Starting phenix.real_space_refine on Sun Mar 10 21:42:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fna_3241/03_2024/5fna_3241.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fna_3241/03_2024/5fna_3241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fna_3241/03_2024/5fna_3241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fna_3241/03_2024/5fna_3241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fna_3241/03_2024/5fna_3241.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fna_3241/03_2024/5fna_3241.pdb" } resolution = 4.8 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 ------------------------------------------------------------------------------- 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= 0.718 sd= 0.877 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 48 5.16 5 C 3312 2.51 5 N 920 2.21 5 O 1048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5328 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "B" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "D" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "E" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "F" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "H" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Time building chain proxies: 3.41, per 1000 atoms: 0.64 Number of scatterers: 5328 At special positions: 0 Unit cell: (80.91, 83.52, 81.78, 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 48 16.00 O 1048 8.00 N 920 7.00 C 3312 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: 1.98 Conformation dependent library (CDL) restraints added in 911.5 milliseconds 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE A 13 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG A 14 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.805A pdb=" N ALA A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 8 Processing helix chain 'B' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE B 13 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.805A pdb=" N ALA B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 8 Processing helix chain 'C' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG C 14 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 42 through 45 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.806A pdb=" N ALA C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.588A pdb=" N CYS C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 8 Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE D 13 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG D 14 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 31 removed outlier: 5.214A pdb=" N GLY D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 41 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 59 removed outlier: 3.805A pdb=" N ALA D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 8 Processing helix chain 'E' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE E 13 " --> pdb=" O LYS E 10 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG E 14 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 42 through 45 Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.806A pdb=" N ALA E 55 " --> pdb=" O ASP E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 8 Processing helix chain 'F' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE F 13 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG F 14 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY F 23 " --> pdb=" O GLY F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 41 Processing helix chain 'F' and resid 42 through 45 Processing helix chain 'F' and resid 48 through 50 No H-bonds generated for 'chain 'F' and resid 48 through 50' Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.806A pdb=" N ALA F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 8 Processing helix chain 'G' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE G 13 " --> pdb=" O LYS G 10 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG G 14 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 31 removed outlier: 5.214A pdb=" N GLY G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 41 Processing helix chain 'G' and resid 42 through 45 Processing helix chain 'G' and resid 48 through 50 No H-bonds generated for 'chain 'G' and resid 48 through 50' Processing helix chain 'G' and resid 51 through 59 removed outlier: 3.806A pdb=" N ALA G 55 " --> pdb=" O ASP G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 8 Processing helix chain 'H' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE H 13 " --> pdb=" O LYS H 10 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG H 14 " --> pdb=" O LEU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 41 Processing helix chain 'H' and resid 42 through 45 Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.805A pdb=" N ALA H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 600 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: 1.30 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1143 1.32 - 1.44: 1112 1.44 - 1.57: 3025 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 5352 Sorted by residual: bond pdb=" CA VAL B 42 " pdb=" C VAL B 42 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.46e-02 4.69e+03 1.47e+01 