Starting phenix.real_space_refine on Wed Mar 5 15:41:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ot1_17166/03_2025/8ot1_17166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ot1_17166/03_2025/8ot1_17166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ot1_17166/03_2025/8ot1_17166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ot1_17166/03_2025/8ot1_17166.map" model { file = "/net/cci-nas-00/data/ceres_data/8ot1_17166/03_2025/8ot1_17166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ot1_17166/03_2025/8ot1_17166.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 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 12 5.16 5 C 1596 2.51 5 N 432 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2460 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 1.70, per 1000 atoms: 0.69 Number of scatterers: 2460 At special positions: 0 Unit cell: (77.522, 83.126, 43.898, 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 12 16.00 O 420 8.00 N 432 7.00 C 1596 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: 0.57 Conformation dependent library (CDL) restraints added in 314.7 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 24 removed outlier: 6.384A pdb=" N LYS A 16 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE C 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA C 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE A 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP C 23 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU A 22 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS C 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA E 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE C 20 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP E 23 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU C 22 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS E 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA G 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE E 20 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP G 23 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU E 22 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS G 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE I 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA I 21 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE G 20 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP I 23 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU G 22 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS I 16 " --> pdb=" O LEU K 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE K 19 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL I 18 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA K 21 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE I 20 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP K 23 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU I 22 " --> pdb=" O ASP K 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 16 through 24 removed outlier: 6.384A pdb=" N LYS B 16 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE D 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA D 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE B 20 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP D 23 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU B 22 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS D 16 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA F 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE D 20 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP F 23 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU D 22 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS F 16 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE H 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA H 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE F 20 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP H 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU F 22 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS H 16 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE J 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA J 21 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE H 20 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP J 23 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLU H 22 " --> pdb=" O ASP J 23 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS J 16 " --> pdb=" O LEU L 17 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE L 19 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL J 18 " --> pdb=" O PHE L 19 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA L 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE J 20 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ASP L 23 " --> pdb=" O PHE J 20 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N GLU J 22 " --> pdb=" O ASP L 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 No hydrogen bonds 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: 0.05 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 540 1.33 - 1.45: 492 1.45 - 1.57: 1440 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 2496 Sorted by residual: bond pdb=" CA GLY A 33 " pdb=" C GLY A 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.52e+01 bond pdb=" CA GLY B 33 " pdb=" C GLY B 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.52e+01 bond pdb=" CA GLY I 33 " pdb=" C GLY I 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.51e+01 bond pdb=" CA GLY J 33 " pdb=" C GLY J 33 " ideal model delta sigma weight residual 1.514 1.459 0.055 1.41e-02 5.03e+03 1.51e+01 bond pdb=" CA GLY D 33 " pdb=" C GLY D 33 " ideal model delta sigma weight residual 1.514 1.460 0.054 1.41e-02 5.03e+03 1.49e+01 ... (remaining 2491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 2280 2.34 - 4.68: 940 4.68 - 7.01: 80 7.01 - 9.35: 24 9.35 - 11.69: 12 Bond angle restraints: 3336 Sorted by residual: angle pdb=" CA GLY F 38 " pdb=" C GLY F 38 " pdb=" O GLY F 38 " ideal model delta sigma weight residual 122.23 118.11 4.12 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY E 38 " pdb=" C GLY E 38 " pdb=" O GLY E 38 " ideal model delta sigma weight residual 122.23 118.11 4.12 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY H 38 " pdb=" C GLY H 38 " pdb=" O GLY H 38 " ideal model delta sigma weight residual 