Starting phenix.real_space_refine on Mon Sep 23 20:14:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mst_9232/09_2024/6mst_9232.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mst_9232/09_2024/6mst_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mst_9232/09_2024/6mst_9232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mst_9232/09_2024/6mst_9232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mst_9232/09_2024/6mst_9232.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mst_9232/09_2024/6mst_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.16, per 1000 atoms: 0.80 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: 2.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.07 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: 1.47 Time building geometry restraints manager: 2.92 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 22.200 Find NCS groups from input model: 0.210 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:18.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.910 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.656 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.8449 time to fit residues: 240.7159 Evaluate side-chains 114 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 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 fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 0.575 Fit side-chains REVERT: B 39 ARG cc_start: 0.8058 (ttt90) cc_final: 0.7552 (tmm-80) REVERT: C 15 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7417 (mpp-170) REVERT: D 39 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7686 (ttp-170) REVERT: H 12 ASP cc_start: 0.8263 (t70) cc_final: 0.7999 (t70) REVERT: L 15 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.5915 (mpt180) REVERT: G 26 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8058 (mt-10) outliers start: 7 outliers final: 4 residues processed: 141 average time/residue: 1.7807 time to fit residues: 258.2554 Evaluate side-chains 134 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 30 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2123 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= 0.338 Angle : 0.546 4.829 7164 Z= 0.314 Chirality : 0.041 0.112 600 Planarity : 0.004 0.044 960 Dihedral : 4.658 16.937 744 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.19 % Allowed : 10.31 % Favored : 87.50 % 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: -3.89 (0.20), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.15), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 53 HIS 0.002 0.000 HIS D 37 PHE 0.012 0.002 PHE D 3 TYR 0.014 0.002 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 141 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: B 39 ARG cc_start: 0.8040 (ttt90) cc_final: 0.7811 (tmm-80) REVERT: C 15 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7396 (mpp-170) REVERT: H 12 ASP cc_start: 0.8230 (t70) cc_final: 0.7980 (t70) REVERT: L 15 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.5930 (mpt180) REVERT: G 26 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8092 (mt-10) outliers start: 10 outliers final: 6 residues processed: 139 average time/residue: 1.5893 time to fit residues: 227.6404 Evaluate side-chains 133 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 5340 Z= 0.380 Angle : 0.544 5.089 7164 Z= 0.315 Chirality : 0.041 0.110 600 Planarity : 0.004 0.038 960 Dihedral : 4.683 17.224 744 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.41 % Allowed : 12.28 % 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 (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: -3.79 (0.20), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 53 HIS 0.001 0.000 HIS J 37 PHE 0.013 0.002 PHE D 3 TYR 0.023 0.002 TYR H 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 140 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 0.581 Fit side-chains REVERT: C 15 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7396 (mpp-170) REVERT: D 39 ARG cc_start: 0.7897 (ttt90) cc_final: 0.7614 (ttt180) REVERT: H 12 ASP cc_start: 0.8322 (t70) cc_final: 0.8011 (t70) REVERT: L 15 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.5922 (mpt180) outliers start: 11 outliers final: 8 residues processed: 137 average time/residue: 1.6922 time to fit residues: 238.5816 Evaluate side-chains 135 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER 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 15 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.034 5340 Z= 0.533 Angle : 0.601 6.144 7164 Z= 0.346 Chirality : 0.043 0.114 600 Planarity : 0.005 0.041 960 Dihedral : 4.922 17.092 744 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.85 % Allowed : 12.06 % 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 (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: -3.72 (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 TRP 0.005 0.001 TRP B 18 HIS 0.002 0.001 HIS J 37 PHE 0.014 0.002 PHE K 11 TYR 0.025 0.002 TYR H 42 ARG 0.005 0.001 ARG I 39 *********************** 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 143 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.601 Fit side-chains REVERT: C 15 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7415 (mpp-170) REVERT: H 12 ASP cc_start: 0.8263 (t70) cc_final: 0.7956 (t70) REVERT: L 15 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.5992 (mpt180) outliers start: 13 outliers final: 8 residues processed: 139 average time/residue: 1.6730 time to fit residues: 239.3356 Evaluate side-chains 137 