Starting phenix.real_space_refine on Fri Aug 22 13:08:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ovk_17218/08_2025/8ovk_17218.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ovk_17218/08_2025/8ovk_17218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ovk_17218/08_2025/8ovk_17218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ovk_17218/08_2025/8ovk_17218.map" model { file = "/net/cci-nas-00/data/ceres_data/8ovk_17218/08_2025/8ovk_17218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ovk_17218/08_2025/8ovk_17218.cif" } resolution = 2.88 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1940 2.51 5 N 530 2.21 5 O 580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3060 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.58, per 1000 atoms: 0.19 Number of scatterers: 3060 At special positions: 0 Unit cell: (100.8, 124.95, 39.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 580 8.00 N 530 7.00 C 1940 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: 0.25 Conformation dependent library (CDL) restraints added in 115.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 47.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 24 removed outlier: 6.224A pdb=" N LYS A 16 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE C 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA C 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE A 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP C 23 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU A 22 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS C 16 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA E 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE C 20 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP E 23 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU C 22 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS E 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA G 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE E 20 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP G 23 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU E 22 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS G 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE I 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA I 21 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE G 20 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP I 23 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLU G 22 " --> pdb=" O ASP I 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 39 removed outlier: 6.785A pdb=" N ILE C 32 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 39 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE E 32 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 33 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 39 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE G 32 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY E 33 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL E 39 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE I 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY G 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL G 39 " --> pdb=" O GLY I 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 24 removed outlier: 6.225A pdb=" N LYS B 16 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE D 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA D 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE B 20 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP D 23 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU B 22 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS D 16 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA F 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE D 20 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP F 23 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU D 22 " --> pdb=" O ASP F 23 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS F 16 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE H 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA H 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE F 20 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP H 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU F 22 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS H 16 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE J 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA J 21 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE H 20 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP J 23 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU H 22 " --> pdb=" O ASP J 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 39 removed outlier: 6.785A pdb=" N ILE D 32 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY B 33 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 39 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE F 32 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY D 33 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL D 39 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE H 