Starting phenix.real_space_refine on Tue Feb 3 12:51:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cki_45647/02_2026/9cki_45647.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cki_45647/02_2026/9cki_45647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cki_45647/02_2026/9cki_45647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cki_45647/02_2026/9cki_45647.map" model { file = "/net/cci-nas-00/data/ceres_data/9cki_45647/02_2026/9cki_45647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cki_45647/02_2026/9cki_45647.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 10 5.16 5 C 1630 2.51 5 N 420 2.21 5 O 450 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2510 Number of models: 1 Model: "" Number of chains: 1 Chain: "J" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Restraints were copied for chains: A, B, C, D, E, F, G, H, I Time building chain proxies: 0.42, per 1000 atoms: 0.17 Number of scatterers: 2510 At special positions: 0 Unit cell: (69.42, 64.08, 46.992, 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 10 16.00 O 450 8.00 N 420 7.00 C 1630 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: 0.19 Conformation dependent library (CDL) restraints added in 110.2 milliseconds 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.351A pdb=" N GLU J 11 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 16 through 20 removed outlier: 6.210A pdb=" N LEU J 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE D 20 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE J 19 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE J 20 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N LEU B 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N PHE F 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N PHE B 19 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N PHE F 20 " --> pdb=" O PHE H 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 30 through 36 removed outlier: 9.246A pdb=" N ALA J 30 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N GLY D 33 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE J 32 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N MET D 35 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU J 34 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE J 31 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE B 32 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY J 33 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 31 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE F 32 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY B 33 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE F 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE H 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY F 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.361A pdb=" N GLU A 11 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 16 through 20 removed outlier: 6.261A pdb=" N LEU A 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE E 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE A 19 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N PHE C 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE A 19 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE C 20 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE G 20 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 30 through 36 removed outlier: 6.289A pdb=" N ILE A 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU E 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLY A 33 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N VAL E 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N MET A 35 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 31 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE C 32 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLY A 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE C 31 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE G 32 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY C 33 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE G 31 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE I 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY G 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.454A pdb=" N VAL C 40 " --> pdb=" O ILE G 41 " (cutoff:3.500A) 62 hydrogen bonds defined for protein. 