Starting phenix.real_space_refine on Mon Feb 10 20:46:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ot1_17166/02_2025/8ot1_17166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ot1_17166/02_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_17166/02_2025/8ot1_17166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ot1_17166/02_2025/8ot1_17166.map" model { file = "/net/cci-nas-00/data/ceres_data/8ot1_17166/02_2025/8ot1_17166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ot1_17166/02_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-5592/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: 1.54, per 1000 atoms: 0.63 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: 0.55 Conformation dependent library (CDL) restraints added in 333.9 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: 0.20 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: 0.65 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: 1.420 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.570 Find NCS groups from input model: 0.050 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- 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 : 0.271 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.6489 time to fit residues: 52.5475 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 : 0.284 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.154842 restraints weight = 3117.410| |-----------------------------------------------------------------------------| 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 : 0.260 Fit side-chains REVERT: C 22 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7553 (tm-30) REVERT: D 22 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7562 (tm-30) REVERT: E 22 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7404 (tm-30) REVERT: E 35 MET cc_start: 0.7327 (mtp) cc_final: 0.6848 (mtt) REVERT: F 22 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7414 (tm-30) REVERT: F 35 MET cc_start: 0.7337 (mtp) cc_final: 0.6849 (mtt) REVERT: G 22 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7406 (tm-30) REVERT: H 22 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7420 (tm-30) REVERT: I 22 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7652 (tm-30) REVERT: J 22 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7660 (tm-30) outliers start: 16 outliers final: 10 residues processed: 70 average time/residue: 0.7123 time to fit residues: 51.7590 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 : 0.277 ------------------------------------------------------------------------------- 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: 2.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.0070 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.8800 ------------------------------------------------------------------------------- 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 = 0.5179 r_free = 0.5179 target = 0.189740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.161314 restraints weight = 3013.368| |-----------------------------------------------------------------------------| r_work (start): 0.4912 rms_B_bonded: 3.71 r_work: 0.4799 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2496 Z= 0.136 Angle : 0.606 4.198 3336 Z= 0.338 Chirality : 0.051 0.126 384 Planarity : 0.002 0.013 420 Dihedral : 4.401 11.371 324 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 26.98 % 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: -2.30 (0.36), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 14 PHE 0.008 0.002 PHE E 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 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.286 Fit side-chains REVERT: C 22 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7723 (tm-30) REVERT: D 22 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7722 (tm-30) REVERT: E 22 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7649 (tm-30) REVERT: F 22 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7654 (tm-30) REVERT: G 22 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7495 (tm-30) REVERT: H 22 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7493 (tm-30) REVERT: I 22 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7348 (tm-30) REVERT: J 22 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7344 (tm-30) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.7523 time to fit residues: 54.5587 Evaluate side-chains 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.5178 r_free = 0.5178 target = 0.184109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.157456 restraints weight = 3181.958| |-----------------------------------------------------------------------------| r_work (start): 0.4904 rms_B_bonded: 3.70 r_work: 0.4798 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2496 Z= 0.189 Angle : 0.652 4.898 3336 Z= 0.358 Chirality : 0.050 0.134 384 Planarity : 0.003 0.012 420 Dihedral : 4.849 11.870 324 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 7.94 % Allowed : 19.84 % 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: -2.03 (0.38), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.29), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 14 PHE 0.010 0.002 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 92 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.267 Fit side-chains REVERT: C 22 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7646 (tm-30) REVERT: D 22 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7629 (tm-30) REVERT: E 22 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7398 (tm-30) REVERT: F 22 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7373 (tm-30) REVERT: G 22 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7589 (tm-30) REVERT: H 22 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7560 (tm-30) REVERT: I 22 