Starting phenix.real_space_refine on Tue Feb 11 09:39:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mst_9232/02_2025/6mst_9232.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mst_9232/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6mst_9232/02_2025/6mst_9232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mst_9232/02_2025/6mst_9232.map" model { file = "/net/cci-nas-00/data/ceres_data/6mst_9232/02_2025/6mst_9232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mst_9232/02_2025/6mst_9232.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 2.11, per 1000 atoms: 0.41 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: 1.14 Conformation dependent library (CDL) restraints added in 766.7 milliseconds 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: 0.79 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: 1.28 Time building geometry restraints manager: 1.35 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.720 Find NCS groups from input model: 0.110 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:15.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.290 ------------------------------------------------------------------------------- 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= 0.390 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.003 TRP E 53 HIS 0.001 0.000 HIS B 37 PHE 0.019 0.004 PHE C 11 TYR 0.037 0.005 TYR E 29 ARG 0.003 0.000 ARG L 25 *********************** 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 : 0.615 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.8388 time to fit residues: 240.0310 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 : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 D 37 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.089724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074695 restraints weight = 6546.661| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.78 r_work: 0.2863 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1746 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= 0.332 Angle : 0.567 4.896 7164 Z= 0.324 Chirality : 0.042 0.112 600 Planarity : 0.004 0.031 960 Dihedral : 4.790 16.958 744 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.54 % Allowed : 5.92 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.19), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.15), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 53 HIS 0.002 0.000 HIS J 37 PHE 0.014 0.002 PHE D 3 TYR 0.020 0.002 TYR C 29 ARG 0.007 0.001 ARG L 39 *********************** 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 143 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.491 Fit side-chains REVERT: A 15 ARG cc_start: 0.8727 (mtt180) cc_final: 0.8265 (mtm180) REVERT: A 34 LYS cc_start: 0.8957 (mttt) cc_final: 0.8662 (mtmt) REVERT: B 39 ARG cc_start: 0.8807 (ttt90) cc_final: 0.8458 (tmm-80) REVERT: C 12 ASP cc_start: 0.8862 (t70) cc_final: 0.8579 (t70) REVERT: C 15 ARG cc_start: 0.8548 (mtt180) cc_final: 0.7182 (mpp-170) REVERT: C 34 LYS cc_start: 0.8923 (mttt) cc_final: 0.8648 (mtmt) REVERT: C 39 ARG cc_start: 0.8715 (ttt180) cc_final: 0.8117 (ttp-170) REVERT: E 12 ASP cc_start: 0.8817 (t70) cc_final: 0.8605 (t70) REVERT: D 39 ARG cc_start: 0.8791 (ttm-80) cc_final: 0.8354 (ttp-170) REVERT: F 39 ARG cc_start: 0.8710 (ttt90) cc_final: 0.7993 (ttp-170) REVERT: F 46 LYS cc_start: 0.8252 (mttt) cc_final: 0.7901 (mttp) REVERT: H 12 ASP cc_start: 0.8919 (t70) cc_final: 0.8623 (t70) REVERT: H 15 ARG cc_start: 0.8472 (mtt180) cc_final: 0.7338 (mpp-170) REVERT: H 26 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8967 (mt-10) REVERT: I 33 ASP cc_start: 0.8962 (m-30) cc_final: 0.8737 (m-30) REVERT: I 34 LYS cc_start: 0.8807 (mttt) cc_final: 0.8555 (mtmt) REVERT: J 34 LYS cc_start: 0.8809 (mttt) cc_final: 0.8567 (mttp) REVERT: L 15 