186 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: 0.33 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 820 1.34 - 1.46: 464 1.46 - 1.57: 1246 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 2550 Sorted by residual: bond pdb=" CG1 ILE G 32 " pdb=" CD1 ILE G 32 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.13e-01 bond pdb=" CG1 ILE H 32 " pdb=" CD1 ILE H 32 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.09e-01 bond pdb=" CG1 ILE I 32 " pdb=" CD1 ILE I 32 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.09e-01 bond pdb=" CG1 ILE B 32 " pdb=" CD1 ILE B 32 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.00e-01 bond pdb=" CG1 ILE E 32 " pdb=" CD1 ILE E 32 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.00e-01 ... (remaining 2545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.53: 2831 0.53 - 1.05: 398 1.05 - 1.58: 141 1.58 - 2.10: 30 2.10 - 2.63: 30 Bond angle restraints: 3430 Sorted by residual: angle pdb=" N HIS C 13 " pdb=" CA HIS C 13 " pdb=" C HIS C 13 " ideal model delta sigma weight residual 108.79 111.10 -2.31 1.53e+00 4.27e-01 2.28e+00 angle pdb=" N HIS H 13 " pdb=" CA HIS H 13 " pdb=" C HIS H 13 " ideal model delta sigma weight residual 108.79 111.08 -2.29 1.53e+00 4.27e-01 2.24e+00 angle pdb=" N HIS A 13 " pdb=" CA HIS A 13 " pdb=" C HIS A 13 " ideal model delta sigma weight residual 108.79 111.07 -2.28 1.53e+00 4.27e-01 2.23e+00 angle pdb=" N HIS G 13 " pdb=" CA HIS G 13 " pdb=" C HIS G 13 " ideal model delta sigma weight residual 108.79 111.05 -2.26 1.53e+00 4.27e-01 2.19e+00 angle pdb=" N HIS B 13 " pdb=" CA HIS B 13 " pdb=" C HIS B 13 " ideal model delta sigma weight residual 108.79 111.05 -2.26 1.53e+00 4.27e-01 2.17e+00 ... (remaining 3425 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 9.92: 1130 9.92 - 19.84: 140 19.84 - 29.75: 100 29.75 - 39.67: 10 39.67 - 49.58: 40 Dihedral angle restraints: 1420 sinusoidal: 520 harmonic: 900 Sorted by residual: dihedral pdb=" CA ASP I 23 " pdb=" CB ASP I 23 " pdb=" CG ASP I 23 " pdb=" OD1 ASP I 23 " ideal model delta sinusoidal sigma weight residual -30.00 -79.58 49.58 1 2.00e+01 2.50e-03 8.44e+00 dihedral pdb=" CA ASP B 23 " pdb=" CB ASP B 23 " pdb=" CG ASP B 23 " pdb=" OD1 ASP B 23 " ideal model delta sinusoidal sigma weight residual -30.00 -79.56 49.56 1 2.00e+01 2.50e-03 8.43e+00 dihedral pdb=" CA ASP F 23 " pdb=" CB ASP F 23 " pdb=" CG ASP F 23 " pdb=" OD1 ASP F 23 " ideal model delta sinusoidal sigma weight residual -30.00 -79.56 49.56 1 2.00e+01 2.50e-03 8.43e+00 ... (remaining 1417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 169 0.026 - 0.053: 101 0.053 - 0.079: 20 0.079 - 0.106: 45 0.106 - 0.132: 55 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA ILE E 31 " pdb=" N ILE E 31 " pdb=" C ILE E 31 " pdb=" CB ILE E 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE C 31 " pdb=" N ILE C 31 " pdb=" C ILE C 31 " pdb=" CB ILE C 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 387 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS H 13 " 0.004 2.00e-02 2.50e+03 3.09e-03 1.43e-01 pdb=" CG HIS H 13 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS H 13 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS H 13 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS H 13 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS H 13 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 13 " 0.004 2.00e-02 2.50e+03 3.02e-03 1.37e-01 pdb=" CG HIS F 13 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS F 13 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS F 13 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS F 13 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS F 13 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 13 " 0.004 2.00e-02 2.50e+03 3.02e-03 1.37e-01 pdb=" CG HIS D 13 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS D 13 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 13 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS D 13 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS D 13 " 0.001 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.67 - 3.11: 1665 3.11 - 3.56: 2571 3.56 - 4.01: 3864 4.01 - 4.45: 4159 4.45 - 4.90: 7441 Nonbonded interactions: 19700 Sorted by model distance: nonbonded pdb=" N GLU A 22 " pdb=" O GLU A 22 " model vdw 2.667 2.496 nonbonded pdb=" N GLU H 22 " pdb=" O GLU H 22 " model vdw 2.667 2.496 nonbonded pdb=" N GLU F 22 " pdb=" O GLU F 22 " model vdw 2.667 2.496 nonbonded pdb=" N GLU B 22 " pdb=" O GLU B 22 " model vdw 2.667 2.496 nonbonded pdb=" N GLU I 22 " pdb=" O GLU I 22 " model vdw 2.667 2.496 ... (remaining 19695 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: 0.01 Found NCS groups: ncs_group { reference = chain 'J' selection = 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' } 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: 0.570 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.520 