Starting phenix.real_space_refine on Fri Aug 22 12:54:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ot1_17166/08_2025/8ot1_17166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ot1_17166/08_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_17166/08_2025/8ot1_17166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ot1_17166/08_2025/8ot1_17166.map" model { file = "/net/cci-nas-00/data/ceres_data/8ot1_17166/08_2025/8ot1_17166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ot1_17166/08_2025/8ot1_17166.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 0.55, per 1000 atoms: 0.22 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: 0.20 Conformation dependent library (CDL) restraints added in 104.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.07 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: 0.02 Time building geometry restraints manager: 0.27 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.190 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.220 Find NCS groups from input model: 0.030 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:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.37 (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 PHE 0.021 0.005 PHE D 20 HIS 0.002 0.001 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.01327 ( 2496) covalent geometry : angle 2.39977 ( 3336) *********************** 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 : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2274 time to fit residues: 18.4171 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 : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.5103 r_free = 0.5103 target = 0.184266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.156329 restraints weight = 3104.151| |-----------------------------------------------------------------------------| r_work (start): 0.4866 rms_B_bonded: 3.89 r_work: 0.4745 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2898 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= 0.148 Angle : 0.647 3.397 3336 Z= 0.362 Chirality : 0.052 0.121 384 Planarity : 0.003 0.016 420 Dihedral : 4.402 11.359 324 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.76 % Allowed : 31.75 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.28), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE H 20 HIS 0.006 0.001 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 2496) covalent geometry : angle 0.64684 ( 3336) *********************** 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 86 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.060 Fit side-chains REVERT: C 22 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7488 (tm-30) REVERT: D 22 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7485 (tm-30) REVERT: E 22 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7486 (tm-30) REVERT: E 35 MET cc_start: 0.7346 (mtp) cc_final: 0.6884 (mtt) REVERT: F 22 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7476 (tm-30) REVERT: F 35 MET cc_start: 0.7357 (mtp) cc_final: 0.6881 (mtt) REVERT: G 22 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7320 (tm-30) REVERT: H 22 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7319 (tm-30) REVERT: I 22 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7660 (tm-30) REVERT: J 22 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7650 (tm-30) outliers start: 12 outliers final: 10 residues processed: 74 average time/residue: 0.3223 time to fit residues: 24.7026 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 : 0.101 ------------------------------------------------------------------------------- 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 19 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 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 = 0.5173 r_free = 0.5173 target = 0.185501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.158463 restraints weight = 3177.415| |-----------------------------------------------------------------------------| r_work (start): 0.4890 rms_B_bonded: 3.69 r_work: 0.4795 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2496 Z= 0.190 Angle : 0.644 3.834 3336 Z= 0.364 Chirality : 0.050 0.128 384 Planarity : 0.003 0.013 420 Dihedral : 4.642 12.510 324 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 7.94 % Allowed : 20.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.35), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE C 20 HIS 0.004 0.001 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 2496) covalent geometry : angle 0.64443 ( 3336) *********************** 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 92 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.076 Fit side-chains REVERT: C 22 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 22 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7786 (tm-30) REVERT: E 22 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7776 (tm-30) REVERT: F 22 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7778 (tm-30) REVERT: G 22 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7451 (tm-30) REVERT: H 22 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7439 (tm-30) REVERT: I 22 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7381 (tm-30) REVERT: J 22 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7381 (tm-30) outliers start: 20 outliers final: 10 residues processed: 82 average time/residue: 0.2872 time to fit residues: 24.5101 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 : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B 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 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 9 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.5214 r_free = 0.5214 target = 0.188918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.162118 restraints weight = 3106.006| |-----------------------------------------------------------------------------| r_work (start): 0.4932 rms_B_bonded: 3.70 r_work: 0.4835 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4354 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= 0.127 Angle : 0.611 5.002 3336 Z= 0.332 Chirality : 0.051 0.124 384 Planarity : 0.002 0.013 420 Dihedral : 4.560 10.501 324 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.76 % Allowed : 23.