122.23 118.12 4.11 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY G 38 " pdb=" C GLY G 38 " pdb=" O GLY G 38 " ideal model delta sigma weight residual 122.23 118.12 4.11 6.90e-01 2.10e+00 3.56e+01 angle pdb=" CA GLY L 38 " pdb=" C GLY L 38 " pdb=" O GLY L 38 " ideal model delta sigma weight residual 122.23 118.12 4.11 6.90e-01 2.10e+00 3.55e+01 ... (remaining 3331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.97: 1152 12.97 - 25.93: 156 25.93 - 38.90: 24 38.90 - 51.86: 36 51.86 - 64.83: 24 Dihedral angle restraints: 1392 sinusoidal: 516 harmonic: 876 Sorted by residual: dihedral pdb=" CA GLU K 22 " pdb=" CB GLU K 22 " pdb=" CG GLU K 22 " pdb=" CD GLU K 22 " ideal model delta sinusoidal sigma weight residual -60.00 -118.23 58.23 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLU L 22 " pdb=" CB GLU L 22 " pdb=" CG GLU L 22 " pdb=" CD GLU L 22 " ideal model delta sinusoidal sigma weight residual -60.00 -118.23 58.23 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLU I 22 " pdb=" CB GLU I 22 " pdb=" CG GLU I 22 " pdb=" CD GLU I 22 " ideal model delta sinusoidal sigma weight residual -60.00 -118.22 58.22 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1389 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.053: 84 0.053 - 0.104: 60 0.104 - 0.155: 132 0.155 - 0.207: 84 0.207 - 0.258: 24 Chirality restraints: 384 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 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE F 31 " pdb=" N ILE F 31 " pdb=" C ILE F 31 " pdb=" CB ILE F 31 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE L 31 " pdb=" N ILE L 31 " pdb=" C ILE L 31 " pdb=" CB ILE L 31 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 381 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 34 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LEU G 34 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU G 34 " -0.021 2.00e-02 2.50e+03 pdb=" N MET G 35 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 34 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LEU H 34 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU H 34 " 0.021 2.00e-02 2.50e+03 pdb=" N MET H 35 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 34 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU K 34 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU K 34 " -0.021 2.00e-02 2.50e+03 pdb=" N MET K 35 " -0.019 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 1042 2.96 - 3.45: 2198 3.45 - 3.93: 4190 3.93 - 4.41: 4504 4.41 - 4.90: 8910 Nonbonded interactions: 20844 Sorted by model distance: nonbonded pdb=" N LEU B 34 " pdb=" O LEU B 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU A 34 " pdb=" O LEU A 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU L 34 " pdb=" O LEU L 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU K 34 " pdb=" O LEU K 34 " model vdw 2.477 2.496 nonbonded pdb=" N LEU E 34 " pdb=" O LEU E 34 " model vdw 2.477 2.496 ... (remaining 20839 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 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 : 0.013 0.055 2496 Z= 0.995 Angle : 2.400 11.686 3336 Z= 1.683 Chirality : 0.128 0.258 384 Planarity : 0.012 0.032 420 Dihedral : 17.351 64.826 840 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 23.81 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.27), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.20), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 14 PHE 0.021 0.005 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.6952 time to fit residues: 56.1795 Evaluate side-chains 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 14 HIS C 14 HIS D 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5091 r_free = 0.5091 target = 0.182640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.154841 restraints weight = 3117.419| |-----------------------------------------------------------------------------| r_work (start): 0.4852 rms_B_bonded: 3.90 r_work: 0.4729 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2496 Z= 0.145 Angle : 0.652 3.466 3336 Z= 0.368 Chirality : 0.052 0.121 384 Planarity : 0.003 0.016 420 Dihedral : 4.392 11.601 324 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.35 % Allowed : 31.75 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.28), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 14 PHE 0.009 0.002 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.290 Fit side-chains REVERT: C 22 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 22 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7565 (tm-30) REVERT: E 22 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7406 (tm-30) REVERT: E 35 MET cc_start: 0.7327 (mtp) cc_final: 0.6848 (mtt) REVERT: F 22 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7417 (tm-30) REVERT: F 35 MET cc_start: 0.7337 (mtp) cc_final: 0.6849 (mtt) REVERT: G 22 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7407 (tm-30) REVERT: H 22 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7421 (tm-30) REVERT: I 22 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7652 (tm-30) REVERT: J 22 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7661 (tm-30) outliers start: 16 outliers final: 10 residues processed: 70 average time/residue: 0.7388 time to fit residues: 53.5818 Evaluate side-chains 70 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain J residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.5185 r_free = 0.5185 target = 0.186511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.160213 restraints weight = 3115.462| |-----------------------------------------------------------------------------| r_work (start): 0.4909 rms_B_bonded: 3.65 r_work: 0.4810 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2496 Z= 0.159 Angle : 0.633 4.377 3336 Z= 0.353 Chirality : 0.051 0.125 384 Planarity : 0.003 0.013 420 Dihedral : 4.594 12.064 324 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.37 % Allowed : 25.79 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.35), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 14 PHE 0.009 0.002 PHE F 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.244 Fit side-chains REVERT: C 22 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7645 (tm-30) REVERT: D 22 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7656 (tm-30) REVERT: E 