Starting phenix.real_space_refine on Fri Aug 22 15:36:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mst_9232/08_2025/6mst_9232.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mst_9232/08_2025/6mst_9232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mst_9232/08_2025/6mst_9232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mst_9232/08_2025/6mst_9232.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mst_9232/08_2025/6mst_9232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mst_9232/08_2025/6mst_9232.map" } resolution = 2.7 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= 0.010 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 24 5.16 5 C 3288 2.51 5 N 924 2.21 5 O 936 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: 5172 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Restraints were copied for chains: B, C, E, D, F, H, I, J, K, L, G Time building chain proxies: 0.64, per 1000 atoms: 0.12 Number of scatterers: 5172 At special positions: 0 Unit cell: (75.92, 92.56, 50.96, 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 24 16.00 O 936 8.00 N 924 7.00 C 3288 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: 0.39 Conformation dependent library (CDL) restraints added in 192.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 9 removed outlier: 6.430A pdb=" N PHE I 6 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLU G 9 " --> pdb=" O PHE I 6 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY I 8 " --> pdb=" O GLU G 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 23 removed outlier: 6.795A pdb=" N ARG C 19 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER E 22 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR C 21 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG E 19 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N SER G 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR E 21 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG I 19 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N SER K 22 " --> pdb=" O ARG I 19 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR I 21 " --> pdb=" O SER K 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.499A pdb=" N TYR A 29 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR C 29 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR E 29 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR I 29 " --> pdb=" O ILE K 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 39 removed outlier: 6.680A pdb=" N ALA A 38 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA C 38 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA E 38 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA I 38 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.669A pdb=" N TYR I 42 " --> pdb=" O ASP G 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.568A pdb=" N LYS I 46 " --> pdb=" O ARG G 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 52 through 54 removed outlier: 6.547A pdb=" N VAL A 52 " --> pdb=" O TRP C 53 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 52 " --> pdb=" O TRP E 53 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL E 52 " --> pdb=" O TRP G 53 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL I 52 " --> pdb=" O TRP K 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 6 through 9 Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 23 removed outlier: 6.809A pdb=" N ARG B 19 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N SER D 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR B 21 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG D 19 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER F 22 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR D 21 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG H 19 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N SER J 22 " --> pdb=" O ARG H 19 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR H 21 " --> pdb=" O SER J 22 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG J 19 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N SER L 22 " --> pdb=" O ARG J 19 