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY F 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL F 39 " --> pdb=" O GLY H 38 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE J 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY H 33 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL H 39 " --> pdb=" O GLY J 38 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.33 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: 1003 1.33 - 1.45: 538 1.45 - 1.57: 1559 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3120 Sorted by residual: bond pdb=" CA GLN D 15 " pdb=" C GLN D 15 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.28e-02 6.10e+03 8.65e+00 bond pdb=" CA GLN B 15 " pdb=" C GLN B 15 " ideal model delta sigma weight residual 1.523 1.485 0.037 1.28e-02 6.10e+03 8.51e+00 bond pdb=" CA GLN I 15 " pdb=" C GLN I 15 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.28e-02 6.10e+03 8.45e+00 bond pdb=" CA GLN G 15 " pdb=" C GLN G 15 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.28e-02 6.10e+03 8.44e+00 bond pdb=" CA GLN E 15 " pdb=" C GLN E 15 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.28e-02 6.10e+03 8.43e+00 ... (remaining 3115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 2778 1.45 - 2.90: 992 2.90 - 4.36: 280 4.36 - 5.81: 90 5.81 - 7.26: 50 Bond angle restraints: 4190 Sorted by residual: angle pdb=" O GLY H 29 " pdb=" C GLY H 29 " pdb=" N ALA H 30 " ideal model delta sigma weight residual 123.59 119.55 4.04 8.70e-01 1.32e+00 2.16e+01 angle pdb=" O GLY E 29 " pdb=" C GLY E 29 " pdb=" N ALA E 30 " ideal model delta sigma weight residual 123.59 119.58 4.01 8.70e-01 1.32e+00 2.12e+01 angle pdb=" O GLY C 29 " pdb=" C GLY C 29 " pdb=" N ALA C 30 " ideal model delta sigma weight residual 123.59 119.58 4.01 8.70e-01 1.32e+00 2.12e+01 angle pdb=" N PHE D 4 " pdb=" CA PHE D 4 " pdb=" C PHE D 4 " ideal model delta sigma weight residual 111.52 117.84 -6.32 1.40e+00 5.10e-01 2.04e+01 angle pdb=" N PHE J 4 " pdb=" CA PHE J 4 " pdb=" C PHE J 4 " ideal model delta sigma weight residual 111.52 117.84 -6.32 1.40e+00 5.10e-01 2.04e+01 ... (remaining 4185 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 10.60: 1390 10.60 - 21.18: 193 21.18 - 31.75: 97 31.75 - 42.33: 50 42.33 - 52.90: 20 Dihedral angle restraints: 1750 sinusoidal: 670 harmonic: 1080 Sorted by residual: dihedral pdb=" CA LEU J 34 " pdb=" C LEU J 34 " pdb=" N MET J 35 " pdb=" CA MET J 35 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU A 34 " pdb=" C LEU A 34 " pdb=" N MET A 35 " pdb=" CA MET A 35 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU G 34 " pdb=" C LEU G 34 " pdb=" N MET G 35 " pdb=" CA MET G 35 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 1747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 90 0.046 - 0.092: 141 0.092 - 0.137: 129 0.137 - 0.183: 50 0.183 - 0.229: 30 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA GLU C 11 " pdb=" N GLU C 11 " pdb=" C GLU C 11 " pdb=" CB GLU C 11 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU B 11 " pdb=" N GLU B 11 " pdb=" C GLU B 11 " pdb=" CB GLU B 11 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU G 11 " pdb=" N GLU G 11 " pdb=" C GLU G 11 " pdb=" CB GLU G 11 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 437 not shown) Planarity restraints: 560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 10 " 0.062 2.00e-02 2.50e+03 3.56e-02 2.54e+01 pdb=" CG TYR H 10 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR H 10 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR H 10 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR H 10 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR H 10 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR H 10 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 10 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 10 " 0.062 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR D 10 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR D 10 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR D 10 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR D 10 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR D 10 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR D 10 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 10 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 10 " -0.061 2.00e-02 2.50e+03 3.55e-02 2.52e+01 pdb=" CG TYR A 10 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 10 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 10 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 10 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 10 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 10 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 10 " -0.058 2.00e-02 2.50e+03 ... (remaining 557 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1120 2.89 - 3.39: 2591 3.39 - 3.89: 5434 3.89 - 4.40: 6090 4.40 - 4.90: 11642 Nonbonded interactions: 26877 Sorted by model distance: nonbonded pdb=" NH2 ARG H 5 " pdb=" OD2 ASP J 7 " model vdw 2.386 3.120 nonbonded pdb=" NH2 ARG A 5 " pdb=" OD2 ASP C 7 " model vdw 2.387 3.120 nonbonded