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.38), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.29), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE C 20 HIS 0.002 0.001 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2496) covalent geometry : angle 0.61094 ( 3336) *********************** 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 84 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.099 Fit side-chains REVERT: C 22 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7664 (tm-30) REVERT: D 22 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7679 (tm-30) REVERT: E 22 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7507 (tm-30) REVERT: F 22 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7492 (tm-30) REVERT: I 22 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7032 (tm-30) REVERT: J 22 GLU cc_start: 0.7748 (tm-30) cc_final: 0.6970 (tm-30) REVERT: K 22 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7616 (tm-30) REVERT: L 22 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7600 (tm-30) outliers start: 12 outliers final: 4 residues processed: 74 average time/residue: 0.3277 time to fit residues: 25.1277 Evaluate side-chains 74 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.184558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.157831 restraints weight = 3174.720| |-----------------------------------------------------------------------------| r_work (start): 0.4892 rms_B_bonded: 3.68 r_work: 0.4784 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2496 Z= 0.183 Angle : 0.635 5.362 3336 Z= 0.345 Chirality : 0.050 0.136 384 Planarity : 0.003 0.012 420 Dihedral : 4.919 11.891 324 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.35 % Allowed : 21.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.38), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.29), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE D 20 HIS 0.003 0.001 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 2496) covalent geometry : angle 0.63498 ( 3336) *********************** 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 86 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.125 Fit side-chains REVERT: C 22 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7582 (tm-30) REVERT: D 22 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7559 (tm-30) REVERT: E 22 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7675 (tm-30) REVERT: F 22 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7667 (tm-30) REVERT: G 22 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7372 (tm-30) REVERT: H 22 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7378 (tm-30) REVERT: I 22 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7028 (tm-30) REVERT: J 22 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7013 (tm-30) REVERT: K 22 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7580 (tm-30) REVERT: L 22 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7581 (tm-30) outliers start: 16 outliers final: 8 residues processed: 78 average time/residue: 0.3372 time to fit residues: 27.3124 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 : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D 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 I residue 39 VAL Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.5212 r_free = 0.5212 target = 0.187658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.160602 restraints weight = 3103.242| |-----------------------------------------------------------------------------| r_work (start): 0.4926 rms_B_bonded: 3.61 r_work: 0.4831 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4799 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= 0.137 Angle : 0.601 5.978 3336 Z= 0.325 Chirality : 0.052 0.131 384 Planarity : 0.002 0.014 420 Dihedral : 4.748 10.749 324 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.76 % Allowed : 23.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.39), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE C 20 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2496) covalent geometry : angle 0.60072 ( 3336) *********************** 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 82 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.071 Fit side-chains REVERT: C 22 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 22 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7588 (tm-30) REVERT: E 22 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 35 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7014 (mtt) REVERT: F 22 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7542 (tm-30) REVERT: F 35 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7025 (mtt) REVERT: G 22 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7525 (tm-30) REVERT: H 22 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7546 (tm-30) REVERT: I 22 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7342 (tm-30) REVERT: J 22 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7353 (tm-30) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.3396 time to fit residues: 25.3237 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 : 0.094 ------------------------------------------------------------------------------- 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 35 MET Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 35 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 2 optimal weight: 0.0270 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.4840 ------------------------------------------------------------------------------- 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 = 0.195147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5023 r_free = 0.5023 target = 0.166951 restraints weight = 3038.083| |-----------------------------------------------------------------------------| r_work (start): 0.5011 rms_B_bonded: 3.58 r_work: 0.4914 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2496 Z= 0.103 Angle : 0.589 6.179 3336 Z= 0.313 Chirality : 0.051 0.125 384 Planarity : 0.003 0.021 420 Dihedral : 4.474 10.500 324 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.17 % Allowed : 26.