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.004 0.025 2550 Z= 0.180 Angle : 0.498 2.627 3430 Z= 0.294 Chirality : 0.062 0.132 390 Planarity : 0.001 0.003 440 Dihedral : 15.627 49.582 860 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.46), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.22 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR G 10 PHE 0.002 0.001 PHE A 20 HIS 0.002 0.001 HIS H 13 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 2550) covalent geometry : angle 0.49771 ( 3430) hydrogen bonds : bond 0.21816 ( 62) hydrogen bonds : angle 7.34617 ( 186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.094 Fit side-chains REVERT: J 11 GLU cc_start: 0.8221 (tt0) cc_final: 0.7999 (tt0) REVERT: J 26 SER cc_start: 0.9027 (t) cc_final: 0.8797 (m) REVERT: A 26 SER cc_start: 0.8709 (t) cc_final: 0.8430 (t) REVERT: A 35 MET cc_start: 0.9109 (ttt) cc_final: 0.8466 (ttp) REVERT: C 10 TYR cc_start: 0.7908 (m-80) cc_final: 0.7649 (m-80) REVERT: C 26 SER cc_start: 0.8685 (t) cc_final: 0.8314 (m) REVERT: D 11 GLU cc_start: 0.8132 (tt0) cc_final: 0.7833 (tt0) REVERT: D 26 SER cc_start: 0.8335 (t) cc_final: 0.8126 (t) REVERT: E 35 MET cc_start: 0.8579 (ttt) cc_final: 0.8337 (ttt) REVERT: G 10 TYR cc_start: 0.7948 (m-80) cc_final: 0.7692 (m-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0640 time to fit residues: 4.7294 Evaluate side-chains 49 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0030 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.0470 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.6094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.103328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084449 restraints weight = 3409.098| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.62 r_work: 0.3120 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2550 Z= 0.126 Angle : 0.506 6.133 3430 Z= 0.281 Chirality : 0.061 0.138 390 Planarity : 0.002 0.006 440 Dihedral : 5.017 17.188 350 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.20 % Allowed : 17.20 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.46), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.26 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 10 PHE 0.007 0.001 PHE I 20 HIS 0.003 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2550) covalent geometry : angle 0.50623 ( 3430) hydrogen bonds : bond 0.02517 ( 62) hydrogen bonds : angle 5.68169 ( 186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.095 Fit side-chains REVERT: J 26 SER cc_start: 0.8761 (t) cc_final: 0.8516 (m) REVERT: B 11 GLU cc_start: 0.8310 (tt0) cc_final: 0.7969 (tt0) REVERT: C 10 TYR cc_start: 0.8052 (m-80) cc_final: 0.7752 (m-80) REVERT: C 26 SER cc_start: 0.8443 (t) cc_final: 0.8048 (m) REVERT: C 35 MET cc_start: 0.8878 (ttp) cc_final: 0.8627 (ttp) REVERT: D 11 GLU cc_start: 0.8214 (tt0) cc_final: 0.7957 (tt0) REVERT: D 22 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7486 (mm-30) REVERT: D 27 ASN cc_start: 0.8579 (t0) cc_final: 0.8374 (t0) REVERT: E 22 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7463 (mm-30) REVERT: G 10 TYR cc_start: 0.8195 (m-80) cc_final: 0.7915 (m-80) REVERT: H 23 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: I 23 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7407 (m-30) outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 0.0371 time to fit residues: 2.9162 Evaluate side-chains 60 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain I residue 23 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077690 restraints weight = 3560.971| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.58 r_work: 0.2995 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 2550 Z= 0.276 Angle : 0.622 5.751 3430 Z= 0.341 Chirality : 0.064 0.143 390 Planarity : 0.002 0.010 440 Dihedral : 6.606 32.306 350 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.40 % Allowed : 19.20 % Favored : 76.40 % 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 are not related in a simple way. whole: -0.51 (0.45), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.38 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR B 10 PHE 0.009 0.002 PHE D 20 HIS 0.006 0.002 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00669 ( 2550) covalent geometry : angle 0.62240 ( 3430) hydrogen bonds : bond 0.02819 ( 62) hydrogen bonds : angle 5.48230 ( 186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.091 Fit side-chains REVERT: J 26 SER cc_start: 0.8638 (t) cc_final: 0.8311 (m) REVERT: B 11 GLU cc_start: 0.8332 (tt0) cc_final: 0.7968 (tt0) REVERT: C 10 TYR cc_start: 0.8217 (m-80) cc_final: 0.7893 (m-80) REVERT: C 26 SER