pdb=" NH2 ARG G 5 " pdb=" OD2 ASP I 7 " model vdw 2.387 3.120 nonbonded pdb=" NH2 ARG D 5 " pdb=" OD2 ASP F 7 " model vdw 2.387 3.120 nonbonded pdb=" NH2 ARG B 5 " pdb=" OD2 ASP D 7 " model vdw 2.387 3.120 ... (remaining 26872 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' } 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.740 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.012 0.038 3120 Z= 0.691 Angle : 1.803 7.261 4190 Z= 1.167 Chirality : 0.109 0.229 440 Planarity : 0.011 0.036 560 Dihedral : 14.992 52.904 1070 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 12.90 % Allowed : 9.68 % Favored : 77.42 % 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 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 5 TYR 0.062 0.030 TYR H 10 PHE 0.027 0.009 PHE B 19 HIS 0.003 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.01194 ( 3120) covalent geometry : angle 1.80262 ( 4190) hydrogen bonds : bond 0.14714 ( 64) hydrogen bonds : angle 8.72647 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: A 5 ARG cc_start: 0.8391 (mtp180) cc_final: 0.6681 (pmt170) REVERT: B 3 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7068 (pm20) REVERT: B 5 ARG cc_start: 0.8356 (mtp180) cc_final: 0.6701 (pmt170) REVERT: C 3 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7026 (mm-30) REVERT: D 3 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6746 (mm-30) REVERT: D 28 LYS cc_start: 0.8549 (mttt) cc_final: 0.8026 (mttm) REVERT: E 3 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: E 15 GLN cc_start: 0.8909 (tt0) cc_final: 0.8641 (tt0) REVERT: F 3 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: G 3 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6991 (mm-30) REVERT: H 3 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6670 (mm-30) REVERT: H 15 GLN cc_start: 0.8933 (tt0) cc_final: 0.8684 (tt0) REVERT: I 3 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: I 5 ARG cc_start: 0.8259 (mtp180) cc_final: 0.6763 (tpm170) REVERT: I 34 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8935 (mt) REVERT: J 3 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: J 5 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7012 (tpm170) outliers start: 40 outliers final: 5 residues processed: 166 average time/residue: 0.5875 time to fit residues: 99.7342 Evaluate side-chains 135 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN F 15 GLN F 27 ASN G 27 ASN H 27 ASN I 27 ASN J 27 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.127463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.098965 restraints weight = 3836.676| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.37 r_work: 0.3606 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3120 Z= 0.132 Angle : 0.514 7.976 4190 Z= 0.277 Chirality : 0.052 0.122 440 Planarity : 0.002 0.010 560 Dihedral : 10.668 59.304 462 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.10 % Allowed : 25.48 % Favored : 67.42 % 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: -2.53 (0.29), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 5 TYR 0.008 0.001 TYR G 10 PHE 0.009 0.001 PHE E 20 HIS 0.001 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3120) covalent geometry : angle 0.51385 ( 4190) hydrogen bonds : bond 0.02480 ( 64) hydrogen bonds : angle 5.78142 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.087 Fit side-chains REVERT: A 3 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6744 (pm20) REVERT: A 5 ARG cc_start: 0.8482 (mtp180) cc_final: 0.6341 (pmt170) REVERT: A 40 VAL cc_start: 0.8758 (m) cc_final: 0.8398 (p) REVERT: B 3 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: B 5 ARG cc_start: 0.8508 (mtp180) cc_final: 0.6195 (pmt170) REVERT: B 28 LYS cc_start: 0.8958 (mttm) cc_final: 0.8397 (mttt) REVERT: C 3 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7355 (mm-30) REVERT: C 5 ARG cc_start: 0.8356 (ttp80) cc_final: 0.7839 (ttt-90) REVERT: D 3 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: D 28 LYS cc_start: 0.8991 (mttt) cc_final: 0.8728 (mttm) REVERT: E 3 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7229 (mm-30) REVERT: E 7 ASP cc_start: 0.8531 (p0) cc_final: 0.8189 (p0) REVERT: E 28 LYS cc_start: 0.8915 (mttt) cc_final: 0.8590 (mttm) REVERT: F 3 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7321 (mm-30) REVERT: F 5 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7805 (tpt-90) REVERT: F 28 LYS cc_start: 0.8834 (mttt) cc_final: 0.8543 (mtpt) REVERT: G 3 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: G 5 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7675 (ttt-90) REVERT: G 7 ASP cc_start: 0.8580 (p0) cc_final: 0.8324 (p0) REVERT: G 28 LYS cc_start: 0.8957 (mttt) cc_final: 0.8705 (mttt) REVERT: H 3 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: H 5 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7757 (ttt-90) REVERT: H 7 ASP cc_start: 0.8586 (p0) cc_final: 0.8229 (p0) REVERT: H 28 LYS cc_start: 0.8994 (mttt) cc_final: 0.8597 (mttm) REVERT: I 3 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: I 5 ARG cc_start: 0.7913 (mtp180) cc_final: 0.6595 (tpm170) REVERT: I 28 LYS cc_start: 0.8918 (mttm) cc_final: 0.8560 (mttm) REVERT: J 3 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: J 5 ARG cc_start: 0.7975 (mtp180) cc_final: 0.6565 (tpm170) outliers start: 22 outliers final: 4 residues processed: 121 average time/residue: 0.5982 time to fit residues: 73.8714 Evaluate side-chains 116 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 0.0770 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS C 6 HIS C 14 HIS D 6 HIS D 14 HIS D 15 GLN E 14 HIS F 6 HIS F 14 HIS G 6 HIS G 14 HIS H 6 HIS H 14 HIS J 6 HIS J 14 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.113202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.085013 restraints weight = 3888.285| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.28 r_work: 0.3318 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 3120 Z= 0.356 Angle : 0.595 7.689 4190 Z= 0.323 Chirality : 0.054 0.133 440 Planarity : 0.002 0.013 560 Dihedral : 10.484 59.886 450 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 8.71 % Allowed : 21.94 % Favored : 69.35 % 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: -2.53 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 5 TYR 0.008 0.001 TYR D 10 PHE 0.015 0.002 PHE D 20 HIS 0.005 0.002 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00820 ( 3120) covalent geometry : angle 0.59521 ( 4190) hydrogen bonds : bond 0.03385 ( 64) hydrogen bonds : angle 5.51130 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.130 Fit side-chains REVERT: A 3 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6627 (pm20) REVERT: A 5 ARG cc_start: 0.8408 (mtp180) cc_final: 0.6300 (pmt170) REVERT: B 3 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6735 (pm20) REVERT: B 5 ARG cc_start: 0.8568 (mtp180) cc_final: 0.6228 (pmt170) REVERT: B 28 LYS cc_start: 0.9070 (mttm) cc_final: 0.8586 (mttt) REVERT: C 3 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: C 5 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7863 (ttt-90) REVERT: D 3 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7056 (mm-30) REVERT: D 5 ARG cc_start: 0.8164 (ttt-90) cc_final: 0.7823 (tpt-90) REVERT: D 7 ASP cc_start: 0.8596 (p0) cc_final: 0.8381 (p0) REVERT: D 28 LYS cc_start: 0.9236 (mttt) cc_final: 0.8943 (mttm) REVERT: E 3 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: E 5 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7775 (tpt-90) REVERT: E 28 LYS cc_start: 0.9055 (mttt) cc_final: 0.8762 (mttp) REVERT: F 3 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: F 5 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7867 (tpt-90) REVERT: F 28 LYS cc_start: 0.9110 (mttt) cc_final: 0.8900 (mttm) REVERT: G 3 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: G 5 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7614 (ttt-90) REVERT: G 7 ASP cc_start: 0.8521 (p0) cc_final: 0.8178 (p0) REVERT: G 28 LYS cc_start: 0.9270 (mttt) cc_final: 0.8998 (mttt) REVERT: G 40 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8600 (t) REVERT: H 3 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: H 5 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7793 (ttt-90) REVERT: H 7 ASP cc_start: 0.8468 (p0) cc_final: 0.8214 (p0) REVERT: H 28 LYS cc_start: 0.9244 (mttt) cc_final: 0.8889 (mttm) REVERT: I 3 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: I 5 ARG cc_start: 0.8004 (mtp180) cc_final: 0.6600 (tpm170) REVERT: I 15 GLN cc_start: 0.9152 (tt0) cc_final: 0.8893 (tt0) REVERT: I 28 LYS cc_start: 0.9157 (mttm) cc_final: 0.8831 (mttm) REVERT: J 3 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: J 5 ARG cc_start: 0.8005 (mtp180) cc_final: 0.6610 (tpm170) outliers start: 27 outliers final: 6 residues processed: 125 average time/residue: 0.6282 time to fit residues: 80.0394 Evaluate side-chains 122 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.116190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.088988 restraints weight = 3830.240| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.19 r_work: 0.3410 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3120 Z= 0.176 Angle : 0.488 7.326 4190 Z= 0.263 Chirality : 0.052 0.149 440 Planarity : 0.002 0.009 560 Dihedral : 10.239 59.874 450 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.39 % Allowed : 22.58 % Favored : 69.03 % 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: -2.66 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 5 TYR 0.005 0.001 TYR G 10 PHE 0.009 0.001 PHE D 20 HIS 0.002 0.001 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3120) covalent geometry : angle 0.48850 ( 4190) hydrogen bonds : bond 0.02243 ( 64) hydrogen bonds : angle 5.27366 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.126 Fit side-chains REVERT: A 3 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6595 (pm20) REVERT: A 5 ARG cc_start: 0.8430 (mtp180) cc_final: 0.6219 (pmt170) REVERT: B 3 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: C 3 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: C 5 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7991 (ttt-90) REVERT: C 28 LYS cc_start: 0.9180 (mttt) cc_final: 0.8785 (mttp) REVERT: D 3 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: D 5 ARG cc_start: 0.8226 (ttt-90) cc_final: 0.7697 (ttt180) REVERT: D 28 LYS cc_start: 0.9209 (mttt) cc_final: 0.8879 (mttp) REVERT: E 3 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: E 5 ARG cc_start: 0.8434 (ttp80) cc_final: 0.7877 (tpt-90) REVERT: E 28 LYS cc_start: 0.8992 (mttt) cc_final: 0.8657 (mttp) REVERT: F 3 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: F 28 LYS cc_start: 0.9071 (mttt) cc_final: 0.8815 (mttm) REVERT: F 40 VAL cc_start: 0.8714 (m) cc_final: 0.8436 (p) REVERT: G 3 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7065 (mm-30) REVERT: G 5 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7763 (ttt-90) REVERT: G 7 ASP cc_start: 0.8519 (p0) cc_final: 0.8164 (p0) REVERT: G 28 LYS cc_start: 0.9207 (mttt) cc_final: 0.8784 (mttp) REVERT: G 40 VAL cc_start: 0.8805 (m) cc_final: 0.8511 (t) REVERT: H 3 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: H 5 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7996 (ttt-90) REVERT: H 28 LYS cc_start: 0.9205 (mttt) cc_final: 0.8833 (mttm) REVERT: I 3 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: I 5 ARG cc_start: 0.7847 (mtp180) cc_final: 0.6564 (tpm170) REVERT: I 28 LYS cc_start: 0.9126 (mttm) cc_final: 0.8795 (mttm) REVERT: J 3 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7781 (mm-30) REVERT: J 5 ARG cc_start: 0.7998 (mtp180) cc_final: 0.6615 (tpm170) outliers start: 26 outliers final: 6 residues processed: 115 average time/residue: 0.6080 time to fit residues: 71.3104 Evaluate side-chains 113 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.116029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.089165 restraints weight = 3865.923| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.22 r_work: 0.3413 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3120 Z= 0.158 Angle : 0.459 4.853 4190 Z= 0.253 Chirality : 0.052 0.155 440 Planarity : 0.001 0.010 560 Dihedral : 9.995 59.399 450 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.06 % Allowed : 25.16 % Favored : 66.77 % 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: -2.70 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 5 TYR 0.014 0.001 TYR J 10 PHE 0.008 0.001 PHE D 20 HIS 0.002 0.001 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3120) covalent geometry : angle 0.45903 ( 4190) hydrogen bonds : bond 0.01977 ( 64) hydrogen bonds : angle 5.28606 ( 192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.151 Fit side-chains REVERT: A 3 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6658 (pm20) REVERT: A 5 ARG cc_start: 0.8422 (mtp180) cc_final: 0.6143 (pmt170) REVERT: B 3 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: C 3 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7542 (mm-30) REVERT: C 28 LYS cc_start: 0.9197 (mttt) cc_final: 0.8810 (mttp) REVERT: D 3 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7468 (mm-30) REVERT: D 5 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7734 (ttt180) REVERT: D 28 LYS cc_start: 0.9212 (mttt) cc_final: 0.8921 (mttm) REVERT: E 3 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: E 5 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8062 (tpt-90) REVERT: E 28 LYS cc_start: 0.8997 (mttt) cc_final: 0.8661 (mttp) REVERT: F 3 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: F 28 LYS cc_start: 0.9010 (mttt) cc_final: 0.8607 (mtpt) REVERT: F 40 VAL cc_start: 0.8595 (m) cc_final: 0.8294 (p) REVERT: G 3 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: G 5 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7831 (ttt-90) REVERT: G 7 ASP cc_start: 0.8542 (p0) cc_final: 0.8129 (p0) REVERT: G 28 LYS cc_start: 0.9174 (mttt) cc_final: 0.8751 (mttp) REVERT: G 40 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8498 (t) REVERT: H 3 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: H 5 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8182 (ttt-90) REVERT: H 28 LYS cc_start: 0.9193 (mttt) cc_final: 0.8816 (mttp) REVERT: I 3 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: I 5 ARG cc_start: 0.7780 (mtp180) cc_final: 0.6640 (tpm170) REVERT: I 15 GLN cc_start: 0.9119 (tt0) cc_final: 0.8808 (tt0) REVERT: I 28 LYS cc_start: 0.9127 (mttm) cc_final: 0.8764 (mttm) REVERT: J 3 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7816 (mm-30) REVERT: J 5 ARG cc_start: 0.7954 (mtp180) cc_final: 0.6586 (tpm170) outliers start: 25 outliers final: 6 residues processed: 106 average time/residue: 0.5816 time to fit residues: 62.9988 Evaluate side-chains 109 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain I residue 3 GLU Chi-restraints excluded: chain J residue 3 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.0470 chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 0.1980 chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8480 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.117897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.091593 restraints weight = 