bond pdb=" CA VAL C 42 " pdb=" C VAL C 42 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.46e-02 4.69e+03 1.45e+01 bond pdb=" CA VAL F 42 " pdb=" C VAL F 42 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.46e-02 4.69e+03 1.43e+01 bond pdb=" CA VAL D 42 " pdb=" C VAL D 42 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.46e-02 4.69e+03 1.43e+01 bond pdb=" CA VAL H 42 " pdb=" C VAL H 42 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.46e-02 4.69e+03 1.42e+01 ... (remaining 5347 not shown) Histogram of bond angle deviations from ideal: 100.84 - 106.39: 72 106.39 - 111.93: 2600 111.93 - 117.48: 1488 117.48 - 123.03: 2329 123.03 - 128.57: 671 Bond angle restraints: 7160 Sorted by residual: angle pdb=" N LYS E 8 " pdb=" CA LYS E 8 " pdb=" C LYS E 8 " ideal model delta sigma weight residual 111.36 123.24 -11.88 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N LYS H 8 " pdb=" CA LYS H 8 " pdb=" C LYS H 8 " ideal model delta sigma weight residual 111.36 123.24 -11.88 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N LYS C 8 " pdb=" CA LYS C 8 " pdb=" C LYS C 8 " ideal model delta sigma weight residual 111.36 123.23 -11.87 1.09e+00 8.42e-01 1.18e+02 angle pdb=" N LYS A 8 " pdb=" CA LYS A 8 " pdb=" C LYS A 8 " ideal model delta sigma weight residual 111.36 123.22 -11.86 1.09e+00 8.42e-01 1.18e+02 angle pdb=" N LYS B 8 " pdb=" CA LYS B 8 " pdb=" C LYS B 8 " ideal model delta sigma weight residual 111.36 123.21 -11.85 1.09e+00 8.42e-01 1.18e+02 ... (remaining 7155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 3184 17.63 - 35.26: 192 35.26 - 52.89: 24 52.89 - 70.52: 8 70.52 - 88.16: 8 Dihedral angle restraints: 3416 sinusoidal: 1448 harmonic: 1968 Sorted by residual: dihedral pdb=" CA LYS D 8 " pdb=" C LYS D 8 " pdb=" N ARG D 9 " pdb=" CA ARG D 9 " ideal model delta harmonic sigma weight residual 0.00 15.63 -15.63 0 5.00e+00 4.00e-02 9.77e+00 dihedral pdb=" CA LYS B 8 " pdb=" C LYS B 8 " pdb=" N ARG B 9 " pdb=" CA ARG B 9 " ideal model delta harmonic sigma weight residual 0.00 15.61 -15.61 0 5.00e+00 4.00e-02 9.75e+00 dihedral pdb=" CA LYS H 8 " pdb=" C LYS H 8 " pdb=" N ARG H 9 " pdb=" CA ARG H 9 " ideal model delta harmonic sigma weight residual 0.00 15.56 -15.56 0 5.00e+00 4.00e-02 9.69e+00 ... (remaining 3413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 595 0.077 - 0.154: 226 0.154 - 0.231: 19 0.231 - 0.308: 8 0.308 - 0.385: 8 Chirality restraints: 856 Sorted by residual: chirality pdb=" CA LYS H 8 " pdb=" N LYS H 8 " pdb=" C LYS H 8 " pdb=" CB LYS H 8 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA LYS B 8 " pdb=" N LYS B 8 " pdb=" C LYS B 8 " pdb=" CB LYS B 8 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA LYS A 8 " pdb=" N LYS A 8 " pdb=" C LYS A 8 " pdb=" CB LYS A 8 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 853 not shown) Planarity restraints: 912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 50 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C MET F 50 " -0.047 2.00e-02 2.50e+03 pdb=" O MET F 50 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP F 51 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET H 50 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C MET H 50 " -0.047 2.00e-02 2.50e+03 pdb=" O MET H 50 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP H 51 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 50 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.17e+00 pdb=" C MET G 50 " 0.046 2.00e-02 2.50e+03 pdb=" O MET G 50 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP G 51 " -0.016 2.00e-02 2.50e+03 ... (remaining 909 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1092 2.76 - 3.29: 6049 3.29 - 3.83: 8159 3.83 - 4.36: 11768 4.36 - 4.90: 15435 Nonbonded interactions: 42503 Sorted by model distance: nonbonded pdb=" CB ALA D 83 " pdb=" CD LYS H 63 " model vdw 2.219 3.860 nonbonded pdb=" CB ALA A 83 " pdb=" CD LYS E 63 " model vdw 2.256 3.860 nonbonded pdb=" CB ALA C 83 " pdb=" CD LYS G 63 " model vdw 2.299 3.860 nonbonded pdb=" CB ALA B 83 " pdb=" CD LYS F 63 " model vdw 2.318 3.860 nonbonded pdb=" CB ALA D 83 " pdb=" CG LYS H 63 " model vdw 2.354 3.860 ... (remaining 42498 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' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.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' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.170 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.760 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 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 : 0.013 0.056 5352 Z= 0.812 Angle : 1.513 11.882 7160 Z= 1.126 Chirality : 0.078 0.385 856 Planarity : 0.006 0.027 912 Dihedral : 12.323 88.156 2136 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 36.