2025/6n3c_0334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n3c_0334/09_2025/6n3c_0334.map" } resolution = 3.3 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 2500 2.51 5 N 840 2.21 5 O 880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4260 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, D, F, H, J, L, N, P, R, T Time building chain proxies: 0.70, per 1000 atoms: 0.16 Number of scatterers: 4260 At special positions: 0 Unit cell: (86.92, 94.34, 47.7, 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 40 16.00 O 880 8.00 N 840 7.00 C 2500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 184.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 292 through 293 removed outlier: 6.461A pdb=" N SER A 292 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 297 through 303 removed outlier: 8.822A pdb=" N ALA A 297 " --> pdb=" O GLY E 298 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N GLY E 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 299 " --> pdb=" O GLY E 300 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASN E 302 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN A 301 " --> pdb=" O ASN E 302 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY A 298 " --> pdb=" O ALA K 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU K 299 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY A 300 " --> pdb=" O LEU K 299 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY K 298 " --> pdb=" O ALA O 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU O 299 " --> pdb=" O GLY K 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY K 300 " --> pdb=" O LEU O 299 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY O 298 " --> pdb=" O ALA S 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU S 299 " --> pdb=" O GLY O 298 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY O 300 " --> pdb=" O LEU S 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 306 through 308 removed outlier: 6.125A pdb=" N ASN A 306 " --> pdb=" O MET E 307 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 311 through 318 removed outlier: 5.950A pdb=" N ASN A 312 " --> pdb=" O PHE E 313 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU E 315 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY A 314 " --> pdb=" O GLU E 315 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER E 317 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 316 " --> pdb=" O SER E 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 292 through 293 removed outlier: 6.563A pdb=" N SER B 292 " --> pdb=" O ARG F 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 312 through 314 removed outlier: 6.179A pdb=" N PHE B 313 " --> pdb=" O GLY L 314 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE L 313 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE P 313 " --> pdb=" O GLY T 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AA8, first strand: chain 'C' and resid 297 through 303 removed outlier: 6.833A pdb=" N GLY C 298 " --> pdb=" O ALA G 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU G 299 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY C 300 " --> pdb=" O LEU G 299 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY G 298 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU I 299 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY G 300 " --> pdb=" O LEU I 299 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY I 298 " --> pdb=" O ALA M 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU M 299 " --> pdb=" O GLY I 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY I 300 " --> pdb=" O LEU M 299 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY M 298 " --> pdb=" O ALA Q 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU Q 299 " --> pdb=" O GLY M 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY M 300 " --> pdb=" O LEU Q 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AB1, first strand: chain 'C' and resid 311 through 318 Processing sheet with id=AB2, first strand: chain 'D' and resid 292 through 293 Processing sheet with id=AB3, first strand: chain 'D' and resid 312 through 314 removed outlier: 6.180A pdb=" N PHE D 313 " --> pdb=" O GLY H 314 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE H 313 " --> pdb=" O GLY J 314 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE J 313 " --> pdb=" O GLY N 314 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE N 313 " --> pdb=" O GLY R 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 100 hydrogen bonds defined for protein. 300 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: 0.56 Time building geometry restraints manager: 0.48 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: 1606 1.34 - 1.45: 742 1.45 - 1.57: 1872 1.57 - 1.68: 0 1.68 - 1.80: 80 Bond restraints: 4300 Sorted by residual: bond pdb=" N GLN S 303 " pdb=" CA GLN S 303 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.24e-02 6.50e+03 7.62e+00 bond pdb=" N GLN E 303 " pdb=" CA GLN E 303 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.24e-02 6.50e+03 7.54e+00 bond pdb=" N PHE C 289 " pdb=" CA PHE C 289 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.45e+00 bond pdb=" N PHE I 289 " pdb=" CA PHE I 289 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.40e+00 bond pdb=" N GLN G 303 " pdb=" CA GLN G 303 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.24e-02 6.50e+03 