Starting phenix.real_space_refine on Thu Sep 18 03:55:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6znh_11311/09_2025/6znh_11311.cif Found real_map, /net/cci-nas-00/data/ceres_data/6znh_11311/09_2025/6znh_11311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6znh_11311/09_2025/6znh_11311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6znh_11311/09_2025/6znh_11311.map" model { file = "/net/cci-nas-00/data/ceres_data/6znh_11311/09_2025/6znh_11311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6znh_11311/09_2025/6znh_11311.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 3 Type Number sf(0) Gaussians C 8970 2.51 5 N 2346 2.21 5 O 2875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14191 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 617 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 75} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W Time building chain proxies: 1.42, per 1000 atoms: 0.10 Number of scatterers: 14191 At special positions: 0 Unit cell: (98.1, 99.19, 173.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2875 8.00 N 2346 7.00 C 8970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 684.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3542 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 0 sheets defined 86.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'B' and resid 7 through 20 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'C' and resid 7 through 20 Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 40 through 76 removed outlier: 3.987A pdb=" N ALA C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 75 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'D' and resid 7 through 20 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 40 through 76 removed outlier: 3.987A pdb=" N ALA D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE D 75 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 76 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 22 through 35 Processing helix chain 'E' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE E 75 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'F' and resid 22 through 35 Processing helix chain 'F' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE F 75 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 76 " --> pdb=" O ASP F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'G' and resid 7 through 20 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE G 75 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE G 76 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 79 No H-bonds generated for 'chain 'G' and resid 77 through 79' Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 22 through 35 Processing helix chain 'H' and resid 40 through 76 removed outlier: 3.985A pdb=" N ALA H 74 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE H 75 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE H 76 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'I' and resid 7 through 20 Processing helix chain 'I' and resid 22 through 35 Processing helix chain 'I' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE I 75 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE I 76 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 79 No H-bonds generated for 'chain 'I' and resid 77 through 79' Processing helix chain 'J' and resid 7 through 20 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 40 through 76 removed outlier: 3.987A pdb=" N ALA J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE J 75 " --> pdb=" O ILE J 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE J 76 " --> pdb=" O ASP J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 79 No H-bonds generated for 'chain 'J' and resid 77 through 79' Processing helix chain 'K' and resid 7 through 20 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE K 75 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE K 76 " --> pdb=" O ASP K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 79 No H-bonds generated for 'chain 'K' and resid 77 through 79' Processing helix chain 'L' and resid 7 through 20 Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE L 75 " --> pdb=" O ILE L 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE L 76 " --> pdb=" O ASP L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 79 No H-bonds generated for 'chain 'L' and resid 77 through 79' Processing helix chain 'M' and resid 7 through 20 Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA M 74 " --> pdb=" O ASP M 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE M 75 " --> pdb=" O ILE M 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE M 76 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 79 No H-bonds generated for 'chain 'M' and resid 77 through 79' Processing helix chain 'N' and resid 7 through 20 Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 40 through 76 removed outlier: 3.987A pdb=" N ALA N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE N 75 " --> pdb=" O ILE N 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 79 No H-bonds generated for 'chain 'N' and resid 77 through 79' Processing helix chain 'O' and resid 7 through 20 Processing helix chain 'O' and resid 22 through 35 Processing helix chain 'O' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA O 74 " --> pdb=" O ASP O 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE O 75 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE O 76 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 79 No H-bonds generated for 'chain 'O' and resid 77 through 79' Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'P' and resid 22 through 35 Processing helix chain 'P' and resid 40 through 76 removed outlier: 3.987A pdb=" N ALA P 74 " --> pdb=" O ASP P 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE P 75 " --> pdb=" O ILE P 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE P 76 " --> pdb=" O ASP P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 79 No H-bonds generated for 'chain 'P' and