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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: -1.83 (0.32), residues: 664 helix: -2.44 (0.21), residues: 432 sheet: None (None), residues: 0 loop : 1.96 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE A 12 TYR 0.001 0.000 TYR A 74 ARG 0.001 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8447 (m-80) cc_final: 0.8245 (m-80) REVERT: A 18 GLU cc_start: 0.8770 (pm20) cc_final: 0.8143 (pp20) REVERT: A 41 LYS cc_start: 0.8697 (mttm) cc_final: 0.8312 (ttpt) REVERT: A 66 GLN cc_start: 0.7935 (pm20) cc_final: 0.7703 (pm20) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2481 time to fit residues: 7.5108 Evaluate side-chains 16 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 19 optimal weight: 0.0570 chunk 30 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 30.0000 overall best weight: 8.6112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5352 Z= 0.229 Angle : 0.799 5.520 7160 Z= 0.458 Chirality : 0.059 0.342 856 Planarity : 0.005 0.023 912 Dihedral : 9.422 60.675 736 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.05 % Allowed : 2.70 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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: 1.16 (0.32), residues: 664 helix: 0.21 (0.27), residues: 328 sheet: None (None), residues: 0 loop : 1.69 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.002 PHE E 12 TYR 0.005 0.002 TYR D 74 ARG 0.005 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 MET cc_start: 0.7672 (tpt) cc_final: 0.7449 (tpt) REVERT: H 18 GLU cc_start: 0.8862 (pm20) cc_final: 0.8257 (pp20) REVERT: H 39 MET cc_start: 0.9097 (tmm) cc_final: 0.8857 (tmm) REVERT: H 51 ASP cc_start: 0.9371 (m-30) cc_final: 0.9151 (m-30) outliers start: 3 outliers final: 0 residues processed: 25 average time/residue: 0.1771 time to fit residues: 4.7075 Evaluate side-chains 15 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 overall best weight: 10.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.8209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5352 Z= 0.242 Angle : 0.733 4.715 7160 Z= 0.415 Chirality : 0.043 0.123 856 Planarity : 0.009 0.074 912 Dihedral : 7.590 30.687 736 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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: 0.86 (0.32), residues: 664 helix: 0.22 (0.29), residues: 328 sheet: None (None), residues: 0 loop : 1.22 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE D 12 TYR 0.005 0.001 TYR C 74 ARG 0.009 0.001 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8821 (pm20) cc_final: 0.7968 (pp20) REVERT: H 50 MET cc_start: 0.7676 (ppp) cc_final: 0.6812 (mpp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1640 time to fit residues: 2.6828 Evaluate side-chains 12 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 0.0030 chunk 55 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 overall best weight: 5.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.9152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5352 Z= 0.186 Angle : 0.670 5.458 7160 Z= 0.370 Chirality : 0.043 0.125 856 Planarity : 0.004 0.023 912 Dihedral : 7.473 25.560 736 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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: 0.95 (0.33), residues: 664 helix: 0.03 (0.28), residues: 336 sheet: None (None), residues: 0 loop : 1.62 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE A 12 TYR 0.007 0.002 TYR C 81 ARG 0.003 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8778 (pm20) cc_final: 0.7993 (pp20) REVERT: H 48 THR cc_start: 0.8306 (p) cc_final: 0.7936 (p) REVERT: H 50 MET cc_start: 0.7510 (ppp) cc_final: 0.6967 (mpp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1795 time to fit residues: 2.9298 Evaluate side-chains 12 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.9656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5352 Z= 0.174 Angle : 0.649 5.488 7160 Z= 0.356 Chirality : 0.041 0.122 856 Planarity : 0.004 0.022 912 Dihedral : 6.813 20.439 736 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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: 0.77 (0.33), residues: 664 helix: 0.04 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 1.45 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.001 PHE C 12 TYR 0.005 0.002 TYR B 74 ARG 0.004 0.001 ARG F 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.082 Fit side-chains REVERT: H 18 GLU cc_start: 0.8733 (pm20) cc_final: 0.7906 (pp20) REVERT: H 50 MET cc_start: 0.7403 (ppp) cc_final: 0.7196 (mpp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1783 time to fit residues: 2.9015 Evaluate side-chains 10 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 51 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 0.0050 overall best weight: 6.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 1.0284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5352 Z= 0.183 Angle : 0.694 5.607 7160 Z= 0.385 Chirality : 0.043 0.121 856 Planarity : 0.004 0.026 912 Dihedral : 6.540 16.845 736 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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: 0.98 (0.34), residues: 664 helix: 0.37 (0.29), residues: 360 sheet: None (None), residues: 0 loop : 1.31 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE C 12 TYR 0.006 0.002 TYR C 74 ARG 0.004 0.001 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.096 Fit side-chains REVERT: H 18 GLU cc_start: 0.8776 (pm20) cc_final: 0.7902 (pp20) REVERT: H 39 MET cc_start: 0.8651 (ppp) cc_final: 0.8155 (ppp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1437 time to fit residues: 2.2300 Evaluate side-chains 9 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 0.0050 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 overall best weight: 5.