Starting phenix.real_space_refine on Sun Mar 10 21:23:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mst_9232/03_2024/6mst_9232.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mst_9232/03_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_9232/03_2024/6mst_9232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mst_9232/03_2024/6mst_9232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mst_9232/03_2024/6mst_9232.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mst_9232/03_2024/6mst_9232.pdb" } 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 Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "F PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "I PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 15": "NH1" <-> "NH2" Residue "J PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 15": "NH1" <-> "NH2" Residue "K PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 15": "NH1" <-> "NH2" Residue "L PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 15": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5172 Number of models: 1 Model: "" Number of chains: 12 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} Chain: "B" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "C" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "E" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "D" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "F" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "H" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "I" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "J" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "K" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "L" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Time building chain proxies: 3.04, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 2.04 Conformation dependent library (CDL) restraints added in 943.9 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: 0.76 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: 2.13 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: 100.82 - 107.45: 254 107.45 - 114.08: 2353 114.08 - 120.71: 2410 120.71 - 127.34: 2075 127.34 - 133.97: 72 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 2.520 nonbonded pdb=" O GLY C 31 " pdb=" N SER F 2 " model vdw 2.307 2.520 nonbonded pdb=" N SER J 2 " pdb=" O GLY G 31 " model vdw 2.307 2.520 nonbonded pdb=" N SER C 2 " pdb=" O GLY D 31 " model vdw 2.308 2.520 nonbonded pdb=" N SER I 2 " pdb=" O GLY J 31 " model vdw 2.316 2.520 ... (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 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: 1.230 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: 4.170 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.560 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- 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 : 0.598 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.7418 time to fit residues: 227.6398 Evaluate side-chains 114 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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: 0.8757 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 5340 Z= 0.444 Angle : 0.613 5.535 7164 Z= 0.346 Chirality : 0.042 0.113 600 Planarity : 0.005 0.030 960 Dihedral : 4.858 15.856 744 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.54 % Allowed : 6.36 % Favored : 92.11 % 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: -4.05 (0.19), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.15), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 53 HIS 0.002 0.001 HIS J 37 PHE 0.013 0.002 PHE J 11 TYR 0.023 0.002 TYR L 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 142 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 1.142 Fit side-chains REVERT: B 39 ARG cc_start: 0.8078 (ttt90) cc_final: 0.7537 (tmm-80) REVERT: C 15 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7461 (mpp-170) REVERT: D 39 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7761 (ttp-170) REVERT: H 12 ASP cc_start: 0.8324 (t70) cc_final: 0.8061 (t70) REVERT: L 15 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.5975 (mpt180) outliers start: 7 outliers final: 2 residues processed: 140 average time/residue: 1.7038 time to fit residues: 245.1001 Evaluate side-chains 134 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain K 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: 1.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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: 0.8758 moved from start: 0.2185 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= 0.339 Angle : 0.545 4.813 7164 Z= 0.312 Chirality : 0.041 0.112 600 Planarity : 0.004 0.037 960 Dihedral : 4.583 14.659 744 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.32 % Allowed : 10.75 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.83 (0.20), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.15), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 53 HIS 0.002 0.001 HIS D 37 PHE 0.011 0.002 PHE J 11 TYR 0.018 0.002 TYR C 42 ARG 0.007 0.001 ARG L 39 *********************** 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 136 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: B 39 ARG cc_start: 0.8056 (ttt90) cc_final: 0.7836 (tmm-80) REVERT: C 15 ARG cc_start: 0.7723 (mtt180) cc_final: 0.7444 (mpp-170) REVERT: H 12 ASP cc_start: 0.8220 (t70) cc_final: 0.7980 (t70) REVERT: H 42 TYR cc_start: 0.8530 (t80) cc_final: 0.8308 (t80) REVERT: L 15 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.5961 (mpt180) outliers start: 6 outliers final: 3 residues processed: 134 average time/residue: 1.7175 time to fit residues: 236.4945 Evaluate side-chains 131 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 15 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.8772 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 5340 Z= 0.424 Angle : 0.571 5.427 7164 Z= 0.326 Chirality : 0.041 0.110 600 Planarity : 0.004 0.032 960 Dihedral : 4.687 15.008 744 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.32 % Allowed : 11.40 % Favored : 87.28 % 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: -3.70 (0.20), 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 0.005 0.001 TRP B 18 HIS 0.002 0.001 HIS F 37 PHE 0.012 0.002 PHE E 3 TYR 0.012 0.002 TYR F 29 ARG 0.005 0.001 ARG L 39 *********************** 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: 6 poor density : 134 time to evaluate : 0.585 Fit side-chains REVERT: C 15 ARG cc_start: 0.7741 (mtt180) cc_final: 0.7454 (mpp-170) REVERT: D 39 ARG cc_start: 0.7875 (ttt90) cc_final: 0.7657 (ttt180) REVERT: H 12 ASP cc_start: 0.8303 (t70) cc_final: 0.8025 (t70) REVERT: I 46 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7862 (mttm) REVERT: L 15 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6032 (mpt180) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 1.6837 time to fit residues: 237.0956 Evaluate side-chains 138 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain K residue 2 SER Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 15 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 0.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.8774 moved from start: 0.2392 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= 0.437 Angle : 0.569 5.739 7164 Z= 0.325 Chirality : 0.041 0.110 600 Planarity : 0.004 0.033 960 Dihedral : 4.724 15.307 744 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.54 % Allowed : 11.18 % Favored : 87.28 % 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: -3.63 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (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 J 37 PHE 0.013 0.002 PHE K 11 TYR 0.021 0.002 TYR H 42 ARG 0.004 0.001 ARG L 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 138 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 0.610 Fit side-chains REVERT: C 15 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7446 (mpp-170) REVERT: D 39 ARG cc_start: 0.7885 (ttt90) cc_final: 0.7544 (ttt180) REVERT: H 12 ASP cc_start: 0.8312 (t70) cc_final: 0.8017 (t70) REVERT: L 15 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6021 (mpt180) outliers start: 7 outliers final: 3 residues processed: 135 average time/residue: 1.7082 time to fit residues: 237.1400 Evaluate side-chains 135 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain K 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: 5.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.8757 moved from start: 0.2407 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= 0.306 Angle : 0.519 5.253 7164 Z= 0.298 Chirality : 0.040 0.111 600 Planarity : 0.004 0.041 960 Dihedral : 4.580 15.734 744 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.10 % Allowed : 11.84 % Favored : 87.06 % 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: -3.57 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (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 0.010 0.001 PHE K 11 TYR 0.022 0.001 TYR H 42 ARG 0.008 0.001 ARG B 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 131 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.623 Fit side-chains REVERT: B 17 MET cc_start: 0.9181 (ttp) cc_final: 0.8870 (ttm) REVERT: C 15 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7455 (mpp-170) REVERT: C 17 MET cc_start: 0.9054 (ttp) cc_final: 0.8824 (ttp) REVERT: H 12 ASP cc_start: 0.8224 (t70) cc_final: 0.7946 (t70) REVERT: L 15 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.5936 (mpt180) outliers start: 5 outliers final: 2 residues processed: 129 average time/residue: 1.7086 time to fit residues: 226.9200 Evaluate side-chains 125 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain K 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 32 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.8779 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 5340 Z= 0.477 Angle : 0.588 5.786 7164 Z= 0.336 Chirality : 0.042 0.112 600 Planarity : 0.005 0.035 960 Dihedral : 4.807 16.158 744 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.10 % Allowed : 13.16 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.56 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (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 D 37 PHE 0.013 0.002 PHE K 11 TYR 0.024 0.002 TYR H 42 ARG 0.008 0.001 ARG I 39 *********************** 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 