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR J 21 " --> pdb=" O SER L 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 29 through 30 removed outlier: 6.468A pdb=" N TYR B 29 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR D 29 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR F 29 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR H 29 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR J 29 " --> pdb=" O ILE L 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 39 removed outlier: 6.876A pdb=" N ALA B 38 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA D 38 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA F 38 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA H 38 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA J 38 " --> pdb=" O ARG L 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'B' and resid 46 through 47 Processing sheet with id=AB5, first strand: chain 'B' and resid 52 through 54 removed outlier: 6.639A pdb=" N VAL B 52 " --> pdb=" O TRP D 53 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 52 " --> pdb=" O TRP F 53 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL F 52 " --> pdb=" O TRP H 53 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL H 52 " --> pdb=" O TRP J 53 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL J 52 " --> pdb=" O TRP L 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 65 hydrogen bonds defined for protein. 195 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: 0.56 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1611 1.34 - 1.45: 1173 1.45 - 1.57: 2508 1.57 - 1.68: 0 1.68 - 1.80: 48 Bond restraints: 5340 Sorted by residual: bond pdb=" CA ALA G 14 " pdb=" CB ALA G 14 " ideal model delta sigma weight residual 1.534 1.517 0.017 1.45e-02 4.76e+03 1.37e+00 bond pdb=" CA ALA F 14 " pdb=" CB ALA F 14 " ideal model delta sigma weight residual 1.534 1.517 0.017 1.45e-02 4.76e+03 1.36e+00 bond pdb=" CA ALA L 14 " pdb=" CB ALA L 14 " ideal model delta sigma weight residual 1.534 1.518 0.017 1.45e-02 4.76e+03 1.33e+00 bond pdb=" CA ALA D 14 " pdb=" CB ALA D 14 " ideal model delta sigma weight residual 1.534 1.518 0.017 1.45e-02 4.76e+03 1.31e+00 bond pdb=" CA ALA C 14 " pdb=" CB ALA C 14 " ideal model delta sigma weight residual 1.534 1.518 0.017 1.45e-02 4.76e+03 1.31e+00 ... (remaining 5335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 6400 1.25 - 2.51: 590 2.51 - 3.76: 137 3.76 - 5.02: 25 5.02 - 6.27: 12 Bond angle restraints: 7164 Sorted by residual: angle pdb=" CA TYR F 21 " pdb=" CB TYR F 21 " pdb=" CG TYR F 21 " ideal model delta sigma weight residual 113.90 118.11 -4.21 1.80e+00 3.09e-01 5.46e+00 angle pdb=" CA TYR J 21 " pdb=" CB TYR J 21 " pdb=" CG TYR J 21 " ideal model delta sigma weight residual 113.90 118.07 -4.17 1.80e+00 3.09e-01 5.36e+00 angle pdb=" CA TYR I 21 " pdb=" CB TYR I 21 " pdb=" CG TYR I 21 " ideal model delta sigma weight residual 113.90 118.05 -4.15 1.80e+00 3.09e-01 5.31e+00 angle pdb=" CA TYR G 21 " pdb=" CB TYR G 21 " pdb=" CG TYR G 21 " ideal model delta sigma weight residual 113.90 118.05 -4.15 1.80e+00 3.09e-01 5.31e+00 angle pdb=" CA TYR H 21 " pdb=" CB TYR H 21 " pdb=" CG TYR H 21 " ideal model delta sigma weight residual 113.90 118.04 -4.14 1.80e+00 3.09e-01 5.30e+00 ... (remaining 7159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.92: 2259 5.92 - 11.84: 465 11.84 - 17.76: 156 17.76 - 23.68: 60 23.68 - 29.60: 12 Dihedral angle restraints: 2952 sinusoidal: 1140 harmonic: 1812 Sorted by residual: dihedral pdb=" CA ASP H 16 " pdb=" C ASP H 16 " pdb=" N MET H 17 " pdb=" CA MET H 17 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ASP L 16 " pdb=" C ASP L 16 " pdb=" N MET L 17 " pdb=" CA MET L 17 " ideal model delta harmonic sigma weight residual -180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ASP F 16 " pdb=" C ASP F 16 " pdb=" N MET F 17 " pdb=" CA MET F 17 " ideal model delta harmonic sigma weight residual 180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 2949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 181 0.024 - 0.047: 171 