3881.896| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.22 r_work: 0.3473 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3120 Z= 0.104 Angle : 0.439 5.386 4190 Z= 0.238 Chirality : 0.051 0.123 440 Planarity : 0.001 0.012 560 Dihedral : 9.668 59.963 450 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 7.10 % Allowed : 27.42 % Favored : 65.48 % 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: -2.83 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 5 TYR 0.016 0.001 TYR J 10 PHE 0.006 0.001 PHE D 20 HIS 0.001 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3120) covalent geometry : angle 0.43920 ( 4190) hydrogen bonds : bond 0.01679 ( 64) hydrogen bonds : angle 5.15471 ( 192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.145 Fit side-chains REVERT: A 3 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.6624 (pm20) REVERT: A 5 ARG cc_start: 0.8466 (mtp180) cc_final: 0.6090 (pmt170) REVERT: B 3 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6536 (pm20) REVERT: C 3 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: C 5 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7799 (ttt-90) REVERT: C 28 LYS cc_start: 0.9179 (mttt) cc_final: 0.8804 (mttp) REVERT: D 3 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7373 (mm-30) REVERT: D 5 ARG cc_start: 0.8239 (ttt-90) cc_final: 0.7902 (ttt180) REVERT: D 28 LYS cc_start: 0.9147 (mttt) cc_final: 0.8838 (mttp) REVERT: E 3 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: E 5 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8140 (tpt-90) REVERT: E 7 ASP cc_start: 0.8486 (p0) cc_final: 0.8264 (p0) REVERT: E 28 LYS cc_start: 0.8920 (mttt) cc_final: 0.8567 (mttp) REVERT: F 3 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: F 28 LYS cc_start: 0.8911 (mttt) cc_final: 0.8513 (mttt) REVERT: F 40 VAL cc_start: 0.8575 (m) cc_final: 0.8319 (p) REVERT: G 3 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: G 5 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7881 (ttt-90) REVERT: G 7 ASP cc_start: 0.8492 (p0) cc_final: 0.8126 (p0) REVERT: G 28 LYS cc_start: 0.9148 (mttt) cc_final: 0.8702 (mttp) REVERT: G 40 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8420 (t) REVERT: H 3 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7191 (mm-30) REVERT: H 5 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8105 (ttt-90) REVERT: H 28 LYS cc_start: 0.9200 (mttt) cc_final: 0.8801 (mttp) REVERT: I 3 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: I 5 ARG cc_start: 0.7741 (mtp180) cc_final: 0.6632 (tpm170) REVERT: I 15 GLN cc_start: 0.9046 (tt0) cc_final: 0.8785 (tt0) REVERT: I 28 LYS cc_start: 0.9141 (mttm) cc_final: 0.8793 (mttm) REVERT: J 5 ARG cc_start: 0.7918 (mtp180) cc_final: 0.6582 (tpm170) outliers start: 22 outliers final: 5 residues processed: 106 average time/residue: 0.6085 time to fit residues: 65.8513 Evaluate side-chains 106 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain I residue 3 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN D 15 GLN F 15 GLN I 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.114544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.087746 restraints weight = 3937.133| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.23 r_work: 0.3400 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3120 Z= 0.174 Angle : 0.482 6.374 4190 Z= 0.257 Chirality : 0.052 0.125 440 Planarity : 0.002 0.013 560 Dihedral : 9.310 58.289 447 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 6.77 % Allowed : 29.03 % Favored : 64.19 % 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: -2.85 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 5 TYR 0.014 0.001 TYR J 10 PHE 0.008 0.001 PHE D 20 HIS 0.002 0.001 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3120) covalent geometry : angle 0.48177 ( 4190) hydrogen bonds : bond 0.01913 ( 64) hydrogen bonds : angle 5.33515 ( 192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.122 Fit side-chains REVERT: A 3 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.6433 (pm20) REVERT: A 5 ARG cc_start: 0.8440 (mtp180) cc_final: 0.6112 (pmt170) REVERT: B 3 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.6576 (pm20) REVERT: C 3 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: C 28 LYS cc_start: 0.9155 (mttt) cc_final: 0.8767 (mttp) REVERT: D 3 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: D 5 ARG cc_start: 0.8258 (ttt-90) cc_final: 0.7884 (tpt-90) REVERT: D 7 ASP cc_start: 0.8554 (p0) cc_final: 0.8350 (p0) REVERT: D 28 LYS cc_start: 0.9167 (mttt) cc_final: 0.8835 (mttp) REVERT: E 3 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: E 5 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8172 (tpt-90) REVERT: E 28 LYS cc_start: 0.9006 (mttt) cc_final: 0.8658 (mttp) REVERT: F 3 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: F 7 ASP cc_start: 0.8482 (p0) cc_final: 0.7977 (p0) REVERT: F 28 LYS cc_start: 0.9047 (mttt) cc_final: 0.8639 (mtpt) REVERT: G 3 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7174 (mm-30) REVERT: G 5 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7891 (ttt-90) REVERT: G 7 ASP