resid 77 through 79' Processing helix chain 'Q' and resid 7 through 20 Processing helix chain 'Q' and resid 22 through 35 Processing helix chain 'Q' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA Q 74 " --> pdb=" O ASP Q 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE Q 75 " --> pdb=" O ILE Q 71 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE Q 76 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 79 No H-bonds generated for 'chain 'Q' and resid 77 through 79' Processing helix chain 'R' and resid 7 through 20 Processing helix chain 'R' and resid 22 through 35 Processing helix chain 'R' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA R 74 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE R 75 " --> pdb=" O ILE R 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE R 76 " --> pdb=" O ASP R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 79 No H-bonds generated for 'chain 'R' and resid 77 through 79' Processing helix chain 'S' and resid 7 through 20 Processing helix chain 'S' and resid 22 through 35 Processing helix chain 'S' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA S 74 " --> pdb=" O ASP S 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE S 75 " --> pdb=" O ILE S 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE S 76 " --> pdb=" O ASP S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 79 No H-bonds generated for 'chain 'S' and resid 77 through 79' Processing helix chain 'T' and resid 7 through 20 Processing helix chain 'T' and resid 22 through 35 Processing helix chain 'T' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA T 74 " --> pdb=" O ASP T 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE T 75 " --> pdb=" O ILE T 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE T 76 " --> pdb=" O ASP T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 79 No H-bonds generated for 'chain 'T' and resid 77 through 79' Processing helix chain 'U' and resid 7 through 20 Processing helix chain 'U' and resid 22 through 35 Processing helix chain 'U' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA U 74 " --> pdb=" O ASP U 70 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE U 75 " --> pdb=" O ILE U 71 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE U 76 " --> pdb=" O ASP U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 79 No H-bonds generated for 'chain 'U' and resid 77 through 79' Processing helix chain 'V' and resid 7 through 20 Processing helix chain 'V' and resid 22 through 35 Processing helix chain 'V' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA V 74 " --> pdb=" O ASP V 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE V 75 " --> pdb=" O ILE V 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE V 76 " --> pdb=" O ASP V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 79 No H-bonds generated for 'chain 'V' and resid 77 through 79' Processing helix chain 'W' and resid 7 through 20 Processing helix chain 'W' and resid 22 through 35 Processing helix chain 'W' and resid 40 through 76 removed outlier: 3.986A pdb=" N ALA W 74 " --> pdb=" O ASP W 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE W 75 " --> pdb=" O ILE W 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE W 76 " --> pdb=" O ASP W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 79 No H-bonds generated for 'chain 'W' and resid 77 through 79' 1150 hydrogen bonds defined for protein. 3450 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: 2.40 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2530 1.29 - 1.35: 2162 1.35 - 1.42: 1403 1.42 - 1.48: 2092 1.48 - 1.54: 6257 Bond restraints: 14444 Sorted by residual: bond pdb=" C ARG K 58 " pdb=" O ARG K 58 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.47e-01 bond pdb=" C ARG T 58 " pdb=" O ARG T 58 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.45e-01 bond pdb=" C ARG A 58 " pdb=" O ARG A 58 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.35e-01 bond pdb=" CA ASP Q 17 " pdb=" C ASP Q 17 " ideal model delta sigma weight residual 1.522 1.509 0.013 1.41e-02 5.03e+03 8.27e-01 bond pdb=" C ARG G 58 " pdb=" O ARG G 58 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 8.22e-01 ... (remaining 14439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 14866 0.87 - 1.73: 3642 1.73 - 2.60: 970 2.60 - 3.46: 164 3.46 - 4.33: 23 Bond angle restraints: 19665 Sorted by residual: angle pdb=" N TYR C 8 " pdb=" CA TYR C 8 " pdb=" C TYR C 8 " ideal model delta sigma weight residual 111.14 114.14 -3.00 1.08e+00 8.57e-01 7.74e+00 angle pdb=" N TYR I 8 " pdb=" CA TYR I 8 " pdb=" C TYR I 8 " ideal model delta sigma weight residual 111.14 114.14 -3.00 1.08e+00 8.57e-01 7.73e+00 angle pdb=" N TYR R 8 " pdb=" CA TYR R 8 " pdb=" C TYR R 8 " ideal model delta sigma weight residual 111.14 114.14 -3.00 1.08e+00 8.57e-01 7.71e+00 angle pdb=" N TYR D 8 " pdb=" CA TYR D 8 " pdb=" C TYR D 8 " ideal model delta sigma weight residual 111.14 114.13 -2.99 1.08e+00 8.57e-01 7.67e+00 angle pdb=" N TYR A 8 " pdb=" CA TYR A 8 " pdb=" C TYR A 8 " ideal model delta sigma weight residual 111.14 114.12 -2.98 1.08e+00 8.57e-01 7.63e+00 ... (remaining 19660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 7802 14.38 - 28.76: 707 28.76 - 43.13: 162 43.13 - 57.51: 69 57.51 - 71.89: 23 Dihedral angle restraints: 8763 sinusoidal: 3335 harmonic: 5428 Sorted by residual: dihedral pdb=" CA VAL T 20 " pdb=" C VAL T 20 " pdb=" N ASP T 21 " pdb=" CA ASP T 21 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA VAL Q 20 " pdb=" C VAL Q 20 " pdb=" N ASP Q 21 " pdb=" CA ASP Q 21 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA VAL M 20 " pdb=" C VAL M 20 " pdb=" N ASP M 21 " pdb=" CA ASP M 21 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 725 0.023 - 0.045: 741 0.045 - 0.068: 518 0.068 - 0.090: 201 0.090 - 0.113: 69 Chirality restraints: 2254 Sorted by residual: chirality pdb=" CA VAL E 20 " pdb=" N VAL E 20 " pdb=" C VAL E 20 " pdb=" CB VAL E 20 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.17e-01 