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6406 (mpt180) REVERT: G 26 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8887 (mt-10) outliers start: 7 outliers final: 4 residues processed: 141 average time/residue: 1.7513 time to fit residues: 253.7181 Evaluate side-chains 133 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 15 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.090835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.075607 restraints weight = 6484.077| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.78 r_work: 0.2889 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5340 Z= 0.223 Angle : 0.487 4.004 7164 Z= 0.282 Chirality : 0.040 0.111 600 Planarity : 0.003 0.036 960 Dihedral : 4.402 16.411 744 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.75 % Allowed : 8.55 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.20), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.15), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 53 HIS 0.001 0.000 HIS D 37 PHE 0.010 0.002 PHE D 3 TYR 0.011 0.001 TYR F 29 ARG 0.008 0.001 ARG E 47 *********************** 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 137 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.595 Fit side-chains REVERT: A 2 SER cc_start: 0.9098 (t) cc_final: 0.8776 (t) REVERT: A 15 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8238 (mtm180) REVERT: A 34 LYS cc_start: 0.8968 (mttt) cc_final: 0.8688 (mtmt) REVERT: B 39 ARG cc_start: 0.8798 (ttt90) cc_final: 0.8449 (tmm-80) REVERT: C 12 ASP cc_start: 0.8914 (t70) cc_final: 0.8642 (t70) REVERT: C 15 ARG cc_start: 0.8537 (mtt180) cc_final: 0.7157 (mpp-170) REVERT: C 16 ASP cc_start: 0.8853 (m-30) cc_final: 0.8649 (m-30) REVERT: C 17 MET cc_start: 0.9319 (ttp) cc_final: 0.9083 (ttp) REVERT: C 34 LYS cc_start: 0.8922 (mttt) cc_final: 0.8660 (mtmt) REVERT: C 39 ARG cc_start: 0.8721 (ttt180) cc_final: 0.8120 (ttp-170) REVERT: D 39 ARG cc_start: 0.8829 (ttm-80) cc_final: 0.8418 (ttp-170) REVERT: F 39 ARG cc_start: 0.8709 (ttt90) cc_final: 0.8355 (ttp-170) REVERT: H 12 ASP cc_start: 0.8823 (t70) cc_final: 0.8611 (t0) REVERT: H 26 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8979 (mt-10) REVERT: H 39 ARG cc_start: 0.8598 (ttt180) cc_final: 0.8345 (ttp-170) REVERT: H 42 TYR cc_start: 0.8926 (t80) cc_final: 0.8656 (t80) REVERT: H 46 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8140 (ttmm) REVERT: J 34 LYS cc_start: 0.8772 (mttt) cc_final: 0.8557 (mttp) REVERT: L 39 ARG cc_start: 0.8546 (ttt90) cc_final: 0.8094 (ttp-170) REVERT: G 26 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8893 (mt-10) outliers start: 8 outliers final: 6 residues processed: 134 average time/residue: 1.7374 time to fit residues: 239.7492 Evaluate side-chains 133 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 H residue 46 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.088521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.073313 restraints weight = 6642.737| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.80 r_work: 0.2844 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 5340 Z= 0.342 Angle : 0.514 4.402 7164 Z= 0.301 Chirality : 0.041 0.112 600 Planarity : 0.004 0.037 960 Dihedral : 4.557 15.877 744 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.63 % Allowed : 9.65 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.20), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.15), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 53 HIS 0.001 0.000 HIS D 37 PHE 0.012 0.002 PHE D 3 TYR 0.012 0.002 TYR C 42 ARG 0.008 0.001 ARG E 47 *********************** 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 141 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.602 Fit side-chains REVERT: A 2 SER cc_start: 0.9010 (t) cc_final: 0.8726 (t) REVERT: A 15 ARG cc_start: 0.8741 (mtt180) cc_final: 0.8249 (mtm180) REVERT: A 34 LYS cc_start: 0.8967 (mttt) cc_final: 0.8673 (mtmt) REVERT: B 39 ARG cc_start: 0.8820 (ttt90) cc_final: 0.8478 (tmm-80) REVERT: C 12 ASP cc_start: 0.8923 (t70) cc_final: 0.8647 (t70) REVERT: C 15 ARG cc_start: 0.8562 (mtt180) cc_final: 0.7192 (mpp-170) REVERT: C 16 ASP cc_start: 0.8904 (m-30) cc_final: 0.8682 (m-30) REVERT: C 34 LYS cc_start: 0.8958 (mttt) cc_final: 0.8701 (mttt) REVERT: C 39 ARG cc_start: 0.8731 (ttt180) cc_final: 0.8107 (ttp-170) REVERT: D 39 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8406 (ttp-170) REVERT: F 39 ARG cc_start: 0.8692 (ttt90) cc_final: 0.7937 (ttp-170) REVERT: H 12 ASP cc_start: 0.8915 (t70) cc_final: 0.8607 (t70) REVERT: H 15 ARG cc_start: 0.8436 (mtt180) cc_final: 0.7276 (mpp-170) REVERT: H 39 ARG cc_start: 0.8615 (ttt180) cc_final: 0.8364 (ttt180) REVERT: H 42 TYR cc_start: 0.8927 (t80) cc_final: 0.8691 (t80) REVERT: J 39 ARG cc_start: 0.8743 (ttp-110) cc_final: 0.8525 (ttm-80) REVERT: L 15 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6647 (mpt180) REVERT: G 26 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8905 (mt-10) outliers start: 12 outliers final: 6 residues processed: 137 average time/residue: 1.7132 time to fit residues: 241.4929 Evaluate side-chains 134 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.087124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.072008 restraints weight = 6581.348| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.77 r_work: 0.2816 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.033 5340 Z= 0.532 Angle : 0.592 5.698 7164 Z= 0.344 Chirality : 0.043 0.111 600 Planarity : 0.005 0.038 960 Dihedral : 4.875 16.276 744 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.19 % Allowed : 11.62 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (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 TRP 0.005 0.001 TRP B 18 HIS 0.002 0.001 HIS G 37 PHE 0.014 0.002 PHE D 3 TYR 0.011 0.002 TYR F 29 ARG 0.006 0.001 ARG E 47 *********************** 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 138 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.574 Fit side-chains REVERT: A 15 ARG cc_start: 0.8766 (mtt180) cc_final: 0.8257 (mtm180) REVERT: A 34 LYS cc_start: 0.8936 (mttt) cc_final: 0.8666 (mttp) REVERT: B 39 ARG cc_start: 0.8830 (ttt90) cc_final: 0.8505 (tmm-80) REVERT: C 12 ASP cc_start: 0.8869 (t70) cc_final: 0.8557 (t70) REVERT: C 15 ARG cc_start: 0.8565 (mtt180) cc_final: 0.7210 (mpp-170) REVERT: C 16 ASP cc_start: 0.8927 (m-30) cc_final: 0.8715 (m-30) REVERT: C 34 LYS cc_start: 0.8956 (mttt) cc_final: 0.8726 (mttp) REVERT: C 39 ARG cc_start: 0.8674 (ttt180) cc_final: 0.8089 (ttp-170) REVERT: D 39 ARG cc_start: 0.8830 (ttm-80) cc_final: 0.8467 (ttp-170) REVERT: F 39 ARG cc_start: 0.8679 (ttt90) cc_final: 0.7975 (ttp-170) REVERT: H 12 ASP cc_start: 0.8819 (t70) cc_final: 0.8506 (t70) REVERT: H 15 ARG cc_start: 0.8442 (mtt180) cc_final: 0.7308 (mpp-170) REVERT: H 42 TYR cc_start: 0.8941 (t80) cc_final: 0.8643 (t80) REVERT: L 15 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6781 (mpt180) REVERT: G 26 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8886 (mt-10) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 1.6667 time to fit residues: 231.4848 Evaluate side-chains 133 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.089902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074638 restraints weight = 6349.025| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.77 r_work: 0.2873 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2303 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= 0.225 Angle : 0.467 4.248 7164 Z= 0.274 Chirality : 0.040 0.114 600 Planarity : 0.003 0.023 960 Dihedral : 4.459 15.723 744 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.19 % Allowed : 11.