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7067 (tm-30) REVERT: J 22 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7017 (tm-30) REVERT: K 22 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7605 (tm-30) REVERT: L 22 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7599 (tm-30) outliers start: 20 outliers final: 8 residues processed: 82 average time/residue: 0.6559 time to fit residues: 55.9464 Evaluate side-chains 80 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 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 = 0.5219 r_free = 0.5219 target = 0.189498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.161675 restraints weight = 3109.930| |-----------------------------------------------------------------------------| r_work (start): 0.4925 rms_B_bonded: 3.67 r_work: 0.4823 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2496 Z= 0.124 Angle : 0.580 5.380 3336 Z= 0.317 Chirality : 0.051 0.128 384 Planarity : 0.002 0.013 420 Dihedral : 4.599 10.370 324 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.97 % Allowed : 24.60 % 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: -1.86 (0.39), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 14 PHE 0.007 0.001 PHE F 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 80 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.285 Fit side-chains REVERT: C 22 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 22 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7557 (tm-30) REVERT: E 22 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7544 (tm-30) REVERT: F 22 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7524 (tm-30) REVERT: I 22 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7334 (tm-30) REVERT: J 22 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7321 (tm-30) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.7073 time to fit residues: 52.8655 Evaluate side-chains 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.5191 r_free = 0.5191 target = 0.184819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.157925 restraints weight = 3166.434| |-----------------------------------------------------------------------------| r_work (start): 0.4908 rms_B_bonded: 3.69 r_work: 0.4803 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2496 Z= 0.188 Angle : 0.636 5.474 3336 Z= 0.347 Chirality : 0.051 0.135 384 Planarity : 0.003 0.019 420 Dihedral : 4.906 11.396 324 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.56 % Allowed : 24.60 % 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: -1.95 (0.40), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 14 PHE 0.010 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 80 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.297 Fit side-chains REVERT: C 22 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 22 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7607 (tm-30) REVERT: E 22 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7671 (tm-30) REVERT: F 22 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7688 (tm-30) REVERT: G 22 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7488 (tm-30) REVERT: H 22 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7517 (tm-30) REVERT: I 22 GLU cc_start: 0.7849 (tm-30) cc_final: 0.6791 (tm-30) REVERT: J 22 GLU cc_start: 0.7858 (tm-30) cc_final: 0.6806 (tm-30) REVERT: K 22 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7548 (tm-30) REVERT: L 22 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7568 (tm-30) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 0.7331 time to fit residues: 54.6996 Evaluate side-chains 72 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.0030 chunk 7 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.5294 r_free = 0.5294 target = 0.194589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.166248 restraints weight = 3106.267| |-----------------------------------------------------------------------------| r_work (start): 0.4996 rms_B_bonded: 3.65 r_work: 0.4895 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2496 Z= 0.106 Angle : 0.579 6.458 3336 Z= 0.311 Chirality : 0.052 0.129 384 Planarity : 0.002 0.013 420 Dihedral : 4.540 10.675 324 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 25.40 % 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: -1.75 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.31), 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 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 78 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.287 Fit side-chains REVERT: A 35 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6763 (mtt) REVERT: B 35 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6780 (mtt) REVERT: C 22 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7502 (tm-30) REVERT: D 22 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7496 (tm-30) REVERT: E 22 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7523 (tm-30) REVERT: F 22 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7501 (tm-30) REVERT: I 22 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7255 (tm-30) REVERT: J 22 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7227 (tm-30) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.7256 time to fit residues: 52.5557 Evaluate side-chains 78 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain E residue 24 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- 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 = 0.5251 r_free = 0.5251 target = 0.189564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.161971 restraints weight = 3143.263| |-----------------------------------------------------------------------------| r_work (start): 0.4970 rms_B_bonded: 3.68 r_work: 0.4866 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2496 Z= 0.140 Angle : 0.625 6.062 3336 Z= 0.335 Chirality : 0.051 0.132 384 