chirality pdb=" CA VAL C 20 " pdb=" N VAL C 20 " pdb=" C VAL C 20 " pdb=" CB VAL C 20 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA VAL U 20 " pdb=" N VAL U 20 " pdb=" C VAL U 20 " pdb=" CB VAL U 20 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.08e-01 ... (remaining 2251 not shown) Planarity restraints: 2576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 57 " -0.015 2.00e-02 2.50e+03 1.04e-02 2.16e+00 pdb=" CG TYR N 57 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR N 57 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR N 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR N 57 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR N 57 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR N 57 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR N 57 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 57 " -0.015 2.00e-02 2.50e+03 1.03e-02 2.14e+00 pdb=" CG TYR J 57 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR J 57 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR J 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR J 57 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR J 57 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR J 57 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR J 57 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 57 " -0.015 2.00e-02 2.50e+03 1.03e-02 2.12e+00 pdb=" CG TYR Q 57 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 57 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 57 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 57 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR Q 57 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR Q 57 " -0.002 2.00e-02 2.50e+03 ... (remaining 2573 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 356 2.71 - 3.26: 14394 3.26 - 3.80: 21903 3.80 - 4.35: 25819 4.35 - 4.90: 46098 Nonbonded interactions: 108570 Sorted by model distance: nonbonded pdb=" OD1 ASP E 10 " pdb=" OG SER K 49 " model vdw 2.160 3.040 nonbonded pdb=" OD2 ASP B 10 " pdb=" NZ LYS H 50 " model vdw 2.197 3.120 nonbonded pdb=" NZ LYS Q 50 " pdb=" OD2 ASP W 10 " model vdw 2.200 3.120 nonbonded pdb=" NZ LYS C 50 " pdb=" OD2 ASP P 10 " model vdw 2.209 3.120 nonbonded pdb=" OG SER F 49 " pdb=" OD1 ASP M 10 " model vdw 2.215 3.040 ... (remaining 108565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } 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 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.980 Find NCS groups from input model: 0.130 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 0.026 14444 Z= 0.267 Angle : 0.836 4.325 19665 Z= 0.624 Chirality : 0.045 0.113 2254 Planarity : 0.004 0.031 2576 Dihedral : 13.444 71.891 5221 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.03 % Allowed : 7.18 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.18), residues: 1771 helix: 1.27 (0.12), residues: 1449 sheet: None (None), residues: 0 loop : -4.04 (0.23), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 58 TYR 0.025 0.003 TYR N 57 PHE 0.006 0.001 PHE T 68 TRP 0.002 0.001 TRP H 5 Details of bonding type rmsd covalent geometry : bond 0.00563 (14444) covalent geometry : angle 0.83572 (19665) hydrogen bonds : bond 0.10352 ( 1150) hydrogen bonds : angle 3.48497 ( 3450) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 245 time to evaluate : 0.543 Fit side-chains REVERT: A 53 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 57 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8041 (t80) REVERT: B 17 ASP cc_start: 0.7579 (m-30) cc_final: 0.7261 (m-30) REVERT: B 22 ASN cc_start: 0.7391 (t0) cc_final: 0.6967 (t0) REVERT: B 57 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8182 (t80) REVERT: C 17 ASP cc_start: 0.7380 (m-30) cc_final: 0.6861 (m-30) REVERT: C 57 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7699 (t80) REVERT: D 17 ASP cc_start: 0.7548 (m-30) cc_final: 0.7320 (m-30) REVERT: D 22 ASN cc_start: 0.7498 (t0) cc_final: 0.7292 (t0) REVERT: E 17 ASP cc_start: 0.7464 (m-30) cc_final: 0.7053 (m-30) REVERT: F 17 ASP cc_start: 0.7607 (m-30) cc_final: 0.7256 (m-30) REVERT: F 53 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7841 (mm-30) REVERT: F 57 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.8289 (t80) REVERT: L 18 THR cc_start: 0.8296 (m) cc_final: 0.8026 (p) REVERT: M 57 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7882 (t80) REVERT: N 53 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7749 (mm-30) REVERT: N 57 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7790 (t80) REVERT: O 17 ASP cc_start: 0.7738 (m-30) cc_final: 0.7389 (m-30) REVERT: O 53 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7680 (mm-30) REVERT: O 57 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8172 (t80) REVERT: P 53 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7388 (mm-30) REVERT: P 57 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8272 (t80) REVERT: Q 53 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7554 (mm-30) REVERT: Q 57 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7655 (t80) REVERT: R 17 ASP cc_start: 0.7659 (m-30) cc_final: 0.7426 (m-30) REVERT: R 53 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7227 (mm-30) REVERT: R 57 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.8346 (t80) REVERT: S 57 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8347 (t80) REVERT: T 57 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8398 (t80) REVERT: U 70 ASP cc_start: 0.7785 (m-30) cc_final: 0.7540 (m-30) outliers start: 46 outliers final: 10 residues processed: 272 average time/residue: 0.1197 time to fit residues: 48.8135 Evaluate side-chains 241 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Chi-restraints excluded: chain W residue 57 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN E 24 GLN F 24 GLN J 24 GLN K 24 GLN N 24 GLN P 24 GLN Q 24 GLN U 24 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099971 restraints weight = 15995.