7.39e+00 ... (remaining 4295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 4938 1.71 - 3.42: 482 3.42 - 5.13: 133 5.13 - 6.84: 77 6.84 - 8.55: 10 Bond angle restraints: 5640 Sorted by residual: angle pdb=" N GLY D 294 " pdb=" CA GLY D 294 " pdb=" C GLY D 294 " ideal model delta sigma weight residual 112.82 107.51 5.31 1.38e+00 5.25e-01 1.48e+01 angle pdb=" N GLY P 294 " pdb=" CA GLY P 294 " pdb=" C GLY P 294 " ideal model delta sigma weight residual 112.82 107.52 5.30 1.38e+00 5.25e-01 1.47e+01 angle pdb=" N GLY F 294 " pdb=" CA GLY F 294 " pdb=" C GLY F 294 " ideal model delta sigma weight residual 112.82 107.54 5.28 1.38e+00 5.25e-01 1.47e+01 angle pdb=" N GLY T 294 " pdb=" CA GLY T 294 " pdb=" C GLY T 294 " ideal model delta sigma weight residual 112.82 107.55 5.27 1.38e+00 5.25e-01 1.46e+01 angle pdb=" N GLY B 294 " pdb=" CA GLY B 294 " pdb=" C GLY B 294 " ideal model delta sigma weight residual 112.82 107.56 5.26 1.38e+00 5.25e-01 1.46e+01 ... (remaining 5635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.42: 1860 12.42 - 24.84: 250 24.84 - 37.25: 130 37.25 - 49.67: 0 49.67 - 62.09: 20 Dihedral angle restraints: 2260 sinusoidal: 840 harmonic: 1420 Sorted by residual: dihedral pdb=" CA ASN B 312 " pdb=" C ASN B 312 " pdb=" N PHE B 313 " pdb=" CA PHE B 313 " ideal model delta harmonic sigma weight residual 180.00 -162.66 -17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASN P 312 " pdb=" C ASN P 312 " pdb=" N PHE P 313 " pdb=" CA PHE P 313 " ideal model delta harmonic sigma weight residual -180.00 -162.66 -17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASN D 312 " pdb=" C ASN D 312 " pdb=" N PHE D 313 " pdb=" CA PHE D 313 " ideal model delta harmonic sigma weight residual -180.00 -162.69 -17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 2257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 310 0.050 - 0.100: 60 0.100 - 0.150: 47 0.150 - 0.200: 13 0.200 - 0.250: 10 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA SER M 305 " pdb=" N SER M 305 " pdb=" C SER M 305 " pdb=" CB SER M 305 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA SER E 305 " pdb=" N SER E 305 " pdb=" C SER E 305 " pdb=" CB SER E 305 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA SER I 305 " pdb=" N SER I 305 " pdb=" C SER I 305 " pdb=" CB SER I 305 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 437 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY O 304 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C GLY O 304 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY O 304 " -0.013 2.00e-02 2.50e+03 pdb=" N SER O 305 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 304 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C GLY G 304 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY G 304 " 0.013 2.00e-02 2.50e+03 pdb=" N SER G 305 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 304 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C GLY M 304 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY M 304 " 0.013 2.00e-02 2.50e+03 pdb=" N SER M 305 " 0.012 2.00e-02 2.50e+03 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1842 2.89 - 3.39: 3758 3.39 - 3.89: 7085 3.89 - 4.40: 8792 4.40 - 4.90: 17058 Nonbonded interactions: 38535 Sorted by model distance: nonbonded pdb=" ND2 ASN A 302 " pdb=" OG SER A 305 " model vdw 2.387 3.120 nonbonded pdb=" ND2 ASN C 302 " pdb=" OG SER C 305 " model vdw 2.387 3.120 nonbonded pdb=" ND2 ASN K 302 " pdb=" OG SER K 305 " model vdw 2.388 3.120 nonbonded pdb=" ND2 ASN I 302 " pdb=" OG SER I 305 " model vdw 2.388 3.120 nonbonded pdb=" ND2 ASN S 302 " pdb=" OG SER S 305 " model vdw 2.388 3.120 ... (remaining 38530 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 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' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.530 Find NCS groups from input model: 0.080 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.009 0.035 4300 Z= 0.507 Angle : 1.311 8.550 5640 Z= 0.786 Chirality : 0.073 0.250 440 Planarity : 0.004 0.020 860 Dihedral : 14.000 62.088 1460 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % 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: -5.01 (0.17), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.13), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 293 PHE 0.015 0.001 PHE M 313 Details of bonding type rmsd covalent geometry : bond 0.00932 ( 4300) covalent geometry : angle 1.31051 ( 5640) hydrogen bonds : bond 0.14059 ( 100) hydrogen bonds : angle 9.80604 ( 300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.167 Fit side-chains REVERT: C 291 ASN cc_start: 0.8565 (p0) cc_final: 0.7128 (m-40) REVERT: C 305 SER cc_start: 0.7761 (p) cc_final: 0.7471 (m) REVERT: C 315 GLU cc_start: 0.8507 (tt0) cc_final: 0.8251 (tt0) REVERT: E 311 MET cc_start: 0.8956 (ttt) cc_final: 0.8665 (ttm) REVERT: F 307 MET cc_start: 0.7926 (mmt) cc_final: 0.7668 (mmt) REVERT: G 311 MET cc_start: 0.8909 (ttt) cc_final: 0.8596 (ttm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0465 time to fit residues: 5.7710 Evaluate side-chains 70 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN I 302 ASN K 302 ASN M 302 ASN N 306 ASN O 302 ASN Q 302 ASN S 302 ASN T 306 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.148606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.136072 restraints weight = 