cc_start: 0.8425 (t) cc_final: 0.8062 (m) REVERT: C 35 MET cc_start: 0.8861 (ttp) cc_final: 0.8592 (ttp) REVERT: D 11 GLU cc_start: 0.8228 (tt0) cc_final: 0.7990 (tt0) REVERT: D 22 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7515 (mm-30) REVERT: E 22 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7704 (mm-30) REVERT: H 23 ASP cc_start: 0.8062 (m-30) cc_final: 0.7846 (m-30) REVERT: I 23 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7615 (m-30) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.0295 time to fit residues: 2.3494 Evaluate side-chains 62 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain I residue 23 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.100991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.082665 restraints weight = 3421.187| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.60 r_work: 0.3093 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2550 Z= 0.126 Angle : 0.497 5.296 3430 Z= 0.277 Chirality : 0.061 0.136 390 Planarity : 0.001 0.006 440 Dihedral : 5.860 26.866 350 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.60 % Allowed : 20.80 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.45), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.42 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR G 10 PHE 0.005 0.001 PHE J 20 HIS 0.003 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2550) covalent geometry : angle 0.49734 ( 3430) hydrogen bonds : bond 0.02028 ( 62) hydrogen bonds : angle 5.12744 ( 186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.056 Fit side-chains REVERT: J 26 SER cc_start: 0.8661 (t) cc_final: 0.8355 (m) REVERT: C 26 SER cc_start: 0.8487 (t) cc_final: 0.8121 (m) REVERT: D 11 GLU cc_start: 0.8191 (tt0) cc_final: 0.7968 (tt0) REVERT: D 17 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8837 (tp) REVERT: D 22 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7703 (mm-30) REVERT: E 22 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7612 (mm-30) REVERT: H 22 GLU cc_start: 0.7932 (mm-30) cc_final: 0.6101 (pt0) REVERT: H 23 ASP cc_start: 0.8050 (m-30) cc_final: 0.7838 (m-30) REVERT: I 23 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7502 (m-30) outliers start: 9 outliers final: 6 residues processed: 62 average time/residue: 0.0304 time to fit residues: 2.3732 Evaluate side-chains 59 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 23 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.095483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.077589 restraints weight = 3551.398| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.58 r_work: 0.3019 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 2550 Z= 0.298 Angle : 0.622 5.460 3430 Z= 0.344 Chirality : 0.065 0.145 390 Planarity : 0.002 0.007 440 Dihedral : 7.013 35.621 350 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.80 % Allowed : 21.20 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.44), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.61 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR C 10 PHE 0.007 0.002 PHE B 19 HIS 0.007 0.003 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00718 ( 2550) covalent geometry : angle 0.62161 ( 3430) hydrogen bonds : bond 0.02615 ( 62) hydrogen bonds : angle 5.18689 ( 186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.092 Fit side-chains REVERT: J 26 SER cc_start: 0.8672 (t) cc_final: 0.8308 (m) REVERT: J 34 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8431 (tp) REVERT: C 26 SER cc_start: 0.8425 (t) cc_final: 0.8072 (m) REVERT: D 11 GLU cc_start: 0.8182 (tt0) cc_final: 0.7936 (tt0) REVERT: D 23 ASP cc_start: 0.7726 (m-30) cc_final: 0.7524 (m-30) REVERT: E 22 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7645 (mm-30) REVERT: H 22 GLU cc_start: 0.7796 (mm-30) cc_final: 0.6072 (pt0) REVERT: H 23 ASP cc_start: 0.8074 (m-30) cc_final: 0.7790 (m-30) REVERT: I 23 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7629 (m-30) outliers start: 12 outliers final: 8 residues processed: 60 average time/residue: 0.0488 time to fit residues: 3.6385 Evaluate side-chains 62 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 23 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088830 restraints weight = 3287.662| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.43 r_work: 0.3201 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2550 Z= 0.079 Angle : 0.447 5.201 3430 Z= 0.256 Chirality : 0.060 0.135 390 Planarity : 0.001 0.006 440 Dihedral : 5.521 24.291 350 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.80 % Allowed : 23.60 