cc_start: 0.8528 (p0) cc_final: 0.8197 (p0) REVERT: G 28 LYS cc_start: 0.9170 (mttt) cc_final: 0.8748 (mttp) REVERT: G 40 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8382 (t) REVERT: H 3 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: H 5 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8197 (ttt-90) REVERT: H 28 LYS cc_start: 0.9201 (mttt) cc_final: 0.8800 (mttp) REVERT: I 3 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7704 (mm-30) REVERT: I 5 ARG cc_start: 0.7794 (mtp180) cc_final: 0.6575 (tpm170) REVERT: I 15 GLN cc_start: 0.9058 (tt0) cc_final: 0.8785 (tt0) REVERT: I 28 LYS cc_start: 0.9167 (mttm) cc_final: 0.8814 (mttm) REVERT: J 5 ARG cc_start: 0.7915 (mtp180) cc_final: 0.6542 (tpm170) outliers start: 21 outliers final: 6 residues processed: 103 average time/residue: 0.6037 time to fit residues: 63.5463 Evaluate side-chains 106 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 3 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 0.0070 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 6 optimal weight: 0.0000 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.114862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.088427 restraints weight = 3934.362| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.27 r_work: 0.3408 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3120 Z= 0.147 Angle : 0.479 6.462 4190 Z= 0.253 Chirality : 0.052 0.125 440 Planarity : 0.002 0.013 560 Dihedral : 9.293 57.898 447 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 6.13 % Allowed : 31.29 % Favored : 62.58 % 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: -2.93 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 5 TYR 0.016 0.001 TYR J 10 PHE 0.008 0.001 PHE D 20 HIS 0.002 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3120) covalent geometry : angle 0.47898 ( 4190) hydrogen bonds : bond 0.01770 ( 64) hydrogen bonds : angle 5.31857 ( 192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.124 Fit side-chains REVERT: A 3 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.6225 (pm20) REVERT: A 5 ARG cc_start: 0.8547 (mtp180) cc_final: 0.5914 (ppt170) REVERT: B 3 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.6553 (pm20) REVERT: B 32 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9090 (mt) REVERT: C 28 LYS cc_start: 0.9148 (mttt) cc_final: 0.8755 (mttp) REVERT: D 3 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7420 (mm-30) REVERT: D 5 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.7904 (tpt-90) REVERT: D 7 ASP cc_start: 0.8511 (p0) cc_final: 0.8297 (p0) REVERT: D 28 LYS cc_start: 0.9157 (mttt) cc_final: 0.8825 (mttp) REVERT: E 3 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: E 5 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8137 (tpt-90) REVERT: E 28 LYS cc_start: 0.8938 (mttt) cc_final: 0.8581 (mttp) REVERT: F 3 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: F 7 ASP cc_start: 0.8434 (p0) cc_final: 0.7899 (p0) REVERT: F 28 LYS cc_start: 0.8976 (mttt) cc_final: 0.8556 (mtpt) REVERT: G 3 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: G 5 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7872 (ttt-90) REVERT: G 7 ASP cc_start: 0.8498 (p0) cc_final: 0.8075 (p0) REVERT: G 28 LYS cc_start: 0.9162 (mttt) cc_final: 0.8730 (mttp) REVERT: G 40 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8104 (t) REVERT: H 28 LYS cc_start: 0.9194 (mttt) cc_final: 0.8782 (mttp) REVERT: I 3 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: I 5 ARG cc_start: 0.7767 (mtp180) cc_final: 0.6564 (tpm170) REVERT: I 15 GLN cc_start: 0.9058 (tt0) cc_final: 0.8799 (tt0) REVERT: I 28 LYS cc_start: 0.9167 (mttm) cc_final: 0.8825 (mttp) REVERT: J 5 ARG cc_start: 0.7879 (mtp180) cc_final: 0.6509 (tpm170) outliers start: 19 outliers final: 5 residues processed: 97 average time/residue: 0.6144 time to fit residues: 60.9302 Evaluate side-chains 98 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain I residue 3 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0170 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.118487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.092413 restraints weight = 3916.896| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.24 r_work: 0.3491 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3120 Z= 0.102 Angle : 0.469 5.730 4190 Z= 0.248 Chirality : 0.052 0.126 440 Planarity : 0.001 0.009 560 Dihedral : 8.358 58.257 441 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.52 % Allowed : 33.87 % Favored : 61.61 % 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: -2.98 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.25), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 5 TYR 0.018 0.001 TYR J 10 PHE 0.009 0.001 PHE A 4 HIS 0.001 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 3120) covalent geometry : angle 0.46910 ( 4190) hydrogen bonds : bond 0.01503 ( 64) hydrogen bonds : angle 5.16334 ( 192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.6198 (pm20) REVERT: A 5 ARG cc_start: 0.8519 (mtp180) cc_final: 0.5928 (ppt170) REVERT: B 3 