22 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7639 (tm-30) REVERT: F 22 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7630 (tm-30) REVERT: G 22 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7602 (tm-30) REVERT: H 22 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7576 (tm-30) REVERT: I 22 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7221 (tm-30) REVERT: J 22 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7187 (tm-30) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 0.7611 time to fit residues: 55.8794 Evaluate side-chains 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- 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 = 0.5150 r_free = 0.5150 target = 0.181222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.155389 restraints weight = 3246.951| |-----------------------------------------------------------------------------| r_work (start): 0.4862 rms_B_bonded: 3.70 r_work: 0.4759 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2496 Z= 0.240 Angle : 0.702 4.830 3336 Z= 0.386 Chirality : 0.051 0.138 384 Planarity : 0.003 0.012 420 Dihedral : 5.207 12.875 324 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 9.52 % Allowed : 18.25 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.36), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.28), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 14 PHE 0.012 0.003 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.290 Fit side-chains REVERT: C 22 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7587 (tm-30) REVERT: D 22 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7601 (tm-30) REVERT: E 22 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7311 (tm-30) REVERT: F 22 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7325 (tm-30) REVERT: G 22 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7584 (tm-30) REVERT: H 22 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7597 (tm-30) REVERT: I 22 GLU cc_start: 0.7763 (tm-30) cc_final: 0.6799 (tm-30) REVERT: J 22 GLU cc_start: 0.7760 (tm-30) cc_final: 0.6791 (tm-30) REVERT: K 22 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7594 (tm-30) REVERT: L 22 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7598 (tm-30) outliers start: 24 outliers final: 12 residues processed: 82 average time/residue: 0.7135 time to fit residues: 60.6900 Evaluate side-chains 86 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain L residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.5238 r_free = 0.5238 target = 0.188539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.161845 restraints weight = 3147.014| |-----------------------------------------------------------------------------| r_work (start): 0.4976 rms_B_bonded: 3.60 r_work: 0.4873 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2496 Z= 0.126 Angle : 0.605 5.787 3336 Z= 0.327 Chirality : 0.051 0.129 384 Planarity : 0.002 0.014 420 Dihedral : 4.734 10.461 324 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 7.14 % Allowed : 20.63 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.39), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 14 PHE 0.007 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.291 Fit side-chains REVERT: C 22 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7647 (tm-30) REVERT: D 22 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7664 (tm-30) REVERT: E 22 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7702 (tm-30) REVERT: F 22 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7711 (tm-30) REVERT: I 22 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7334 (tm-30) REVERT: J 22 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7349 (tm-30) outliers start: 18 outliers final: 10 residues processed: 80 average time/residue: 0.6476 time to fit residues: 53.8307 Evaluate side-chains 82 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.5142 r_free = 0.5142 target = 0.182233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.156250 restraints weight = 3214.278| |-----------------------------------------------------------------------------| r_work (start): 0.4865 rms_B_bonded: 3.59 r_work: 0.4763 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2496 Z= 0.219 Angle : 0.694 6.092 3336 Z= 0.373 Chirality : 0.052 0.138 384 Planarity : 0.003 0.020 420 Dihedral : 5.115 11.926 324 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.35 % Allowed : 22.22 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.39), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.29), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 14 PHE 0.011 0.002 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.273 Fit side-chains REVERT: C 22 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7652 (tm-30) REVERT: D 22 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7664 (tm-30) REVERT: E 22 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7688 (tm-30) REVERT: F 22 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7696 (tm-30) REVERT: I 22 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7054 (tm-30) REVERT: J 22 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7057 (tm-30) outliers start: 16 outliers final: 14 residues processed: 76 average time/residue: 0.6798 time to fit residues: 53.6227 Evaluate side-chains 78 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 36 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.5220 r_free = 0.5220 target = 0.189061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.162050 restraints weight = 3158.050| |-----------------------------------------------------------------------------| r_work (start): 0.4941 rms_B_bonded: 3.63 r_work: 0.4841 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2496 Z= 0.132 Angle : 0.660 6.876 3336 Z= 0.350 Chirality : 0.052 0.131 384 Planarity : 0.002 0.012 420 Dihedral : 4.775 11.226 324 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.57 % Allowed : 25.79 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 14 PHE 0.008 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.312 Fit side-chains REVERT: C 22 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7631 (tm-30) REVERT: D 22 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7644 (tm-30) REVERT: E 22 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7658 (tm-30) REVERT: F 22 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7667 (tm-30) REVERT: G 22 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7401 (tm-30) REVERT: G 35 MET cc_start: 0.7693 (mtp) cc_final: 0.7397 (mtt) REVERT: H 22 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7411 (tm-30) REVERT: H 35 MET cc_start: 0.7728 (mtp) cc_final: 0.7432 (mtt) REVERT: I 22 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7305 (tm-30) REVERT: J 22 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7310 (tm-30) outliers start: 9 outliers final: 11 residues processed: 71 average time/residue: 0.7248 time to fit residues: 53.2999 Evaluate side-chains 79 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.5165 r_free = 0.5165 target = 0.184058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.157733 restraints weight = 3236.460| |-----------------------------------------------------------------------------| r_work (start): 0.4889 rms_B_bonded: 3.59 r_work: 0.4786 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2496 Z= 0.194 Angle : 0.712 6.832 3336 Z= 0.379 Chirality : 0.052 0.138 384 Planarity : 0.003 0.026 420 Dihedral : 4.981 11.367 324 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.97 % Allowed : 25.40 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.40), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 14 PHE 0.010 0.002 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.305 Fit side-chains REVERT: C 22 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7561 (tm-30) REVERT: D 22 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7543 (tm-30) REVERT: E 22 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7756 (tm-30) REVERT: F 22 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7742 (tm-30) REVERT: G 22 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7467 (tm-30) REVERT: G 35 MET cc_start: 0.7688 (mtp) cc_final: 0.7408 (mtt) REVERT: H 22 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7459 (tm-30) REVERT: H 35 MET cc_start: 0.7706 (mtp) cc_final: 0.7431 (mtt) REVERT: I 22 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7277 (tm-30) REVERT: J 22 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7274 (tm-30) outliers start: 10 outliers final: 9 residues processed: 74 average time/residue: 0.7467 time to fit residues: 57.1679 Evaluate side-chains 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.5220 r_free = 0.5220 target = 0.187755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.160835 restraints weight = 3199.881| |-----------------------------------------------------------------------------| r_work (start): 0.4945 rms_B_bonded: 3.58 r_work: 0.4843 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2496 Z= 0.144 Angle : 0.690 7.628 3336 Z= 0.363 Chirality : 0.052 0.133 384 Planarity : 0.002 0.011 420 Dihedral : 4.841 11.160 324 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.97 % Allowed : 25.40 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 14 PHE 0.008 0.001 PHE D 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.364 Fit side-chains REVERT: C 22 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7543 (tm-30) REVERT: D 22 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7535 (tm-30) REVERT: E 22 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7669 (tm-30) REVERT: F 22 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7655 (tm-30) REVERT: G 22 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7528 (tm-30) REVERT: G 35 MET cc_start: 0.7641 (mtp) cc_final: 0.7314 (mtt) REVERT: H 22 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7520 (tm-30) REVERT: H 35 MET cc_start: 0.7661 (mtp) cc_final: 0.7330 (mtt) REVERT: I 22 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7387 (tm-30) REVERT: J 22 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7376 (tm-30) outliers start: 10 outliers final: 10 residues processed: 71 average time/residue: 0.7248 time to fit residues: 53.3609 Evaluate side-chains 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 21 optimal weight: 0.0000 chunk 22 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.5276 r_free = 0.5276 target = 0.191701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.164441 restraints weight = 3027.601| |-----------------------------------------------------------------------------| r_work (start): 0.5013 rms_B_bonded: 3.50 r_work: 0.4919 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2496 Z= 0.116 Angle : 0.659 7.446 3336 Z= 0.345 Chirality : 0.052 0.130 384 Planarity : 0.003 0.029 420 Dihedral : 4.596 11.054 324 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.57 % Allowed : 26.59 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.42), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 14 PHE 0.007 0.001 PHE D 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.294 Fit side-chains REVERT: C 22 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 22 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7557 (tm-30) REVERT: E 22 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7665 (tm-30) REVERT: F 22 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7660 (tm-30) REVERT: G 35 MET cc_start: 0.7686 (mtp) cc_final: 0.7311 (mtt) REVERT: H 35 MET cc_start: 0.7689 (mtp) cc_final: 0.7306 (mtt) REVERT: I 22 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7250 (tm-30) REVERT: J 22 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7236 (tm-30) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.6889 time to fit residues: 49.9972 Evaluate side-chains 75 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.5198 r_free = 0.5198 target = 0.184941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.158721 restraints weight = 3202.009| |-----------------------------------------------------------------------------| r_work (start): 0.4921 rms_B_bonded: 3.60 r_work: 0.4818 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2496 Z= 0.201 Angle : 0.758 7.948 3336 Z= 0.399 Chirality : 0.052 0.137 384 Planarity : 0.003 0.028 420 Dihedral : 5.007 11.881 324 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.78 % Allowed : 28.17 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 14 PHE 0.010 0.002 PHE C 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2931.85 seconds wall clock time: 50 minutes 29.47 seconds (3029.47 seconds total)