6351.476| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.14 r_work: 0.4017 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4300 Z= 0.191 Angle : 0.593 8.107 5640 Z= 0.300 Chirality : 0.045 0.133 440 Planarity : 0.002 0.008 860 Dihedral : 5.636 16.892 640 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 4.74 % Allowed : 21.32 % Favored : 73.95 % 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: -4.43 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 293 PHE 0.017 0.002 PHE G 313 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 4300) covalent geometry : angle 0.59257 ( 5640) hydrogen bonds : bond 0.04103 ( 100) hydrogen bonds : angle 6.59771 ( 300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: C 291 ASN cc_start: 0.8621 (p0) cc_final: 0.6970 (m-40) REVERT: E 291 ASN cc_start: 0.8734 (p0) cc_final: 0.6929 (m-40) REVERT: J 306 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8554 (m-40) outliers start: 18 outliers final: 11 residues processed: 89 average time/residue: 0.0428 time to fit residues: 5.4895 Evaluate side-chains 82 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 306 ASN Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain S residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 57 optimal weight: 30.0000 chunk 8 optimal weight: 0.0970 overall best weight: 13.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.143765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.130342 restraints weight = 6359.960| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.20 r_work: 0.3907 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 4300 Z= 0.364 Angle : 0.719 9.376 5640 Z= 0.361 Chirality : 0.046 0.148 440 Planarity : 0.003 0.015 860 Dihedral : 6.084 19.047 640 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 7.37 % Allowed : 25.79 % Favored : 66.84 % 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: -4.22 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 293 PHE 0.020 0.002 PHE O 313 Details of bonding type rmsd covalent geometry : bond 0.00831 ( 4300) covalent geometry : angle 0.71927 ( 5640) hydrogen bonds : bond 0.04737 ( 100) hydrogen bonds : angle 6.78503 ( 300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.158 Fit side-chains REVERT: D 307 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8313 (ttm) REVERT: G 311 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8824 (ttm) REVERT: Q 303 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7523 (mt0) outliers start: 28 outliers final: 21 residues processed: 86 average time/residue: 0.0454 time to fit residues: 5.5461 Evaluate side-chains 92 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 291 ASN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain T residue 292 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 291 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.149392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.136272 restraints weight = 6098.147| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.20 r_work: 0.4123 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4018 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4300 Z= 0.178 Angle : 0.576 8.337 5640 Z= 0.291 Chirality : 0.041 0.138 440 Planarity : 0.002 0.007 860 Dihedral : 5.459 17.429 640 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 6.58 % Allowed : 25.26 % Favored : 68.16 % 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: -3.93 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 293 PHE 0.016 0.002 PHE O 313 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 4300) covalent geometry : angle 0.57610 ( 5640) hydrogen bonds : bond 0.03625 ( 100) hydrogen bonds : angle 6.33504 ( 300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.120 Fit side-chains REVERT: C 291 ASN cc_start: 0.8837 (p0) cc_final: 0.6787 (m-40) REVERT: E 291 ASN cc_start: 0.8773 (p0) cc_final: 0.6742 (m-40) REVERT: G 311 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8722 (ttm) REVERT: S 303 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7867 (mt0) outliers start: 25 outliers final: 17 residues processed: 93 average time/residue: 0.0414 time to fit residues: 5.5453 Evaluate side-chains 94 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.0270 chunk 8 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 56 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 55 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 45 optimal weight: 40.0000 chunk 43 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 overall best weight: 7.4646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN F 312 ASN N 306 ASN ** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 291 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.149773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.136477 restraints weight = 6229.891| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.21 r_work: 0.4126 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4022 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4300 Z= 0.210 Angle : 0.599 8.439 5640 Z= 0.300 Chirality : 0.041 0.157 440 Planarity : 0.002 0.013 860 Dihedral : 5.511 16.926 640 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 7.63 % Allowed : 24.47 % Favored : 67.89 % 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: -3.83 (0.27), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 293 PHE 0.016 0.002 PHE M 313 