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (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 TRP 0.003 0.001 TRP B 18 HIS 0.001 0.000 HIS J 37 PHE 0.009 0.001 PHE K 11 TYR 0.010 0.001 TYR I 42 ARG 0.005 0.000 ARG E 47 *********************** 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 136 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.544 Fit side-chains REVERT: A 2 SER cc_start: 0.9000 (t) cc_final: 0.8685 (t) REVERT: A 15 ARG cc_start: 0.8703 (mtt180) cc_final: 0.8233 (mtm180) REVERT: A 34 LYS cc_start: 0.8971 (mttt) cc_final: 0.8746 (mttp) REVERT: B 12 ASP cc_start: 0.8694 (t70) cc_final: 0.8467 (t70) REVERT: B 39 ARG cc_start: 0.8822 (ttt90) cc_final: 0.8500 (tmm-80) REVERT: C 12 ASP cc_start: 0.8872 (t70) cc_final: 0.8583 (t70) REVERT: C 15 ARG cc_start: 0.8551 (mtt180) cc_final: 0.7178 (mpp-170) REVERT: C 16 ASP cc_start: 0.8968 (m-30) cc_final: 0.8720 (m-30) REVERT: C 34 LYS cc_start: 0.8942 (mttt) cc_final: 0.8699 (mttt) REVERT: C 39 ARG cc_start: 0.8686 (ttt180) cc_final: 0.8091 (ttp-170) REVERT: D 39 ARG cc_start: 0.8845 (ttm-80) cc_final: 0.8454 (ttp-170) REVERT: D 46 LYS cc_start: 0.8547 (mttm) cc_final: 0.7754 (tttt) REVERT: F 39 ARG cc_start: 0.8687 (ttt90) cc_final: 0.8354 (ttp-170) REVERT: H 12 ASP cc_start: 0.8916 (t70) cc_final: 0.8634 (t0) REVERT: H 39 ARG cc_start: 0.8664 (ttm-80) cc_final: 0.8251 (ttp-170) REVERT: H 42 TYR cc_start: 0.8881 (t80) cc_final: 0.8603 (t80) REVERT: J 39 ARG cc_start: 0.8801 (ttt180) cc_final: 0.8516 (ttp-110) REVERT: L 15 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6363 (mpt180) REVERT: L 39 ARG cc_start: 0.8520 (ttt90) cc_final: 0.8042 (ttp-170) REVERT: G 26 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8857 (mt-10) outliers start: 10 outliers final: 6 residues processed: 133 average time/residue: 1.5892 time to fit residues: 218.1885 Evaluate side-chains 129 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.089135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074016 restraints weight = 6495.952| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.76 r_work: 0.2862 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5340 Z= 0.271 Angle : 0.486 4.868 7164 Z= 0.285 Chirality : 0.040 0.113 600 Planarity : 0.003 0.032 960 Dihedral : 4.486 16.169 744 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.97 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (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 TRP 0.004 0.001 TRP B 18 HIS 0.001 0.000 HIS I 37 PHE 0.009 0.001 PHE K 11 TYR 0.021 0.001 TYR E 42 ARG 0.008 0.001 ARG B 47 *********************** 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 135 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.594 Fit side-chains REVERT: A 2 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8749 (t) REVERT: A 15 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8248 (mtm180) REVERT: A 34 LYS cc_start: 0.8966 (mttt) cc_final: 0.8723 (mttp) REVERT: B 12 ASP cc_start: 0.8669 (t70) cc_final: 0.8421 (t70) REVERT: B 39 ARG cc_start: 0.8827 (ttt90) cc_final: 0.8517 (tmm-80) REVERT: C 12 ASP cc_start: 0.8873 (t70) cc_final: 0.8579 (t70) REVERT: C 15 ARG cc_start: 0.8546 (mtt180) cc_final: 0.7180 (mpp-170) REVERT: C 16 ASP cc_start: 0.9056 (m-30) cc_final: 0.8809 (m-30) REVERT: C 34 LYS cc_start: 0.8951 (mttt) cc_final: 0.8700 (mttp) REVERT: C 39 ARG cc_start: 0.8685 (ttt180) cc_final: 0.8098 (ttp-170) REVERT: D 39 ARG cc_start: 0.8872 (ttm-80) cc_final: 0.8473 (ttp-170) REVERT: D 46 LYS cc_start: 0.8523 (mttm) cc_final: 0.7753 (tttt) REVERT: F 39 ARG cc_start: 0.8685 (ttt90) cc_final: 0.8338 (ttp-170) REVERT: H 12 ASP cc_start: 0.8915 (t70) cc_final: 0.8630 (t0) REVERT: H 15 ARG cc_start: 0.8444 (mtt180) cc_final: 0.7240 (mpp-170) REVERT: H 39 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.8262 (ttp-170) REVERT: H 42 TYR cc_start: 0.8890 (t80) cc_final: 0.8667 (t80) REVERT: J 39 ARG cc_start: 0.8739 (ttt180) cc_final: 0.8522 (ttp-110) REVERT: K 39 ARG cc_start: 0.8349 (ttp-170) cc_final: 0.7938 (ttp-110) REVERT: L 15 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6393 (mpt180) REVERT: L 39 ARG cc_start: 0.8536 (ttt90) cc_final: 0.8052 (ttp-170) REVERT: G 26 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8844 (mt-10) outliers start: 9 outliers final: 6 residues processed: 132 average time/residue: 1.7173 time to fit residues: 233.4463 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 : 0.540 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3263 r_free = 0.3263 target = 0.088621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.073487 restraints weight = 6436.276| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.75 r_work: 0.2846 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 5340 Z= 0.338 Angle : 0.510 5.404 7164 Z= 0.298 Chirality : 0.041 0.113 600 Planarity : 0.004 0.027 960 Dihedral : 4.601 16.523 744 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.19 % Allowed : 12.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (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 TRP 0.005 0.001 TRP B 18 HIS 0.001 0.000 HIS J 37 PHE 0.011 0.002 PHE D 3 TYR 0.022 0.002 TYR G 42 ARG 0.006 0.000 ARG B 47 *********************** 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 140 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.549 Fit side-chains REVERT: A 2 SER cc_start: 0.9097 (OUTLIER) cc_final: 0.8783 (t) REVERT: A 15 ARG cc_start: 0.8752 (mtt180) cc_final: 0.8261 (mtm180) REVERT: B 39 ARG cc_start: 0.8835 (ttt90) cc_final: 0.8522 (tmm-80) REVERT: C 12 ASP cc_start: 0.8891 (t70) cc_final: 0.8605 (t70) REVERT: C 15 ARG cc_start: 0.8548 (mtt180) cc_final: 0.7188 (mpp-170) REVERT: C 16 ASP cc_start: 0.9076 (m-30) cc_final: 0.8836 (m-30) REVERT: C 34 LYS cc_start: 0.8939 (mttt) cc_final: 0.8693 (mttp) REVERT: C 39 ARG cc_start: 0.8668 (ttt180) cc_final: 0.8103 (ttp-170) REVERT: D 39 ARG cc_start: 0.8867 (ttm-80) cc_final: 0.8477 (ttp-170) REVERT: D 46 LYS cc_start: 0.8530 (mttm) cc_final: 0.7758 (tttt) REVERT: F 39 ARG cc_start: 0.8688 (ttt90) cc_final: 0.7952 (ttp-170) REVERT: H 12 ASP cc_start: 0.8836 (t70) cc_final: 0.8513 (t70) REVERT: H 15 ARG cc_start: 0.8446 (mtt180) cc_final: 0.7256 (mpp-170) REVERT: H 42 TYR cc_start: 0.8873 (t80) cc_final: 0.8666 (t80) REVERT: L 15 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6511 (mpt180) REVERT: G 26 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8840 (mt-10) outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 1.6976 time to fit residues: 239.4217 Evaluate side-chains 134 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.089633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.074598 restraints weight = 6487.090| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.75 r_work: 0.2874 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2426 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= 0.243 Angle : 0.473 4.883 7164 Z= 0.277 Chirality : 0.040 0.113 600 Planarity : 0.003 0.025 960 Dihedral : 4.434 15.972 744 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.75 % Allowed : 13.60 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (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 TRP 0.004 0.001 TRP B 18 HIS 0.001 0.000 HIS D 37 PHE 0.009 0.001 PHE I 3 TYR 0.022 0.001 TYR I 42 ARG 0.007 0.000 ARG B 47 *********************** 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 136 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.567 Fit side-chains REVERT: A 2 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8723 (t) REVERT: A 15 ARG cc_start: 0.8710 (mtt180) cc_final: 0.8230 (mtm180) REVERT: B 12 ASP cc_start: 0.8675 (t70) cc_final: 0.8450 (t70) REVERT: B 39 ARG cc_start: 0.8792 (ttt90) cc_final: 0.8508 (tmm-80) REVERT: C 12 ASP cc_start: 0.8885 (t70) cc_final: 0.8604 (t70) REVERT: C 15 ARG cc_start: 0.8545 (mtt180) cc_final: 0.7163 (mpp-170) REVERT: C 16 ASP cc_start: 0.9043 (m-30) cc_final: 0.8803 (m-30) REVERT: C 34 LYS cc_start: 0.8896 (mttt) cc_final: 0.8691 (mttt) REVERT: C 39 ARG cc_start: 0.8677 (ttt180) cc_final: 0.8097 (ttp-170) REVERT: E 15 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8024 (mtm180) REVERT: D 39 ARG cc_start: 0.8870 (ttm-80) cc_final: 0.8478 (ttp-170) REVERT: D 46 LYS cc_start: 0.8505 (mttm) cc_final: 0.7734 (tttt) REVERT: F 39 ARG cc_start: 0.8665 (ttt90) cc_final: 0.7965 (ttp-170) REVERT: H 12 ASP cc_start: 0.8917 (t70) cc_final: 0.8629 (t0) REVERT: H 15 ARG cc_start: 0.8437 (mtt180) cc_final: 0.7288 (mpp-170) REVERT: L 15 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6358 (mpt180) REVERT: G 26 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8855 (mt-10) outliers start: 8 outliers final: 6 residues processed: 134 average time/residue: 1.6086 time to fit residues: 222.1128 Evaluate side-chains 134 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.087511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.072396 restraints weight = 6584.638| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.77 r_work: 0.2830 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2400 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= 0.487 Angle : 0.572 6.373 7164 Z= 0.333 Chirality : 0.042 0.113 600 Planarity : 0.005 0.034 960 Dihedral : 4.812 17.889 744 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.97 % Allowed : 13.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.002 0.001 HIS J 37 PHE 0.014 0.002 PHE I 3 TYR 0.035 0.002 TYR G 42 ARG 0.007 0.001 ARG I 39 ********************** 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 135 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.531 Fit side-chains REVERT: A 15 ARG cc_start: 0.8765 (mtt180) cc_final: 0.8203 (mtm-85) REVERT: B 39 ARG cc_start: 0.8840 (ttt90) cc_final: 0.8525 (tmm-80) REVERT: C 12 ASP cc_start: 0.8866 (t70) cc_final: 0.8572 (t70) REVERT: C 15 ARG cc_start: 0.8570 (mtt180) cc_final: 0.7192 (mpp-170) REVERT: C 16 ASP cc_start: 0.9071 (m-30) cc_final: 0.8788 (m-30) REVERT: C 39 ARG cc_start: 0.8717 (ttt180) cc_final: 0.8122 (ttp-170) REVERT: D 39 ARG cc_start: 0.8873 (ttm-80) cc_final: 0.8516 (ttp-170) REVERT: D 46 LYS cc_start: 0.8534 (mttm) cc_final: 0.7722 (tttt) REVERT: F 39 ARG cc_start: 0.8686 (ttt90) cc_final: 0.7929 (ttp-170) REVERT: H 12 ASP cc_start: 0.8832 (t70) cc_final: 0.8522 (t70) REVERT: H 15 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7259 (mpp-170) REVERT: L 15 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6708 (mpt180) REVERT: G 26 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8870 (mt-10) outliers start: 9 outliers final: 8 residues processed: 133 average time/residue: 1.6769 time to fit residues: 229.5224 Evaluate side-chains 132 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 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 = 0.3293 r_free = 0.3293 target = 0.089688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.074601 restraints weight = 6563.742| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.78 r_work: 0.2881 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2441 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= 0.232 Angle : 0.475 5.335 7164 Z= 0.279 Chirality : 0.040 0.113 600 Planarity : 0.003 0.032 960 Dihedral : 4.462 16.682 744 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.41 % Allowed : 13.82 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 18 HIS 0.001 0.000 HIS D 37 PHE 0.009 0.001 PHE I 3 TYR 0.030 0.002 TYR G 42 ARG 0.007 0.001 ARG I 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4781.71 seconds wall clock time: 84 minutes 50.62 seconds (5090.62 seconds total)