134 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.599 Fit side-chains REVERT: B 17 MET cc_start: 0.9211 (ttp) cc_final: 0.8890 (ttm) REVERT: C 15 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7457 (mpp-170) REVERT: C 17 MET cc_start: 0.9050 (ttp) cc_final: 0.8832 (ttp) REVERT: H 12 ASP cc_start: 0.8263 (t70) cc_final: 0.7947 (t70) REVERT: I 46 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7850 (mttm) REVERT: L 15 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6043 (mpt180) outliers start: 5 outliers final: 2 residues processed: 132 average time/residue: 1.6836 time to fit residues: 228.5323 Evaluate side-chains 132 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain K 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 28 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8735 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5340 Z= 0.184 Angle : 0.470 4.222 7164 Z= 0.272 Chirality : 0.040 0.112 600 Planarity : 0.003 0.029 960 Dihedral : 4.305 16.655 744 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.10 % Allowed : 12.72 % 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: -3.56 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 18 HIS 0.001 0.000 HIS D 37 PHE 0.008 0.001 PHE K 11 TYR 0.019 0.001 TYR E 42 ARG 0.007 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 131 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.595 Fit side-chains REVERT: C 15 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7426 (mpp-170) REVERT: H 12 ASP cc_start: 0.8222 (t70) cc_final: 0.7922 (t70) outliers start: 5 outliers final: 2 residues processed: 128 average time/residue: 1.5717 time to fit residues: 207.3098 Evaluate side-chains 126 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain L residue 17 MET 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: 3.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8736 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5340 Z= 0.211 Angle : 0.475 4.161 7164 Z= 0.276 Chirality : 0.040 0.111 600 Planarity : 0.003 0.028 960 Dihedral : 4.326 16.736 744 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.44 % Allowed : 14.69 % 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: -3.54 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (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 L 37 PHE 0.008 0.001 PHE E 3 TYR 0.028 0.001 TYR G 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 126 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.611 Fit side-chains REVERT: C 15 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7419 (mpp-170) REVERT: H 12 ASP cc_start: 0.8222 (t70) cc_final: 0.7922 (t70) outliers start: 2 outliers final: 2 residues processed: 125 average time/residue: 1.5986 time to fit residues: 205.8533 Evaluate side-chains 125 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain L residue 17 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 0.0070 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 chunk 19 optimal weight: 0.6980 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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: 0.8729 moved from start: 0.2623 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= 0.196 Angle : 0.471 4.157 7164 Z= 0.274 Chirality : 0.040 0.111 600 Planarity : 0.003 0.028 960 Dihedral : 4.273 16.708 744 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.44 % Allowed : 14.69 % 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: -3.53 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (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 L 37 PHE 0.008 0.001 PHE E 3 TYR 0.028 0.001 TYR E 42 ARG 0.007 0.000 ARG B 47 ********************** 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 128 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.598 Fit side-chains REVERT: C 15 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7414 (mpp-170) REVERT: C 46 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7852 (tmtm) REVERT: H 12 ASP cc_start: 0.8214 (t70) cc_final: 0.7907 (t70) outliers start: 2 outliers final: 2 residues processed: 127 average time/residue: 1.5908 time to fit residues: 208.2980 Evaluate side-chains 126 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain L residue 17 MET 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: 2.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.086673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.071860 restraints weight = 6591.643| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.73 r_work: 0.2820 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 5340 Z= 0.610 Angle : 0.630 6.518 7164 Z= 0.362 Chirality : 0.044 0.116 600 Planarity : 0.005 0.042 960 Dihedral : 4.875 16.524 744 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.66 % Allowed : 14.91 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.54 (0.21), residues: 624 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.16), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 18 HIS 0.002 0.001 HIS G 37 PHE 0.015 0.002 PHE E 3 TYR 0.038 0.003 TYR E 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: 3525.95 seconds wall clock time: 62 minutes 20.14 seconds (3740.14 seconds total)