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER 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 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 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 5340 Z= 0.205 Angle : 0.463 4.103 7164 Z= 0.271 Chirality : 0.040 0.114 600 Planarity : 0.003 0.027 960 Dihedral : 4.430 16.589 744 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.41 % Allowed : 12.94 % 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: -3.68 (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 0.003 0.001 TRP B 18 HIS 0.001 0.000 HIS D 37 PHE 0.009 0.001 PHE D 3 TYR 0.020 0.001 TYR H 42 ARG 0.006 0.000 ARG I 39 *********************** 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 fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 0.750 Fit side-chains REVERT: H 12 ASP cc_start: 0.8330 (t70) cc_final: 0.7987 (t70) REVERT: G 42 TYR cc_start: 0.8351 (t80) cc_final: 0.8059 (t80) outliers start: 11 outliers final: 7 residues processed: 135 average time/residue: 1.7999 time to fit residues: 251.2237 Evaluate side-chains 132 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2549 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= 0.483 Angle : 0.573 5.735 7164 Z= 0.332 Chirality : 0.042 0.111 600 Planarity : 0.004 0.032 960 Dihedral : 4.818 16.945 744 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.75 % Allowed : 14.47 % 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: -3.69 (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 TRP 0.005 0.001 TRP B 18 HIS 0.001 0.001 HIS F 37 PHE 0.014 0.002 PHE D 3 TYR 0.029 0.002 TYR H 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 138 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 0.547 Fit side-chains REVERT: H 12 ASP cc_start: 0.8286 (t70) cc_final: 0.7980 (t70) outliers start: 8 outliers final: 7 residues processed: 137 average time/residue: 1.5869 time to fit residues: 223.9187 Evaluate side-chains 135 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 5340 Z= 0.166 Angle : 0.447 3.880 7164 Z= 0.262 Chirality : 0.040 0.117 600 Planarity : 0.003 0.034 960 Dihedral : 4.291 15.593 744 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.54 % Allowed : 14.47 % Favored : 83.99 % 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 : -2.80 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP L 18 HIS 0.001 0.000 HIS D 37 PHE 0.008 0.001 PHE D 3 TYR 0.025 0.001 TYR C 42 ARG 0.008 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 137 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.593 Fit side-chains REVERT: D 39 ARG cc_start: 0.7818 (ttt90) cc_final: 0.7445 (ttp-170) REVERT: H 12 ASP cc_start: 0.8341 (t70) cc_final: 0.8081 (t0) REVERT: I 26 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7941 (mt-10) REVERT: G 42 TYR cc_start: 0.8323 (t80) cc_final: 0.8066 (t80) outliers start: 7 outliers final: 7 residues processed: 136 average time/residue: 1.6752 time to fit residues: 234.9655 Evaluate side-chains 133 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 5340 Z= 0.391 Angle : 0.544 5.799 7164 Z= 0.315 Chirality : 0.041 0.112 600 Planarity : 0.004 0.044 960 Dihedral : 4.685 16.843 744 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.97 % Allowed : 14.47 % Favored : 83.55 % 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 0.005 0.001 TRP B 18 HIS 0.001 0.000 HIS L 37 PHE 0.013 0.002 PHE D 3 TYR 0.032 0.002 TYR H 42 ARG 0.008 0.001 ARG I 39 *********************** 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 140 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: H 12 ASP cc_start: 0.8310 (t70) cc_final: 0.7986 (t70) REVERT: L 15 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.5879 (mpt180) outliers start: 9 outliers final: 7 residues processed: 139 average time/residue: 1.6281 time to fit residues: 233.1380 Evaluate side-chains 135 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2626 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= 0.209 Angle : 0.479 4.724 7164 Z= 0.280 Chirality : 0.040 0.114 600 Planarity : 0.003 0.034 960 Dihedral : 4.428 16.556 744 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.75 % Allowed : 14.91 % Favored : 83.33 % 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 0.003 0.001 TRP G 53 HIS 0.001 0.000 HIS L 37 PHE 0.010 0.001 PHE D 3 TYR 0.029 0.002 TYR C 42 ARG 0.014 0.001 ARG D 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 138 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 0.584 Fit side-chains REVERT: H 12 ASP cc_start: 0.8349 (t70) cc_final: 0.8068 (t0) REVERT: I 26 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7930 (mt-10) REVERT: L 15 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.5872 (mpt180) outliers start: 8 outliers final: 7 residues processed: 137 average time/residue: 1.5225 time to fit residues: 215.1414 Evaluate side-chains 135 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073902 restraints weight = 6588.014| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.76 r_work: 0.2874 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 5340 Z= 0.345 Angle : 0.527 6.051 7164 Z= 0.306 Chirality : 0.041 0.114 600 Planarity : 0.004 0.035 960 Dihedral : 4.643 17.370 744 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.19 % Allowed : 14.47 % Favored : 83.33 % 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 L 37 PHE 0.012 0.002 PHE D 3 TYR 0.037 0.002 TYR H 42 ARG 0.007 0.000 ARG I 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3715.18 seconds wall clock time: 65 minutes 41.42 seconds (3941.42 seconds total)