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.103140 restraints weight = 10203.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105372 restraints weight = 7469.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.106936 restraints weight = 5999.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108166 restraints weight = 5085.138| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 14444 Z= 0.213 Angle : 0.517 4.232 19665 Z= 0.290 Chirality : 0.039 0.125 2254 Planarity : 0.005 0.035 2576 Dihedral : 8.308 64.836 1999 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.31 % Allowed : 11.26 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.19), residues: 1771 helix: 2.64 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -2.79 (0.29), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 58 TYR 0.026 0.003 TYR E 57 PHE 0.010 0.002 PHE F 68 TRP 0.005 0.001 TRP K 5 Details of bonding type rmsd covalent geometry : bond 0.00480 (14444) covalent geometry : angle 0.51750 (19665) hydrogen bonds : bond 0.09202 ( 1150) hydrogen bonds : angle 3.06271 ( 3450) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.602 Fit side-chains REVERT: A 53 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7470 (mm-30) REVERT: A 57 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8087 (t80) REVERT: C 57 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7776 (t80) REVERT: D 17 ASP cc_start: 0.7601 (m-30) cc_final: 0.7325 (m-30) REVERT: D 57 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.8218 (t80) REVERT: E 53 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7570 (mm-30) REVERT: J 6 SER cc_start: 0.9184 (p) cc_final: 0.8902 (p) REVERT: J 53 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7368 (mm-30) REVERT: K 53 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7354 (mm-30) REVERT: L 18 THR cc_start: 0.8445 (m) cc_final: 0.8190 (p) REVERT: M 57 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7886 (t80) REVERT: N 53 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7700 (mm-30) REVERT: N 57 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7795 (t80) REVERT: O 17 ASP cc_start: 0.7683 (m-30) cc_final: 0.7350 (m-30) REVERT: O 53 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7702 (mm-30) REVERT: O 57 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8004 (t80) REVERT: P 53 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7541 (mm-30) REVERT: P 57 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8276 (t80) REVERT: Q 53 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7573 (mm-30) REVERT: Q 57 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7821 (t80) REVERT: R 53 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7103 (mm-30) REVERT: R 72 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8013 (t0) REVERT: S 17 ASP cc_start: 0.7723 (m-30) cc_final: 0.7498 (m-30) REVERT: S 57 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8204 (t80) REVERT: T 57 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7778 (t80) REVERT: U 5 TRP cc_start: 0.8718 (t60) cc_final: 0.8379 (t60) REVERT: U 53 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7342 (mm-30) REVERT: U 70 ASP cc_start: 0.7777 (m-30) cc_final: 0.7563 (m-30) REVERT: V 53 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7361 (mm-30) REVERT: V 77 GLN cc_start: 0.8312 (tt0) cc_final: 0.8105 (tt0) outliers start: 35 outliers final: 17 residues processed: 243 average time/residue: 0.1106 time to fit residues: 41.5255 Evaluate side-chains 233 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain S residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Chi-restraints excluded: chain W residue 57 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 160 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102707 restraints weight = 16022.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106276 restraints weight = 9933.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108826 restraints weight = 7147.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110552 restraints weight = 5650.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111883 restraints weight = 4758.930| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 14444 Z= 0.171 Angle : 0.452 3.942 19665 Z= 0.253 Chirality : 0.037 0.121 2254 Planarity : 0.004 0.035 2576 Dihedral : 7.670 63.623 1995 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.70 % Allowed : 14.76 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.63 (0.20), residues: 1771 helix: 3.18 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -2.05 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 58 TYR 0.021 0.002 TYR P 57 PHE 0.007 0.001 PHE F 68 TRP 0.004 0.001 TRP A 5 Details of bonding type rmsd covalent geometry : bond 0.00371 (14444) covalent geometry : angle 0.45164 (19665) hydrogen bonds : bond 0.08140 ( 1150) hydrogen bonds : angle 2.79844 ( 3450) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 0.652 Fit side-chains REVERT: A 57 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8076 (t80) REVERT: B 57 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8172 (t80) REVERT: C 57 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7830 (t80) REVERT: D 17 ASP cc_start: 0.7539 (m-30) cc_final: 0.7284 (m-30) REVERT: D 57 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.8246 (t80) REVERT: E 53 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7606 (mm-30) REVERT: F 53 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7651 (mm-30) REVERT: J 6 SER cc_start: 0.9160 (p) cc_final: 0.8907 (p) REVERT: J 53 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7344 (mm-30) REVERT: K 53 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7400 (mm-30) REVERT: L 18 THR cc_start: 0.8462 (m) cc_final: 0.8197 (p) REVERT: M 57 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7888 (t80) REVERT: N 57 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7747 (t80) REVERT: O 17 ASP cc_start: 0.7647 (m-30) cc_final: 0.7302 (m-30) REVERT: O 53 