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.45), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR C 10 PHE 0.005 0.001 PHE J 20 HIS 0.003 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 2550) covalent geometry : angle 0.44741 ( 3430) hydrogen bonds : bond 0.01933 ( 62) hydrogen bonds : angle 4.92180 ( 186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.058 Fit side-chains REVERT: J 26 SER cc_start: 0.8620 (t) cc_final: 0.8284 (m) REVERT: B 11 GLU cc_start: 0.8251 (tt0) cc_final: 0.7802 (tt0) REVERT: B 28 LYS cc_start: 0.8855 (mtmm) cc_final: 0.8649 (mttp) REVERT: C 26 SER cc_start: 0.8431 (t) cc_final: 0.8050 (m) REVERT: D 11 GLU cc_start: 0.8157 (tt0) cc_final: 0.7944 (tt0) REVERT: D 23 ASP cc_start: 0.7433 (m-30) cc_final: 0.7204 (m-30) REVERT: E 22 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7310 (mm-30) REVERT: H 22 GLU cc_start: 0.7944 (mm-30) cc_final: 0.6081 (pt0) REVERT: H 23 ASP cc_start: 0.7900 (m-30) cc_final: 0.7643 (m-30) REVERT: I 23 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7325 (m-30) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 0.0590 time to fit residues: 4.5123 Evaluate side-chains 60 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 23 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.095747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.078017 restraints weight = 3550.654| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.55 r_work: 0.3035 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 2550 Z= 0.299 Angle : 0.627 5.274 3430 Z= 0.347 Chirality : 0.065 0.142 390 Planarity : 0.002 0.008 440 Dihedral : 6.945 35.065 350 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.60 % Allowed : 19.20 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.43), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.70 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR G 10 PHE 0.008 0.002 PHE B 19 HIS 0.007 0.003 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00728 ( 2550) covalent geometry : angle 0.62747 ( 3430) hydrogen bonds : bond 0.02518 ( 62) hydrogen bonds : angle 5.03157 ( 186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.097 Fit side-chains REVERT: J 26 SER cc_start: 0.8743 (t) cc_final: 0.8377 (m) REVERT: J 34 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8463 (tp) REVERT: C 26 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8117 (m) REVERT: C 35 MET cc_start: 0.8872 (ttp) cc_final: 0.8641 (ttp) REVERT: D 11 GLU cc_start: 0.8196 (tt0) cc_final: 0.7944 (tt0) REVERT: D 23 ASP cc_start: 0.7799 (m-30) cc_final: 0.7594 (m-30) REVERT: E 22 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7637 (mm-30) REVERT: H 22 GLU cc_start: 0.7805 (mm-30) cc_final: 0.6124 (pt0) REVERT: H 23 ASP cc_start: 0.8083 (m-30) cc_final: 0.7808 (m-30) REVERT: I 23 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7644 (m-30) outliers start: 14 outliers final: 10 residues processed: 64 average time/residue: 0.0508 time to fit residues: 4.0446 Evaluate side-chains 66 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.103006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083829 restraints weight = 3308.261| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.61 r_work: 0.3118 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2550 Z= 0.147 Angle : 0.518 5.088 3430 Z= 0.289 Chirality : 0.061 0.131 390 Planarity : 0.002 0.006 440 Dihedral : 6.322 30.129 350 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.80 % Allowed : 20.40 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.44), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR G 10 PHE 0.005 0.001 PHE D 20 HIS 0.003 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 2550) covalent geometry : angle 0.51789 ( 3430) hydrogen bonds : bond 0.02001 ( 62) hydrogen bonds : angle 4.86728 ( 186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.098 Fit side-chains REVERT: J 26 SER cc_start: 0.8653 (t) cc_final: 0.8333 (m) REVERT: B 11 GLU cc_start: 0.8279 (tt0) cc_final: 0.7957 (tt0) REVERT: C 26 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8055 (m) REVERT: C 31 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8593 (mm) REVERT: D 11 GLU cc_start: 0.8129 (tt0) cc_final: 0.7891 (tt0) REVERT: D 22 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7676 (mm-30) REVERT: D 23 ASP cc_start: 0.7650 (m-30) cc_final: 0.7337 (m-30) REVERT: E 17 LEU cc_start: 0.8492 (tp) cc_final: 0.8171 (tp) REVERT: E 22 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7458 (mm-30) REVERT: G 35 MET cc_start: 0.8494 (ttt) cc_final: 0.8054 (ttt) REVERT: H 22 GLU cc_start: 0.7917 (mm-30) cc_final: 0.6136 (pt0) REVERT: H 23 ASP cc_start: 