0.047 - 0.071: 142 0.071 - 0.095: 74 0.095 - 0.118: 32 Chirality restraints: 600 Sorted by residual: chirality pdb=" CA ILE G 30 " pdb=" N ILE G 30 " pdb=" C ILE G 30 " pdb=" CB ILE G 30 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE C 30 " pdb=" N ILE C 30 " pdb=" C ILE C 30 " pdb=" CB ILE C 30 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA ILE L 30 " pdb=" N ILE L 30 " pdb=" C ILE L 30 " pdb=" CB ILE L 30 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 597 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 29 " 0.016 2.00e-02 2.50e+03 1.56e-02 4.86e+00 pdb=" CG TYR E 29 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR E 29 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 29 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR E 29 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 29 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 29 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 29 " 0.016 2.00e-02 2.50e+03 1.56e-02 4.85e+00 pdb=" CG TYR G 29 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR G 29 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR G 29 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR G 29 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR G 29 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR G 29 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 29 " -0.015 2.00e-02 2.50e+03 1.56e-02 4.85e+00 pdb=" CG TYR H 29 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR H 29 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR H 29 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR H 29 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR H 29 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR H 29 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 29 " -0.002 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1438 2.82 - 3.34: 3763 3.34 - 3.86: 9950 3.86 - 4.38: 11608 4.38 - 4.90: 20727 Nonbonded interactions: 47486 Sorted by model distance: nonbonded pdb=" N SER A 2 " pdb=" O GLY B 31 " model vdw 2.294 3.120 nonbonded pdb=" O GLY C 31 " pdb=" N SER F 2 " model vdw 2.307 3.120 nonbonded pdb=" N SER J 2 " pdb=" O GLY G 31 " model vdw 2.307 3.120 nonbonded pdb=" N SER C 2 " pdb=" O GLY D 31 " model vdw 2.308 3.120 nonbonded pdb=" N SER I 2 " pdb=" O GLY J 31 " model vdw 2.316 3.120 ... (remaining 47481 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 'E' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'G' } 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: 1.390 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: 0.030 Set scattering table: 0.010 Process input model: 4.740 Find NCS groups from input model: 0.030 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:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 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 : 0.006 0.030 5340 Z= 0.289 Angle : 0.852 6.273 7164 Z= 0.525 Chirality : 0.052 0.118 600 Planarity : 0.004 0.016 960 Dihedral : 7.677 29.598 1824 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.58 (0.18), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.14), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 25 TYR 0.037 0.005 TYR E 29 PHE 0.019 0.004 PHE C 11 TRP 0.016 0.003 TRP E 53 HIS 0.001 0.000 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00600 ( 5340) covalent geometry : angle 0.85178 ( 7164) hydrogen bonds : bond 0.15671 ( 65) hydrogen bonds : angle 7.26243 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.115 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.7771 time to fit residues: 101.2362 Evaluate side-chains 114 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.090449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.075374 restraints weight = 6663.413| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.79 r_work: 0.2872 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5340 Z= 0.193 Angle : 0.549 4.625 7164 Z= 0.314 Chirality : 0.042 0.113 600 Planarity : 0.004 0.030 960 Dihedral : 4.741 16.906 744 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.32 % Allowed : 5.92 % Favored : 92.76 % 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: -4.16 (0.19), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.15), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 39 TYR 0.018 0.002 TYR A 29 PHE 0.013 0.002 PHE D 3 TRP 0.007 0.001 TRP G 53 HIS 0.001 0.000 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 5340) covalent geometry : angle 0.54906 ( 7164) hydrogen bonds : bond 0.03219 ( 65) hydrogen bonds : angle 4.80453 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.153 Fit side-chains REVERT: A 15 ARG cc_start: 0.8706 (mtt180) cc_final: 0.8246 (mtm180) REVERT: A 26 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8806 (mt-10) REVERT: A 34 LYS cc_start: 0.8957 (mttt) cc_final: 0.8746 (mtmt) REVERT: B 26 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8795 (mt-10) REVERT: B 39 ARG cc_start: 0.8794 (ttt90) cc_final: 0.8437 (tmm-80) REVERT: C 12 ASP cc_start: 0.8869 (t70) cc_final: 0.8544 (t70) REVERT: C 15 ARG cc_start: 0.8593 (mtt180) cc_final: 0.7215 (mpp-170) REVERT: C 34 LYS cc_start: 0.8949 (mttt) cc_final: 0.8654 (mttp) REVERT: C 39 ARG cc_start: 0.8683 (ttt180) cc_final: 0.8105 (ttp-170) REVERT: E 42 TYR cc_start: 0.8785 (t80) cc_final: 0.8519 (t80) REVERT: D 39 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8338 (ttp-170) REVERT: F 39 ARG cc_start: 0.8721 (ttt90) cc_final: 0.8357 (ttp-170) REVERT: H 12 ASP cc_start: 0.8958 (t70) cc_final: 0.8734 (t0) REVERT: H 26 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8968 (mt-10) REVERT: H 39 ARG cc_start: 0.8590 (ttt180) cc_final: 0.8343 (ttp-170) REVERT: I 33 ASP cc_start: 0.8909 (m-30) cc_final: 0.8698 (m-30) REVERT: I 34 LYS cc_start: 0.8801 (mttt) cc_final: 0.8549 (mtmt) REVERT: J 34 LYS cc_start: 0.8780 (mttt) cc_final: 0.8544 (mtmp) REVERT: J 39 ARG cc_start: 0.8764 (ttm-80) cc_final: 0.8556 (ttp-110) REVERT: L 39 ARG cc_start: 0.8576 (ttt90) cc_final: 0.8138 (ttp-170) REVERT: G 26 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8883 (mt-10) outliers start: 6 outliers final: 4 residues processed: 136 average time/residue: 0.7275 time to fit residues: 101.6110 Evaluate side-chains 126 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain L residue 2 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.087907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.072735 restraints weight = 6495.653| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.77 r_work: 0.2825 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 5340 Z= 0.322 Angle : 0.598 5.464 7164 Z= 0.343 Chirality : 0.042 0.109 600 Planarity : 0.004 0.033 960 Dihedral : 4.865 17.396 744 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.41 % Allowed : 8.33 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.91 (0.20), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.15), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 47 TYR 0.017 0.002 TYR F 29 PHE 0.015 0.002 PHE D 3 TRP 0.006 0.001 TRP G 53 HIS 0.002 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00730 ( 5340) covalent geometry : angle 0.59761 ( 7164) hydrogen bonds : bond 0.03161 ( 65) hydrogen bonds : angle 4.64567 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.226 Fit side-chains REVERT: A 15 ARG cc_start: 0.8720 (mtt180) cc_final: 0.8248 (mtm180) REVERT: A 34 LYS cc_start: 0.8951 (mttt) cc_final: 0.8663 (mtmt) REVERT: B 39 ARG cc_start: 0.8799 (ttt90) cc_final: 0.8451 (tmm-80) REVERT: C 12 ASP cc_start: 0.8883 (t70) cc_final: 0.8610 (t70) REVERT: C 15 ARG cc_start: 0.8560 (mtt180) cc_final: 0.7194 (mpp-170) REVERT: C 34 LYS cc_start: 0.8964 (mttt) cc_final: 0.8696 (mttp) REVERT: C 39 ARG cc_start: 0.8674 (ttt180) cc_final: 0.8057 (ttp-170) REVERT: D 39 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8373 (ttp-170) REVERT: F 39 ARG cc_start: 0.8667 (ttt90) cc_final: 0.7956 (ttp-170) REVERT: F 46 LYS cc_start: 0.8225 (mttt) cc_final: 0.7843 (mttp) REVERT: H 12 ASP cc_start: 0.8931 (t70) cc_final: 0.8626 (t70) REVERT: H 15 ARG cc_start: 0.8417 (mtt180) cc_final: 0.7304 (mpp-170) REVERT: H 42 TYR cc_start: 0.8932 (t80) cc_final: 0.8678 (t80) REVERT: I 33 ASP cc_start: 0.8974 (m-30) cc_final: 0.8702 (m-30) REVERT: L 15 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6730 (mpt180) REVERT: G 26 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8904 (mt-10) outliers start: 11 outliers final: 8 residues processed: 137 average time/residue: 0.7394 time to fit residues: 104.1028 Evaluate side-chains 135 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 15 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.090235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.075041 restraints weight = 6473.397| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.77 r_work: 0.2885 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5340 Z= 0.152 Angle : 0.474 4.133 7164 Z= 0.276 Chirality : 0.040 0.113 600 Planarity : 0.003 0.026 960 Dihedral : 4.408 16.617 744 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.41 % Allowed : 9.65 % Favored : 87.94 % 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: -3.80 (0.20), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 39 TYR 0.012 0.001 TYR C 42 PHE 0.009 0.001 PHE D 3 TRP 0.004 0.001 TRP G 53 HIS 0.001 0.000 HIS I 37 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5340) covalent geometry : angle 0.47416 ( 7164) hydrogen bonds : bond 0.02316 ( 65) hydrogen bonds : angle 4.45989 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.147 Fit side-chains REVERT: A 15 ARG cc_start: 0.8671 (mtt180) cc_final: 0.8274 (mtm180) REVERT: A 34 LYS cc_start: 0.8975 (mttt) cc_final: 0.8679 (mtmt) REVERT: B 39 ARG cc_start: 0.8798 (ttt90) cc_final: 0.8474 (tmm-80) REVERT: C 12 ASP cc_start: 0.8895 (t70) cc_final: 0.8631 (t70) REVERT: C 15 ARG cc_start: 0.8519 (mtt180) cc_final: 0.7436 (mtm-85) REVERT: C 34 LYS cc_start: 0.8933 (mttt) cc_final: 0.8682 (mtmt) REVERT: C 39 ARG cc_start: 0.8711 (ttt180) cc_final: 0.8109 (ttp-170) REVERT: D 39 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8420 (ttp-170) REVERT: F 39 ARG cc_start: 0.8693 (ttt90) cc_final: 0.8319 (ttp-170) REVERT: H 12 ASP cc_start: 0.8942 (t70) cc_final: 0.8687 (t0) REVERT: H 39 ARG cc_start: 0.8570 (ttt180) cc_final: 0.8349 (ttm170) REVERT: J 39 ARG cc_start: 0.8722 (ttm-80) cc_final: 0.8481 (ttp-110) REVERT: L 39 ARG cc_start: 0.8480 (ttt90) cc_final: 0.8055 (ttp-170) REVERT: G 26 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8861 (mt-10) outliers start: 11 outliers final: 7 residues processed: 131 average time/residue: 0.6579 time to fit residues: 88.7431 Evaluate side-chains 130 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain L residue 2 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.087724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.072447 restraints weight = 6615.707| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.78 r_work: 0.2822 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 5340 Z= 0.328 Angle : 0.572 5.686 7164 Z= 0.332 Chirality : 0.042 0.111 600 Planarity : 0.004 0.032 960 Dihedral : 4.790 16.246 744 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.85 % Allowed : 10.75 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.74 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 39 TYR 0.024 0.002 TYR H 42 PHE 0.013 0.002 PHE K 11 TRP 0.005 0.001 TRP B 18 HIS 0.002 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00744 ( 5340) covalent geometry : angle 0.57165 ( 7164) hydrogen bonds : bond 0.02851 ( 65) hydrogen bonds : angle 4.53767 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.171 Fit side-chains REVERT: A 15 ARG cc_start: 0.8733 (mtt180) cc_final: 0.8246 (mtm-85) REVERT: A 34 LYS cc_start: 0.8962 (mttt) cc_final: 0.8738 (mttp) REVERT: B 39 ARG cc_start: 0.8816 (ttt90) cc_final: 0.8463 (tmm-80) REVERT: C 12 ASP cc_start: 0.8919 (t70) cc_final: 0.8609 (t70) REVERT: C 15 ARG cc_start: 0.8555 (mtt180) cc_final: 0.8193 (mtm180) REVERT: C 34 LYS cc_start: 0.8970 (mttt) cc_final: 0.8739 (mttp) REVERT: C 39 ARG cc_start: 0.8674 (ttt180) cc_final: 0.8066 (ttp-170) REVERT: D 39 ARG cc_start: 0.8834 (ttm-80) cc_final: 0.8486 (ttp-170) REVERT: F 39 ARG cc_start: 0.8666 (ttt90) cc_final: 