Planarity : 0.002 0.013 420 Dihedral : 4.664 10.971 324 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.17 % Allowed : 27.78 % 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: -1.85 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 14 PHE 0.008 0.001 PHE C 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 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.288 Fit side-chains REVERT: C 22 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7596 (tm-30) REVERT: D 22 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7567 (tm-30) REVERT: E 22 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7636 (tm-30) REVERT: F 22 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7652 (tm-30) REVERT: G 22 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7401 (tm-30) REVERT: G 35 MET cc_start: 0.7653 (mtp) cc_final: 0.7354 (mtt) REVERT: H 22 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7429 (tm-30) REVERT: H 35 MET cc_start: 0.7658 (mtp) cc_final: 0.7358 (mtt) REVERT: I 22 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7316 (tm-30) REVERT: J 22 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7328 (tm-30) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.7541 time to fit residues: 53.0439 Evaluate side-chains 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 VAL 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: 0.0670 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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 = 0.5333 r_free = 0.5333 target = 0.195655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.167818 restraints weight = 3029.484| |-----------------------------------------------------------------------------| r_work (start): 0.5057 rms_B_bonded: 3.58 r_work: 0.4953 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2496 Z= 0.101 Angle : 0.599 6.736 3336 Z= 0.318 Chirality : 0.051 0.128 384 Planarity : 0.003 0.028 420 Dihedral : 4.382 10.448 324 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.38 % Allowed : 27.78 % 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: -1.71 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 14 PHE 0.006 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 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.281 Fit side-chains REVERT: C 22 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7613 (tm-30) REVERT: D 22 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7613 (tm-30) REVERT: E 22 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7553 (tm-30) REVERT: F 22 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7547 (tm-30) REVERT: G 22 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7565 (tm-30) REVERT: G 35 MET cc_start: 0.7596 (mtp) cc_final: 0.7308 (mtt) REVERT: H 22 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7557 (tm-30) REVERT: H 35 MET cc_start: 0.7597 (mtp) cc_final: 0.7312 (mtt) REVERT: I 22 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7272 (tm-30) REVERT: J 22 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7270 (tm-30) outliers start: 6 outliers final: 6 residues processed: 70 average time/residue: 0.7309 time to fit residues: 53.0575 Evaluate side-chains 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 VAL 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: 0.6980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.5221 r_free = 0.5221 target = 0.187464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.160478 restraints weight = 3119.962| |-----------------------------------------------------------------------------| r_work (start): 0.4960 rms_B_bonded: 3.62 r_work: 0.4856 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2496 Z= 0.159 Angle : 0.697 7.999 3336 Z= 0.368 Chirality : 0.052 0.133 384 Planarity : 0.002 0.011 420 Dihedral : 4.708 11.042 324 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.38 % Allowed : 28.57 % 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: -1.85 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 14 PHE 0.010 0.002 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 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.288 Fit side-chains REVERT: C 22 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7611 (tm-30) REVERT: D 22 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7621 (tm-30) REVERT: E 22 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7620 (tm-30) REVERT: F 22 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7609 (tm-30) REVERT: G 35 MET cc_start: 0.7697 (mtp) cc_final: 0.7442 (mtt) REVERT: H 35 MET cc_start: 0.7699 (mtp) cc_final: 0.7439 (mtt) REVERT: I 22 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7233 (tm-30) REVERT: J 22 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7246 (tm-30) outliers start: 6 outliers final: 6 residues processed: 68 average time/residue: 0.7181 time to fit residues: 50.6020 Evaluate side-chains 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 VAL 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: 6.9990 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.5163 r_free = 0.5163 target = 0.182918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.156633 restraints weight = 3231.979| |-----------------------------------------------------------------------------| r_work (start): 0.4879 rms_B_bonded: 3.65 r_work: 0.4775 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2496 Z= 0.237 Angle : 0.794 8.316 3336 Z= 0.420 Chirality : 0.053 0.141 384 Planarity : 0.003 0.012 420 Dihedral : 5.066 12.769 324 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.57 % Allowed : 28.17 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.10 (0.40), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 14 PHE 0.012 0.002 PHE D 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2843.02 seconds wall clock time: 50 minutes 34.58 seconds (3034.58 seconds total)