0.7967 (m-30) cc_final: 0.7703 (m-30) REVERT: I 23 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7473 (m-30) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 0.0507 time to fit residues: 3.9958 Evaluate side-chains 62 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 23 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.080144 restraints weight = 3573.655| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.59 r_work: 0.3077 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 2550 Z= 0.232 Angle : 0.635 9.593 3430 Z= 0.335 Chirality : 0.063 0.137 390 Planarity : 0.002 0.006 440 Dihedral : 6.723 33.131 350 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.20 % Allowed : 21.60 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.44), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR G 10 PHE 0.006 0.001 PHE D 19 HIS 0.006 0.002 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 2550) covalent geometry : angle 0.63548 ( 3430) hydrogen bonds : bond 0.02337 ( 62) hydrogen bonds : angle 4.87778 ( 186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.092 Fit side-chains REVERT: J 26 SER cc_start: 0.8710 (t) cc_final: 0.8352 (m) REVERT: B 11 GLU cc_start: 0.8268 (tt0) cc_final: 0.7943 (tt0) REVERT: C 26 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8077 (m) REVERT: C 31 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8597 (mm) REVERT: D 11 GLU cc_start: 0.8158 (tt0) cc_final: 0.7917 (tt0) REVERT: D 23 ASP cc_start: 0.7784 (m-30) cc_final: 0.7566 (m-30) REVERT: E 22 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7646 (mm-30) REVERT: G 35 MET cc_start: 0.8626 (ttt) cc_final: 0.8378 (ttt) REVERT: H 22 GLU cc_start: 0.7804 (mm-30) cc_final: 0.6102 (pt0) REVERT: H 23 ASP cc_start: 0.8083 (m-30) cc_final: 0.7805 (m-30) REVERT: I 23 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7645 (m-30) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.0511 time to fit residues: 3.6815 Evaluate side-chains 59 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 23 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083370 restraints weight = 3284.290| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.63 r_work: 0.3117 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2550 Z= 0.174 Angle : 0.595 9.292 3430 Z= 0.315 Chirality : 0.062 0.132 390 Planarity : 0.002 0.010 440 Dihedral : 6.449 31.039 350 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.80 % Allowed : 21.20 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.44), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR G 10 PHE 0.005 0.001 PHE D 20 HIS 0.004 0.002 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 2550) covalent geometry : angle 0.59532 ( 3430) hydrogen bonds : bond 0.02317 ( 62) hydrogen bonds : angle 4.83660 ( 186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.098 Fit side-chains REVERT: J 26 SER cc_start: 0.8650 (t) cc_final: 0.8323 (m) REVERT: C 26 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8047 (m) REVERT: C 31 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8583 (mm) REVERT: D 11 GLU cc_start: 0.8144 (tt0) cc_final: 0.7915 (tt0) REVERT: D 23 ASP cc_start: 0.7757 (m-30) cc_final: 0.7530 (m-30) REVERT: E 22 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7581 (mm-30) REVERT: G 35 MET cc_start: 0.8557 (ttt) cc_final: 0.8167 (ttt) REVERT: H 22 GLU cc_start: 0.7932 (mm-30) cc_final: 0.6163 (pt0) REVERT: H 23 ASP cc_start: 0.7998 (m-30) cc_final: 0.7736 (m-30) REVERT: I 23 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7580 (m-30) outliers start: 12 outliers final: 6 residues processed: 60 average time/residue: 0.0557 time to fit residues: 4.1098 Evaluate side-chains 60 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 23 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.081306 restraints weight = 3383.104| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.60 r_work: 0.3084 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2550 Z= 0.218 Angle : 0.626 9.018 3430 Z= 0.331 Chirality : 0.063 0.137 390 Planarity : 0.002 0.009 440 Dihedral : 6.637 31.681 350 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.40 % Allowed : 22.00 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.44), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR G 10 PHE 0.005 0.001 PHE D 20 HIS 0.005 0.002 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 2550) covalent geometry : angle 0.62555 ( 3430) hydrogen bonds : bond 0.02396 ( 62) hydrogen bonds : angle 4.84265 ( 186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 701.85 seconds wall clock time: 12 minutes 42.75 seconds (762.75 seconds total)