0.7964 (ttp-170) REVERT: F 46 LYS cc_start: 0.8216 (mttt) cc_final: 0.7991 (mttm) REVERT: H 12 ASP cc_start: 0.8826 (t70) cc_final: 0.8518 (t70) REVERT: H 15 ARG cc_start: 0.8457 (mtt180) cc_final: 0.7328 (mpp-170) REVERT: L 15 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6453 (mpt180) REVERT: G 26 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8903 (mt-10) outliers start: 13 outliers final: 9 residues processed: 139 average time/residue: 0.6918 time to fit residues: 98.8324 Evaluate side-chains 138 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 15 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.090012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074878 restraints weight = 6520.939| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.76 r_work: 0.2879 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 5340 Z= 0.161 Angle : 0.471 4.329 7164 Z= 0.276 Chirality : 0.040 0.114 600 Planarity : 0.003 0.022 960 Dihedral : 4.450 15.931 744 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.41 % Allowed : 12.06 % Favored : 85.53 % 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: -3.71 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 39 TYR 0.010 0.001 TYR C 42 PHE 0.009 0.001 PHE J 11 TRP 0.003 0.001 TRP G 53 HIS 0.001 0.000 HIS D 37 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5340) covalent geometry : angle 0.47138 ( 7164) hydrogen bonds : bond 0.02251 ( 65) hydrogen bonds : angle 4.40464 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.201 Fit side-chains REVERT: A 15 ARG cc_start: 0.8712 (mtt180) cc_final: 0.8303 (mtm180) REVERT: A 34 LYS cc_start: 0.9001 (mttt) cc_final: 0.8757 (mttp) REVERT: B 12 ASP cc_start: 0.8689 (t70) cc_final: 0.8460 (t70) REVERT: B 39 ARG cc_start: 0.8824 (ttt90) cc_final: 0.8530 (tmm-80) REVERT: C 12 ASP cc_start: 0.8884 (t70) cc_final: 0.8612 (t70) REVERT: C 15 ARG cc_start: 0.8528 (mtt180) cc_final: 0.7427 (mtm-85) REVERT: C 34 LYS cc_start: 0.8940 (mttt) cc_final: 0.8706 (mttt) REVERT: C 39 ARG cc_start: 0.8688 (ttt180) cc_final: 0.8095 (ttp-170) REVERT: D 39 ARG cc_start: 0.8868 (ttm-80) cc_final: 0.8469 (ttp-170) REVERT: F 39 ARG cc_start: 0.8695 (ttt90) cc_final: 0.8000 (ttp-170) REVERT: H 12 ASP cc_start: 0.8924 (t70) cc_final: 0.8645 (t0) REVERT: G 26 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8855 (mt-10) outliers start: 11 outliers final: 8 residues processed: 133 average time/residue: 0.6725 time to fit residues: 92.1753 Evaluate side-chains 132 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain L residue 2 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.0000 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.090711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.075542 restraints weight = 6475.579| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.76 r_work: 0.2905 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5340 Z= 0.134 Angle : 0.454 3.966 7164 Z= 0.267 Chirality : 0.040 0.114 600 Planarity : 0.003 0.035 960 Dihedral : 4.300 15.606 744 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.97 % Allowed : 12.72 % Favored : 85.31 % 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: -3.70 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 47 TYR 0.020 0.001 TYR E 42 PHE 0.008 0.001 PHE J 11 TRP 0.003 0.000 TRP G 53 HIS 0.001 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5340) covalent geometry : angle 0.45394 ( 7164) hydrogen bonds : bond 0.02233 ( 65) hydrogen bonds : angle 4.34181 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.149 Fit side-chains REVERT: A 15 ARG cc_start: 0.8683 (mtt180) cc_final: 0.7673 (mtm-85) REVERT: A 34 LYS cc_start: 0.8985 (mttt) cc_final: 0.8740 (mttp) REVERT: B 12 ASP cc_start: 0.8683 (t70) cc_final: 0.8463 (t70) REVERT: B 39 ARG cc_start: 0.8781 (ttt90) cc_final: 0.8509 (tmm-80) REVERT: C 12 ASP cc_start: 0.8875 (t70) cc_final: 0.8601 (t70) REVERT: C 34 LYS cc_start: 0.8955 (mttt) cc_final: 0.8718 (mttt) REVERT: C 39 ARG cc_start: 0.8697 (ttt180) cc_final: 0.8138 (ttp-170) REVERT: E 15 ARG cc_start: 0.8560 (mtt180) cc_final: 0.7254 (mpp-170) REVERT: E 39 ARG cc_start: 0.8767 (ttt90) cc_final: 0.8531 (ttt90) REVERT: D 39 ARG cc_start: 0.8865 (ttm-80) cc_final: 0.8496 (ttp-170) REVERT: D 46 LYS cc_start: 0.8533 (mttm) cc_final: 0.7739 (tttt) REVERT: F 39 ARG cc_start: 0.8661 (ttt90) cc_final: 0.7982 (ttp-170) REVERT: H 12 ASP cc_start: 0.8925 (t70) cc_final: 0.8650 (t0) REVERT: G 26 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8854 (mt-10) outliers start: 9 outliers final: 9 residues processed: 135 average time/residue: 0.6818 time to fit residues: 94.8334 Evaluate side-chains 135 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 17 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.088389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.073118 restraints weight = 6540.269| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.78 r_work: 0.2846 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 5340 Z= 0.269 Angle : 0.534 5.426 7164 Z= 0.312 Chirality : 0.041 0.113 600 Planarity : 0.004 0.031 960 Dihedral : 4.657 16.472 744 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.19 % Allowed : 12.72 % Favored : 85.09 % 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: -3.68 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 39 TYR 0.029 0.002 TYR E 42 PHE 0.012 0.002 PHE D 3 TRP 0.005 0.001 TRP B 18 HIS 0.001 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00608 ( 5340) covalent geometry : angle 0.53439 ( 7164) hydrogen bonds : bond 0.02708 ( 65) hydrogen bonds : angle 4.43972 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8757 (mtt180) cc_final: 0.8241 (mtm-85) REVERT: B 12 ASP cc_start: 0.8711 (t70) cc_final: 0.8486 (t70) REVERT: B 39 ARG cc_start: 0.8804 (ttt90) cc_final: 0.8360 (tmm-80) REVERT: C 12 ASP cc_start: 0.8900 (t70) cc_final: 0.8604 (t70) REVERT: C 15 ARG cc_start: 0.8511 (mtt180) cc_final: 0.7427 (mtm-85) REVERT: C 34 LYS cc_start: 0.8966 (mttt) cc_final: 0.8715 (mttp) REVERT: C 39 ARG cc_start: 0.8660 (ttt180) cc_final: 0.8054 (ttp-170) REVERT: D 46 LYS cc_start: 0.8539 (mttm) cc_final: 0.7740 (tttt) REVERT: F 46 LYS cc_start: 0.8380 (mttt) cc_final: 0.8139 (mttm) REVERT: H 12 ASP cc_start: 0.8833 (t70) cc_final: 0.8514 (t70) REVERT: H 15 ARG cc_start: 0.8423 (mtt180) cc_final: 0.7209 (mpp-170) REVERT: L 15 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.6362 (mpt180) REVERT: G 26 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8872 (mt-10) outliers start: 10 outliers final: 8 residues processed: 142 average time/residue: 0.8233 time to fit residues: 120.2564 Evaluate side-chains 140 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 15 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.088791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073608 restraints weight = 6564.596| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.77 r_work: 0.2852 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5340 Z= 0.230 Angle : 0.517 5.584 7164 Z= 0.301 Chirality : 0.041 0.113 600 Planarity : 0.004 0.030 960 Dihedral : 4.639 16.411 744 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.75 % Allowed : 12.50 % Favored : 85.75 % 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: -3.68 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 47 TYR 0.029 0.002 TYR G 42 PHE 0.011 0.002 PHE D 3 TRP 0.004 0.001 TRP B 18 HIS 0.001 0.000 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 5340) covalent geometry : angle 0.51663 ( 7164) hydrogen bonds : bond 0.02672 ( 65) hydrogen bonds : angle 4.38811 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.208 Fit side-chains REVERT: A 15 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8299 (mtm180) REVERT: B 12 ASP cc_start: 0.8721 (t70) cc_final: 0.8504 (t70) REVERT: B 39 ARG cc_start: 0.8797 (ttt90) cc_final: 0.8512 (tmm-80) REVERT: C 12 ASP cc_start: 0.8906 (t70) cc_final: 0.8610 (t70) REVERT: C 15 ARG cc_start: 0.8520 (mtt180) cc_final: 0.7417 (mtm-85) REVERT: C 34 LYS cc_start: 0.8907 (mttt) cc_final: 0.8672 (mttp) REVERT: C 39 ARG cc_start: 0.8663 (ttt180) cc_final: 0.8086 (ttp-170) REVERT: D 39 ARG cc_start: 0.8881 (ttm-80) cc_final: 