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7659 (mm-30) REVERT: O 57 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8034 (t80) REVERT: P 53 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7403 (mm-30) REVERT: P 57 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8265 (t80) REVERT: Q 53 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7338 (mm-30) REVERT: Q 57 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7782 (t80) REVERT: R 53 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7075 (mm-30) REVERT: R 72 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7945 (t0) REVERT: T 57 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7757 (t80) REVERT: U 5 TRP cc_start: 0.8642 (t60) cc_final: 0.8407 (t60) REVERT: V 53 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7358 (mm-30) REVERT: V 72 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7926 (t0) REVERT: V 77 GLN cc_start: 0.8382 (tt0) cc_final: 0.8078 (tt0) outliers start: 41 outliers final: 24 residues processed: 240 average time/residue: 0.1125 time to fit residues: 41.5426 Evaluate side-chains 240 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Chi-restraints excluded: chain V residue 72 ASP Chi-restraints excluded: chain W residue 57 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 151 optimal weight: 3.9990 chunk 133 optimal weight: 0.0570 chunk 81 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN R 24 GLN S 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.137475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.115101 restraints weight = 15508.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119111 restraints weight = 9287.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121887 restraints weight = 6489.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123766 restraints weight = 5020.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125223 restraints weight = 4150.725| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 14444 Z= 0.109 Angle : 0.370 3.785 19665 Z= 0.206 Chirality : 0.034 0.120 2254 Planarity : 0.004 0.036 2576 Dihedral : 6.643 56.206 1991 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.50 % Allowed : 15.35 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.09 (0.20), residues: 1771 helix: 3.49 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.82 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 80 TYR 0.014 0.001 TYR B 57 PHE 0.004 0.001 PHE L 68 TRP 0.002 0.000 TRP E 5 Details of bonding type rmsd covalent geometry : bond 0.00204 (14444) covalent geometry : angle 0.37038 (19665) hydrogen bonds : bond 0.05401 ( 1150) hydrogen bonds : angle 2.46815 ( 3450) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 0.687 Fit side-chains REVERT: A 57 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.8135 (t80) REVERT: B 17 ASP cc_start: 0.7490 (m-30) cc_final: 0.7224 (m-30) REVERT: B 57 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8159 (t80) REVERT: C 57 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7909 (t80) REVERT: E 53 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7465 (mm-30) REVERT: F 53 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7560 (mm-30) REVERT: H 69 LYS cc_start: 0.7921 (tmtt) cc_final: 0.7458 (tttp) REVERT: J 6 SER cc_start: 0.9069 (p) cc_final: 0.8820 (p) REVERT: J 53 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7174 (mm-30) REVERT: K 53 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7195 (mm-30) REVERT: L 53 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7114 (mm-30) REVERT: M 57 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7840 (t80) REVERT: M 69 LYS cc_start: 0.7870 (tmtt) cc_final: 0.7538 (tttm) REVERT: N 57 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7787 (t80) REVERT: O 57 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7860 (t80) REVERT: P 53 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7204 (mm-30) REVERT: P 57 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8159 (t80) REVERT: Q 53 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7182 (mm-30) REVERT: Q 57 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7736 (t80) REVERT: R 53 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7150 (mm-30) REVERT: T 57 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7544 (t80) REVERT: V 72 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7389 (t0) outliers start: 38 outliers final: 17 residues processed: 277 average time/residue: 0.1450 time to fit residues: 56.8114 Evaluate side-chains 245 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain F residue 57 TYR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 6 SER Chi-restraints excluded: chain V residue 57 TYR Chi-restraints excluded: chain V residue 72 ASP Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain W residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN I 24 GLN W 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098154 restraints weight = 16236.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.101525 restraints weight = 10148.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.103958 restraints weight = 7374.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105631 restraints weight = 5881.