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE C 20 HIS 0.001 0.000 HIS J 14 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 2496) covalent geometry : angle 0.58874 ( 3336) *********************** 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 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.137 Fit side-chains REVERT: A 35 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6891 (mtt) REVERT: C 22 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 22 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7530 (tm-30) REVERT: E 22 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7533 (tm-30) REVERT: F 22 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7549 (tm-30) REVERT: G 22 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7458 (tm-30) REVERT: H 22 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7454 (tm-30) REVERT: I 22 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7221 (tm-30) REVERT: J 22 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7229 (tm-30) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.3553 time to fit residues: 24.9941 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 : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 0.0370 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.5286 r_free = 0.5286 target = 0.193957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.165562 restraints weight = 3063.007| |-----------------------------------------------------------------------------| r_work (start): 0.4993 rms_B_bonded: 3.59 r_work: 0.4899 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2496 Z= 0.110 Angle : 0.607 6.670 3336 Z= 0.325 Chirality : 0.051 0.129 384 Planarity : 0.002 0.013 420 Dihedral : 4.469 10.527 324 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.37 % Allowed : 25.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.40), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE D 20 HIS 0.002 0.000 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 2496) covalent geometry : angle 0.60743 ( 3336) *********************** 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 81 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.098 Fit side-chains REVERT: C 22 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7599 (tm-30) REVERT: D 22 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7636 (tm-30) REVERT: E 22 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7550 (tm-30) REVERT: F 22 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7588 (tm-30) REVERT: G 22 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7507 (tm-30) REVERT: H 22 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7537 (tm-30) REVERT: I 22 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7284 (tm-30) REVERT: J 22 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7313 (tm-30) outliers start: 11 outliers final: 8 residues processed: 72 average time/residue: 0.3564 time to fit residues: 26.5707 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 : 0.100 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.5261 r_free = 0.5261 target = 0.192602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.164309 restraints weight = 3085.062| |-----------------------------------------------------------------------------| r_work (start): 0.4973 rms_B_bonded: 3.64 r_work: 0.4878 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2496 Z= 0.121 Angle : 0.627 7.030 3336 Z= 0.333 Chirality : 0.051 0.128 384 Planarity : 0.003 0.028 420 Dihedral : 4.534 10.730 324 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.17 % Allowed : 26.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE C 20 HIS 0.002 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2496) covalent geometry : angle 0.62709 ( 3336) *********************** 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: 8 poor density : 68 time to evaluate : 0.099 Fit side-chains REVERT: C 22 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 22 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7597 (tm-30) REVERT: E 22 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7594 (tm-30) REVERT: F 22 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7593 (tm-30) REVERT: G 22 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7462 (tm-30) REVERT: H 22 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7461 (tm-30) REVERT: I 22 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7269 (tm-30) REVERT: J 22 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7273 (tm-30) outliers start: 8 outliers final: 8 residues processed: 68 average time/residue: 0.3489 time to fit residues: 24.5431 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 : 0.108 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.5210 r_free = 0.5210 target = 0.186906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.159802 restraints weight = 3189.652| |-----------------------------------------------------------------------------| r_work (start): 0.4935 rms_B_bonded: 3.68 r_work: 0.4833 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2496 Z= 0.179 Angle : 0.700 7.991 3336 Z= 0.372 Chirality : 0.052 0.137 384 Planarity : 0.002 0.011 420 Dihedral : 4.878 11.048 324 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.17 % Allowed : 26.59 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE C 20 HIS 0.003 0.001 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 2496) covalent geometry : angle 0.70029 ( 3336) ********************** 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 76 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.103 Fit side-chains REVERT: C 22 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7616 (tm-30) REVERT: D 22 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7618 (tm-30) REVERT: E 22 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7579 (tm-30) REVERT: F 22 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7574 (tm-30) REVERT: G 22 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7559 (tm-30) REVERT: H 22 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7563 (tm-30) REVERT: I 22 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7222 (tm-30) REVERT: J 22 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7238 (tm-30) outliers start: 8 outliers final: 6 residues processed: 68 average time/residue: 0.3476 time to fit residues: 24.4091 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 : 0.098 ------------------------------------------------------------------------------- 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 19 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.5254 r_free = 0.5254 target = 0.190806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.162964 restraints weight = 3145.069| |-----------------------------------------------------------------------------| r_work (start): 0.4966 rms_B_bonded: 3.66 r_work: 0.4876 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.5198 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= 0.136 Angle : 0.667 7.926 3336 Z= 0.352 Chirality : 0.052 0.132 384 Planarity : 0.002 0.012 420 Dihedral : 4.742 10.962 324 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.41), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE C 20 HIS 0.002 0.001 HIS J 14 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 2496) covalent geometry : angle 0.66675 ( 3336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1447.53 seconds wall clock time: 25 minutes 24.84 seconds (1524.84 seconds total)