0.8467 (ttp-170) REVERT: D 46 LYS cc_start: 0.8548 (mttm) cc_final: 0.7753 (tttt) REVERT: F 39 ARG cc_start: 0.8706 (ttt90) cc_final: 0.7978 (ttp-170) REVERT: F 46 LYS cc_start: 0.8360 (mttt) cc_final: 0.8123 (mttm) REVERT: H 12 ASP cc_start: 0.8849 (t70) cc_final: 0.8531 (t70) REVERT: G 26 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8864 (mt-10) outliers start: 8 outliers final: 8 residues processed: 136 average time/residue: 0.6750 time to fit residues: 94.5721 Evaluate side-chains 136 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain L residue 2 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 16 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 = 0.3283 r_free = 0.3283 target = 0.088867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.073733 restraints weight = 6587.349| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.77 r_work: 0.2861 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5340 Z= 0.228 Angle : 0.518 5.637 7164 Z= 0.302 Chirality : 0.041 0.113 600 Planarity : 0.004 0.031 960 Dihedral : 4.667 16.498 744 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.63 % Allowed : 12.94 % Favored : 84.43 % 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: -3.68 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 47 TYR 0.030 0.002 TYR H 42 PHE 0.011 0.002 PHE D 3 TRP 0.004 0.001 TRP B 18 HIS 0.001 0.000 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 5340) covalent geometry : angle 0.51818 ( 7164) hydrogen bonds : bond 0.02664 ( 65) hydrogen bonds : angle 4.32890 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.213 Fit side-chains REVERT: A 15 ARG cc_start: 0.8730 (mtt180) cc_final: 0.8304 (mtm180) REVERT: B 12 ASP cc_start: 0.8744 (t70) cc_final: 0.8519 (t70) REVERT: B 39 ARG cc_start: 0.8798 (ttt90) cc_final: 0.8517 (tmm-80) REVERT: C 12 ASP cc_start: 0.8906 (t70) cc_final: 0.8608 (t70) REVERT: C 15 ARG cc_start: 0.8521 (mtt180) cc_final: 0.7413 (mtm-85) REVERT: C 34 LYS cc_start: 0.8911 (mttt) cc_final: 0.8678 (mttp) REVERT: C 39 ARG cc_start: 0.8705 (ttt180) cc_final: 0.8098 (ttp-170) REVERT: E 15 ARG cc_start: 0.8549 (mtt180) cc_final: 0.7167 (mpp-170) REVERT: D 39 ARG cc_start: 0.8893 (ttm-80) cc_final: 0.8480 (ttp-170) REVERT: D 46 LYS cc_start: 0.8550 (mttm) cc_final: 0.7758 (tttt) REVERT: F 39 ARG cc_start: 0.8720 (ttt90) cc_final: 0.7991 (ttp-170) REVERT: F 46 LYS cc_start: 0.8373 (mttt) cc_final: 0.8133 (mttm) REVERT: H 12 ASP cc_start: 0.8849 (t70) cc_final: 0.8522 (t70) REVERT: H 15 ARG cc_start: 0.8433 (mtt180) cc_final: 0.7224 (mpp-170) REVERT: K 39 ARG cc_start: 0.8269 (ttp-110) cc_final: 0.7780 (ttp-110) REVERT: L 15 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6192 (mpt180) REVERT: G 26 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8881 (mt-10) outliers start: 12 outliers final: 10 residues processed: 138 average time/residue: 0.8016 time to fit residues: 113.7560 Evaluate side-chains 140 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 15 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 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 = 0.3321 r_free = 0.3321 target = 0.090760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075632 restraints weight = 6597.862| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.77 r_work: 0.2907 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5340 Z= 0.139 Angle : 0.466 4.628 7164 Z= 0.273 Chirality : 0.040 0.114 600 Planarity : 0.003 0.029 960 Dihedral : 4.420 16.164 744 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.41 % Allowed : 12.72 % Favored : 84.87 % 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: -3.69 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 47 TYR 0.027 0.002 TYR E 42 PHE 0.008 0.001 PHE K 11 TRP 0.003 0.001 TRP G 53 HIS 0.001 0.000 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5340) covalent geometry : angle 0.46556 ( 7164) hydrogen bonds : bond 0.02603 ( 65) hydrogen bonds : angle 4.31789 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.47 seconds wall clock time: 39 minutes 2.52 seconds (2342.52 seconds total)