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.6590 (pm20) REVERT: B 28 LYS cc_start: 0.8843 (mttt) cc_final: 0.8633 (mttp) REVERT: C 5 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7961 (ttt-90) REVERT: C 28 LYS cc_start: 0.9118 (mttt) cc_final: 0.8712 (mttp) REVERT: D 5 ARG cc_start: 0.8310 (ttt-90) cc_final: 0.8039 (tpt-90) REVERT: D 28 LYS cc_start: 0.9166 (mttt) cc_final: 0.8855 (mttm) REVERT: E 3 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: E 28 LYS cc_start: 0.8955 (mttt) cc_final: 0.8561 (mttm) REVERT: F 7 ASP cc_start: 0.8380 (p0) cc_final: 0.7792 (p0) REVERT: F 28 LYS cc_start: 0.8896 (mttt) cc_final: 0.8492 (mttp) REVERT: G 3 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: G 7 ASP cc_start: 0.8514 (p0) cc_final: 0.8199 (p0) REVERT: G 28 LYS cc_start: 0.9145 (mttt) cc_final: 0.8704 (mttp) REVERT: G 40 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.8073 (t) REVERT: I 3 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: I 5 ARG cc_start: 0.7718 (mtp180) cc_final: 0.6573 (tpm170) REVERT: I 15 GLN cc_start: 0.8992 (tt0) cc_final: 0.8754 (tt0) REVERT: I 28 LYS cc_start: 0.9124 (mttm) cc_final: 0.8780 (mttm) REVERT: J 5 ARG cc_start: 0.7875 (mtp180) cc_final: 0.6557 (tpm170) outliers start: 14 outliers final: 2 residues processed: 96 average time/residue: 0.6134 time to fit residues: 60.1529 Evaluate side-chains 91 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain I residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 0.0050 chunk 26 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.112239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.086064 restraints weight = 3917.987| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.24 r_work: 0.3351 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3120 Z= 0.231 Angle : 0.534 5.470 4190 Z= 0.286 Chirality : 0.053 0.129 440 Planarity : 0.002 0.021 560 Dihedral : 7.780 57.283 435 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.90 % Allowed : 35.16 % Favored : 61.94 % 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: -2.93 (0.33), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.25), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 5 TYR 0.014 0.002 TYR J 10 PHE 0.011 0.001 PHE A 4 HIS 0.003 0.001 HIS I 14 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 3120) covalent geometry : angle 0.53389 ( 4190) hydrogen bonds : bond 0.01950 ( 64) hydrogen bonds : angle 5.45001 ( 192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.115 Fit side-chains REVERT: A 3 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.6083 (pm20) REVERT: A 5 ARG cc_start: 0.8549 (mtp180) cc_final: 0.6013 (pmt-80) REVERT: B 3 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.6491 (pm20) REVERT: B 28 LYS cc_start: 0.9177 (mttt) cc_final: 0.8851 (mttp) REVERT: C 28 LYS cc_start: 0.9218 (mttt) cc_final: 0.8827 (mttp) REVERT: D 5 ARG cc_start: 0.8263 (ttt-90) cc_final: 0.7939 (tpt-90) REVERT: D 7 ASP cc_start: 0.8521 (p0) cc_final: 0.8310 (p0) REVERT: D 28 LYS cc_start: 0.9139 (mttt) cc_final: 0.8799 (mttp) REVERT: E 3 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: E 28 LYS cc_start: 0.8986 (mttt) cc_final: 0.8587 (mttp) REVERT: F 7 ASP cc_start: 0.8366 (p0) cc_final: 0.7844 (p0) REVERT: F 28 LYS cc_start: 0.8932 (mttt) cc_final: 0.8433 (mttp) REVERT: G 3 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: G 28 LYS cc_start: 0.9166 (mttt) cc_final: 0.8744 (mttp) REVERT: G 40 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7899 (t) REVERT: H 28 LYS cc_start: 0.9189 (mttt) cc_final: 0.8749 (mttp) REVERT: I 3 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7744 (mm-30) REVERT: I 5 ARG cc_start: 0.8007 (mtp180) cc_final: 0.6548 (tpm170) REVERT: I 28 LYS cc_start: 0.9182 (mttm) cc_final: 0.8843 (mttp) outliers start: 9 outliers final: 2 residues processed: 92 average time/residue: 0.5891 time to fit residues: 55.4800 Evaluate side-chains 87 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain E residue 3 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain I residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.116822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.090918 restraints weight = 3961.864| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.23 r_work: 0.3466 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3120 Z= 0.112 Angle : 0.500 5.628 4190 Z= 0.264 Chirality : 0.053 0.163 440 Planarity : 0.002 0.021 560 Dihedral : 7.656 57.094 435 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.87 % Allowed : 35.48 % Favored : 60.65 % 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: -3.00 (0.33), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.25), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 5 TYR 0.016 0.001 TYR J 10 PHE 0.013 0.001 PHE A 4 HIS 0.001 0.000 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3120) covalent geometry : angle 0.50007 ( 4190) hydrogen bonds : bond 0.01590 ( 64) hydrogen bonds : angle 5.22294 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1721.16 seconds wall clock time: 29 minutes 59.62 seconds (1799.62 seconds total)