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.106698 restraints weight = 5006.517| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 14444 Z= 0.217 Angle : 0.489 4.453 19665 Z= 0.269 Chirality : 0.039 0.122 2254 Planarity : 0.004 0.036 2576 Dihedral : 7.334 69.710 1989 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.50 % Allowed : 16.93 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.97 (0.20), residues: 1771 helix: 3.43 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -2.01 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 58 TYR 0.027 0.003 TYR S 57 PHE 0.008 0.002 PHE H 68 TRP 0.004 0.001 TRP E 5 Details of bonding type rmsd covalent geometry : bond 0.00500 (14444) covalent geometry : angle 0.48940 (19665) hydrogen bonds : bond 0.09343 ( 1150) hydrogen bonds : angle 2.83230 ( 3450) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.612 Fit side-chains REVERT: A 57 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8093 (t80) REVERT: B 57 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.8130 (t80) REVERT: C 57 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7876 (t80) REVERT: D 17 ASP cc_start: 0.7640 (m-30) cc_final: 0.7307 (m-30) REVERT: D 57 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8124 (t80) REVERT: E 53 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7564 (mm-30) REVERT: F 37 LYS cc_start: 0.7752 (ttmt) cc_final: 0.7523 (ttmm) REVERT: F 53 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7662 (mm-30) REVERT: J 6 SER cc_start: 0.9186 (p) cc_final: 0.8962 (p) REVERT: J 53 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7342 (mm-30) REVERT: K 53 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7480 (mm-30) REVERT: M 57 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7872 (t80) REVERT: N 57 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7828 (t80) REVERT: P 53 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7410 (mm-30) REVERT: P 57 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8279 (t80) REVERT: Q 53 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7372 (mm-30) REVERT: Q 57 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.7797 (t80) REVERT: R 53 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7029 (mm-30) REVERT: T 53 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7617 (mm-30) REVERT: T 57 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7787 (t80) REVERT: V 72 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7996 (t0) outliers start: 38 outliers final: 21 residues processed: 238 average time/residue: 0.1147 time to fit residues: 41.5647 Evaluate side-chains 244 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain S residue 33 LYS Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain T residue 77 GLN Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 57 TYR Chi-restraints excluded: chain V residue 72 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 109 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.110643 restraints weight = 15653.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114416 restraints weight = 9493.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117083 restraints weight = 6737.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118967 restraints weight = 5261.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120164 restraints weight = 4368.016| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 14444 Z= 0.117 Angle : 0.370 3.675 19665 Z= 0.207 Chirality : 0.034 0.120 2254 Planarity : 0.004 0.039 2576 Dihedral : 6.672 66.065 1985 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.04 % Allowed : 17.79 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.26 (0.20), residues: 1771 helix: 3.62 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.86 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG T 58 TYR 0.015 0.001 TYR B 57 PHE 0.005 0.001 PHE L 68 TRP 0.002 0.000 TRP H 5 Details of bonding type rmsd covalent geometry : bond 0.00225 (14444) covalent geometry : angle 0.36985 (19665) hydrogen bonds : bond 0.05969 ( 1150) hydrogen bonds : angle 2.49147 ( 3450) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.912 Fit side-chains REVERT: A 57 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8129 (t80) REVERT: B 57 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8209 (t80) REVERT: C 17 ASP cc_start: 0.7342 (m-30) cc_final: 0.6896 (m-30) REVERT: C 57 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7815 (t80) REVERT: D 17 ASP cc_start: 0.7437 (m-30) cc_final: 0.7229 (m-30) REVERT: D 33 LYS cc_start: 0.8269 (mtmm) cc_final: 0.8035 (mtmt) REVERT: E 53 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7505 (mm-30) REVERT: F 53 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7520 (mm-30) REVERT: H 69 LYS cc_start: 0.7931 (tmtt) cc_final: 0.7501 (tttp) REVERT: M 57 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7891 (t80) REVERT: M 69 LYS cc_start: 0.7957 (tmtt) cc_final: 0.7618 (tttm) REVERT: N 57 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7905 (t80) REVERT: O 57 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7955 (t80) REVERT: P 53 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7193 (mm-30) REVERT: P 57 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8138 (t80) REVERT: Q 53 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7196 (mm-30) REVERT: Q 57 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7765 (t80) REVERT: R 53 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7093 (mm-30) REVERT: T 57 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7645 (t80) outliers start: 31 outliers final: 12 residues processed: 246 average time/residue: 0.1329 time to fit residues: 49.0038 Evaluate side-chains 240 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.0770 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 24 GLN O 24 GLN V 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114554 restraints weight = 15505.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118089 restraints weight = 9788.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120555 restraints weight = 7084.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122311 restraints weight = 5600.