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 1.0486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 5352 Z= 0.173 Angle : 0.671 5.782 7160 Z= 0.382 Chirality : 0.045 0.154 856 Planarity : 0.004 0.027 912 Dihedral : 6.592 16.242 736 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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: 1.10 (0.34), residues: 664 helix: 0.60 (0.29), residues: 352 sheet: None (None), residues: 0 loop : 1.17 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE E 12 TYR 0.008 0.002 TYR C 74 ARG 0.004 0.001 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.091 Fit side-chains REVERT: H 18 GLU cc_start: 0.8199 (pm20) cc_final: 0.7973 (pp20) REVERT: H 39 MET cc_start: 0.8541 (ppp) cc_final: 0.8096 (ppp) REVERT: H 40 GLU cc_start: 0.8603 (pm20) cc_final: 0.8379 (tm-30) REVERT: H 50 MET cc_start: 0.8442 (mpp) cc_final: 0.7888 (mpp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1588 time to fit residues: 2.4515 Evaluate side-chains 9 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 30 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 1.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 5352 Z= 0.162 Angle : 0.648 5.264 7160 Z= 0.368 Chirality : 0.044 0.126 856 Planarity : 0.004 0.028 912 Dihedral : 6.166 14.853 736 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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: 0.84 (0.33), residues: 664 helix: 0.48 (0.29), residues: 352 sheet: None (None), residues: 0 loop : 0.90 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE D 12 TYR 0.012 0.002 TYR G 74 ARG 0.004 0.001 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: G 18 GLU cc_start: 0.8467 (pm20) cc_final: 0.8096 (pp20) REVERT: G 39 MET cc_start: 0.8445 (ppp) cc_final: 0.7928 (ppp) REVERT: G 50 MET cc_start: 0.8651 (mpp) cc_final: 0.8106 (mpp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1508 time to fit residues: 2.3467 Evaluate side-chains 11 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 25 optimal weight: 0.1980 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 1.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5352 Z= 0.175 Angle : 0.700 5.879 7160 Z= 0.392 Chirality : 0.044 0.119 856 Planarity : 0.004 0.028 912 Dihedral : 6.159 14.086 736 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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: 0.58 (0.34), residues: 664 helix: 0.36 (0.29), residues: 344 sheet: None (None), residues: 0 loop : 0.65 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE B 12 TYR 0.008 0.002 TYR H 74 ARG 0.005 0.001 ARG D 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.088 Fit side-chains REVERT: C 39 MET cc_start: 0.8407 (ppp) cc_final: 0.7851 (ppp) REVERT: C 50 MET cc_start: 0.8508 (mpp) cc_final: 0.8091 (mpp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.2189 time to fit residues: 3.7589 Evaluate side-chains 8 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 46 optimal weight: 40.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 1.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5352 Z= 0.219 Angle : 0.721 5.349 7160 Z= 0.406 Chirality : 0.043 0.121 856 Planarity : 0.004 0.025 912 Dihedral : 6.260 14.281 736 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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: 0.44 (0.35), residues: 664 helix: 0.09 (0.29), residues: 352 sheet: None (None), residues: 0 loop : 0.80 (0.39), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE G 12 TYR 0.012 0.002 TYR G 74 ARG 0.006 0.001 ARG C 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.088 Fit side-chains REVERT: C 16 MET cc_start: 0.7835 (tpt) cc_final: 0.7516 (tpt) REVERT: C 39 MET cc_start: 0.8367 (ppp) cc_final: 0.7781 (ppp) REVERT: C 48 THR cc_start: 0.7922 (p) cc_final: 0.7600 (p) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1857 time to fit residues: 2.6269 Evaluate side-chains 9 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 50 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 6 optimal weight: 40.0000 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.057136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.049011 restraints weight = 5203.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.049573 restraints weight = 4575.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.049916 restraints weight = 4094.426| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 1.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5352 Z= 0.179 Angle : 0.692 5.790 7160 Z= 0.387 Chirality : 0.042 0.120 856 Planarity : 0.004 0.027 912 Dihedral : 6.038 13.112 736 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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: 0.38 (0.35), residues: 664 helix: -0.06 (0.29), residues: 352 sheet: None (None), residues: 0 loop : 0.92 (0.40), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE B 12 TYR 0.009 0.002 TYR G 74 ARG 0.005 0.001 ARG D 9 =============================================================================== Job complete usr+sys time: 1067.56 seconds wall clock time: 20 minutes 22.19 seconds (1222.19 seconds total)