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 4300) covalent geometry : angle 0.59879 ( 5640) hydrogen bonds : bond 0.03711 ( 100) hydrogen bonds : angle 6.35839 ( 300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.157 Fit side-chains REVERT: E 291 ASN cc_start: 0.8797 (p0) cc_final: 0.6758 (m-40) REVERT: E 302 ASN cc_start: 0.8618 (t0) cc_final: 0.8185 (t0) REVERT: G 311 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8765 (ttm) REVERT: K 311 MET cc_start: 0.8994 (ttm) cc_final: 0.8737 (ttt) REVERT: Q 303 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: S 303 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7899 (mt0) outliers start: 29 outliers final: 22 residues processed: 94 average time/residue: 0.0442 time to fit residues: 5.9927 Evaluate side-chains 99 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 292 SER Chi-restraints excluded: chain P residue 311 MET Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 20.0000 chunk 42 optimal weight: 40.0000 chunk 18 optimal weight: 30.0000 chunk 15 optimal weight: 40.0000 chunk 23 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 41 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 overall best weight: 10.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 291 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.146120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.132646 restraints weight = 6469.728| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.25 r_work: 0.4075 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3972 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 4300 Z= 0.289 Angle : 0.647 8.756 5640 Z= 0.330 Chirality : 0.042 0.152 440 Planarity : 0.002 0.011 860 Dihedral : 5.715 17.236 640 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 9.47 % Allowed : 22.63 % Favored : 67.89 % 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: -3.90 (0.26), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 293 PHE 0.018 0.002 PHE S 313 Details of bonding type rmsd covalent geometry : bond 0.00664 ( 4300) covalent geometry : angle 0.64733 ( 5640) hydrogen bonds : bond 0.04012 ( 100) hydrogen bonds : angle 6.52937 ( 300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 0.188 Fit side-chains REVERT: E 291 ASN cc_start: 0.8876 (p0) cc_final: 0.6694 (m-40) REVERT: G 311 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8840 (ttm) REVERT: Q 303 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.7637 (mt0) REVERT: S 291 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8318 (m-40) REVERT: S 303 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7849 (mt0) outliers start: 36 outliers final: 26 residues processed: 94 average time/residue: 0.0433 time to fit residues: 5.8799 Evaluate side-chains 102 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain N residue 318 ILE Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 292 SER Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain T residue 292 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 40.0000 chunk 19 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 291 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.148659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.135382 restraints weight = 6288.849| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.21 r_work: 0.4106 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4300 Z= 0.231 Angle : 0.623 8.235 5640 Z= 0.313 Chirality : 0.042 0.152 440 Planarity : 0.002 0.009 860 Dihedral : 5.658 16.251 640 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 9.74 % Allowed : 23.42 % Favored : 66.84 % 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: -3.85 (0.26), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 293 PHE 0.017 0.002 PHE M 313 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 4300) covalent geometry : angle 0.62314 ( 5640) hydrogen bonds : bond 0.03770 ( 100) hydrogen bonds : angle 6.39559 ( 300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 0.157 Fit side-chains REVERT: E 318 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8544 (mt) REVERT: G 311 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8797 (ttm) REVERT: Q 303 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7558 (mt0) REVERT: S 303 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7791 (mt0) outliers start: 37 outliers final: 28 residues processed: 94 average time/residue: 0.0372 time to fit residues: 5.1313 Evaluate side-chains 104 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain N residue 318 ILE Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 292 SER Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain R residue 311 MET Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain T residue 292 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 40.0000 chunk 24 optimal weight: 30.0000 chunk 45 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.144921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.131670 restraints weight = 6367.503| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.19 r_work: 0.4051 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 4300 Z= 0.353 Angle : 0.717 9.016 5640 Z= 0.360 Chirality : 0.044 0.147 440 Planarity : 0.002 0.013 860 Dihedral : 6.056 16.620 640 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 9.47 % Allowed : 23.42 % Favored : 67.11 % 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: -4.02 