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123531 restraints weight = 4693.140| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 14444 Z= 0.108 Angle : 0.359 2.942 19665 Z= 0.197 Chirality : 0.033 0.119 2254 Planarity : 0.004 0.043 2576 Dihedral : 6.209 63.135 1985 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.52 % Allowed : 18.12 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.41 (0.20), residues: 1771 helix: 3.72 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.79 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG Q 80 TYR 0.015 0.001 TYR B 57 PHE 0.004 0.001 PHE L 68 TRP 0.003 0.000 TRP W 5 Details of bonding type rmsd covalent geometry : bond 0.00205 (14444) covalent geometry : angle 0.35870 (19665) hydrogen bonds : bond 0.05512 ( 1150) hydrogen bonds : angle 2.38103 ( 3450) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.597 Fit side-chains REVERT: A 57 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.8094 (t80) REVERT: B 57 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8239 (t80) REVERT: C 57 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7889 (t80) REVERT: D 17 ASP cc_start: 0.7413 (m-30) cc_final: 0.7146 (m-30) REVERT: D 57 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7710 (t80) REVERT: E 53 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7441 (mm-30) REVERT: F 53 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7479 (mm-30) REVERT: M 57 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7901 (t80) REVERT: N 57 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7900 (t80) REVERT: P 53 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7163 (mm-30) REVERT: P 57 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8207 (t80) REVERT: Q 53 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7184 (mm-30) REVERT: Q 57 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7790 (t80) REVERT: R 53 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7008 (mm-30) REVERT: T 53 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7369 (mm-30) REVERT: T 57 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7614 (t80) outliers start: 23 outliers final: 9 residues processed: 236 average time/residue: 0.1238 time to fit residues: 43.3374 Evaluate side-chains 231 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain S residue 33 LYS Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 113 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.125976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104148 restraints weight = 15916.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.107480 restraints weight = 10124.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109855 restraints weight = 7404.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.111521 restraints weight = 5917.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112677 restraints weight = 5013.123| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14444 Z= 0.160 Angle : 0.425 4.229 19665 Z= 0.234 Chirality : 0.036 0.121 2254 Planarity : 0.004 0.044 2576 Dihedral : 6.253 67.042 1981 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.45 % Allowed : 18.77 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.32 (0.20), residues: 1771 helix: 3.66 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.83 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 58 TYR 0.021 0.002 TYR S 57 PHE 0.006 0.001 PHE F 68 TRP 0.003 0.001 TRP P 5 Details of bonding type rmsd covalent geometry : bond 0.00346 (14444) covalent geometry : angle 0.42483 (19665) hydrogen bonds : bond 0.07858 ( 1150) hydrogen bonds : angle 2.57977 ( 3450) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.554 Fit side-chains REVERT: A 57 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8186 (t80) REVERT: B 57 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8161 (t80) REVERT: C 57 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7958 (t80) REVERT: D 57 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7858 (t80) REVERT: E 53 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7489 (mm-30) REVERT: F 53 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7584 (mm-30) REVERT: M 57 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7974 (t80) REVERT: N 57 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.7906 (t80) REVERT: O 57 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8042 (t80) REVERT: P 53 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7287 (mm-30) REVERT: P 57 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8253 (t80) REVERT: Q 53 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7317 (mm-30) REVERT: Q 57 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7917 (t80) REVERT: R 53 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7065 (mm-30) REVERT: T 53 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7377 (mm-30) REVERT: T 57 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7824 (t80) outliers start: 22 outliers final: 9 residues processed: 229 average time/residue: 0.1102 time to fit residues: 38.9756 Evaluate side-chains 228 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain S residue 33 LYS Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 97 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.131582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110019 restraints weight = 15646.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113491 restraints weight = 9912.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.115960 restraints weight = 7204.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117633 restraints weight = 5712.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118951 restraints weight = 4809.747| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14444 Z= 0.121 Angle : 0.378 3.372 19665 Z= 0.208 Chirality : 0.034 0.120 2254 Planarity : 0.004 0.044 2576 Dihedral : 6.025 65.596 1981 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.25 % Allowed : 19.37 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.42 (0.20), residues: 1771 helix: 3.73 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.78 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 80 TYR 0.016 0.002 TYR B 57 PHE 0.005 0.001 PHE L 68 TRP 0.006 0.000 TRP W 5 Details of bonding type rmsd covalent geometry : bond 0.00235 (14444) covalent geometry : angle 0.37761 (19665) hydrogen bonds : bond 0.06343 ( 1150) hydrogen bonds : angle 2.44764 ( 3450) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.591 Fit side-chains REVERT: A 57 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.8131 (t80) REVERT: B 57 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8211 (t80) REVERT: C 17 ASP cc_start: 0.7320 (m-30) cc_final: 0.6839 (m-30) REVERT: C 57 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7824 (t80) REVERT: E 53 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7537 (mm-30) REVERT: F 53 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7528 (mm-30) REVERT: H 69 LYS cc_start: 0.7960 (tmtt) cc_final: 0.7594 (tmtt) REVERT: M 57 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7931 (t80) REVERT: N 17 ASP cc_start: 0.7401 (m-30) cc_final: 0.7049 (m-30) REVERT: N 57 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7977 (t80) REVERT: O 57 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7991 (t80) REVERT: P 53 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7186 (mm-30) REVERT: P 57 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.8200 (t80) REVERT: Q 53 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7234 (mm-30) REVERT: Q 57 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7851 (t80) REVERT: R 53 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7061 (mm-30) REVERT: T 53 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7334 (mm-30) REVERT: T 57 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7621 (t80) outliers start: 19 outliers final: 7 residues processed: 223 average time/residue: 0.1172 time to fit residues: 39.7707 Evaluate side-chains 221 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 36 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.129915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.108831 restraints weight = 15736.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112142 restraints weight = 10119.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114481 restraints weight = 7430.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116121 restraints weight = 5932.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117282 restraints weight = 5017.259| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 14444 Z= 0.133 Angle : 0.392 3.511 19665 Z= 0.216 Chirality : 0.035 0.121 2254 Planarity : 0.004 0.043 2576 Dihedral : 5.959 65.625 1981 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.12 % Allowed : 19.37 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.43 (0.20), residues: 1771 helix: 3.73 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.78 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 58 TYR 0.017 0.002 TYR B 57 PHE 0.005 0.001 PHE L 68 TRP 0.004 0.001 TRP W 5 Details of bonding type rmsd covalent geometry : bond 0.00270 (14444) covalent geometry : angle 0.39201 (19665) hydrogen bonds : bond 0.06795 ( 1150) hydrogen bonds : angle 2.47120 ( 3450) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3542 Ramachandran restraints generated. 1771 Oldfield, 0 Emsley, 1771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.601 Fit side-chains REVERT: A 57 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.8148 (t80) REVERT: B 57 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8110 (t80) REVERT: C 57 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7732 (t80) REVERT: D 57 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7634 (t80) REVERT: E 53 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7540 (mm-30) REVERT: F 53 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7544 (mm-30) REVERT: H 69 LYS cc_start: 0.7993 (tmtt) cc_final: 0.7604 (tmtt) REVERT: M 57 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.8005 (t80) REVERT: N 57 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7894 (t80) REVERT: O 57 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8033 (t80) REVERT: P 53 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7245 (mm-30) REVERT: P 57 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8289 (t80) REVERT: Q 53 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7267 (mm-30) REVERT: Q 57 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7889 (t80) REVERT: R 53 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7049 (mm-30) REVERT: T 53 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7315 (mm-30) REVERT: T 57 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7765 (t80) outliers start: 17 outliers final: 7 residues processed: 224 average time/residue: 0.1170 time to fit residues: 39.7820 Evaluate side-chains 225 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain P residue 57 TYR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain T residue 57 TYR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 57 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 21 optimal weight: 8.9990 chunk 157 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.132683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111532 restraints weight = 15695.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114963 restraints weight = 9925.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117442 restraints weight = 7186.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119116 restraints weight = 5692.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120373 restraints weight = 4787.053| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14444 Z= 0.118 Angle : 0.372 3.267 19665 Z= 0.205 Chirality : 0.034 0.119 2254 Planarity : 0.004 0.046 2576 Dihedral : 5.759 63.725 1981 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.12 % Allowed : 19.37 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.52 (0.20), residues: 1771 helix: 3.78 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.69 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 80 TYR 0.016 0.002 TYR B 57 PHE 0.004 0.001 PHE L 68 TRP 0.003 0.000 TRP W 5 Details of bonding type rmsd covalent geometry : bond 0.00232 (14444) covalent geometry : angle 0.37155 (19665) hydrogen bonds : bond 0.06061 ( 1150) hydrogen bonds : angle 2.40584 ( 3450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2171.09 seconds wall clock time: 38 minutes 45.48 seconds (2325.48 seconds total)