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.18), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 293 PHE 0.019 0.002 PHE O 313 Details of bonding type rmsd covalent geometry : bond 0.00807 ( 4300) covalent geometry : angle 0.71655 ( 5640) hydrogen bonds : bond 0.04270 ( 100) hydrogen bonds : angle 6.63924 ( 300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.174 Fit side-chains REVERT: E 318 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8494 (mt) REVERT: G 311 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8846 (ttm) REVERT: Q 303 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: S 303 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7691 (mt0) outliers start: 36 outliers final: 27 residues processed: 93 average time/residue: 0.0436 time to fit residues: 5.8461 Evaluate side-chains 104 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 292 SER Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain R residue 311 MET Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain T residue 292 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 40.0000 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.159504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.144573 restraints weight = 6099.209| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.14 r_work: 0.4190 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4087 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4300 Z= 0.141 Angle : 0.567 8.003 5640 Z= 0.286 Chirality : 0.040 0.145 440 Planarity : 0.001 0.007 860 Dihedral : 5.457 18.815 640 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 7.63 % Allowed : 24.74 % Favored : 67.63 % 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: -3.72 (0.27), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 293 PHE 0.015 0.001 PHE K 313 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4300) covalent geometry : angle 0.56725 ( 5640) hydrogen bonds : bond 0.03192 ( 100) hydrogen bonds : angle 6.08384 ( 300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.191 Fit side-chains REVERT: E 291 ASN cc_start: 0.8773 (p0) cc_final: 0.6735 (m-40) REVERT: E 302 ASN cc_start: 0.8631 (t0) cc_final: 0.8165 (t0) REVERT: G 311 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8823 (ttm) REVERT: J 307 MET cc_start: 0.8391 (tpp) cc_final: 0.7900 (tpt) REVERT: Q 303 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: S 303 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7890 (mt0) outliers start: 29 outliers final: 20 residues processed: 92 average time/residue: 0.0414 time to fit residues: 5.5206 Evaluate side-chains 99 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 318 ILE Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 311 MET Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 45 optimal weight: 40.0000 chunk 37 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.145681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.132335 restraints weight = 6344.506| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 2.32 r_work: 0.4060 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3956 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 4300 Z= 0.301 Angle : 0.670 8.809 5640 Z= 0.338 Chirality : 0.042 0.157 440 Planarity : 0.002 0.011 860 Dihedral : 5.771 16.641 640 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 6.05 % Allowed : 25.26 % Favored : 68.68 % 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: -3.78 (0.26), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 293 PHE 0.018 0.002 PHE M 313 Details of bonding type rmsd covalent geometry : bond 0.00695 ( 4300) covalent geometry : angle 0.67019 ( 5640) hydrogen bonds : bond 0.04015 ( 100) hydrogen bonds : angle 6.48708 ( 300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.183 Fit side-chains REVERT: G 311 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8734 (ttm) REVERT: Q 303 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: S 303 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.7810 (mt0) outliers start: 23 outliers final: 19 residues processed: 86 average time/residue: 0.0474 time to fit residues: 5.8588 Evaluate side-chains 93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain Q residue 305 SER Chi-restraints excluded: chain R residue 311 MET Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 48 optimal weight: 30.0000 chunk 7 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.149805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.136746 restraints weight = 6178.378| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.19 r_work: 0.4110 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4300 Z= 0.204 Angle : 0.623 9.631 5640 Z= 0.311 Chirality : 0.041 0.158 440 Planarity : 0.002 0.007 860 Dihedral : 5.606 19.225 640 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 6.32 % Allowed : 24.47 % Favored : 69.21 % 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: -3.67 (0.27), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 293 PHE 0.017 0.002 PHE G 313 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 4300) covalent geometry : angle 0.62300 ( 5640) hydrogen bonds : bond 0.03579 ( 100) hydrogen bonds : angle 6.27714 ( 300) =============================================================================== Job complete usr+sys time: 938.07 seconds wall clock time: 16 minutes 53.05 seconds (1013.05 seconds total)