Starting phenix.real_space_refine on Sat Sep 12 00:57:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s6f_54626/09_2026/9s6f_54626.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s6f_54626/09_2026/9s6f_54626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s6f_54626/09_2026/9s6f_54626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s6f_54626/09_2026/9s6f_54626.map" model { file = "/net/cci-nas-00/data/ceres_data/9s6f_54626/09_2026/9s6f_54626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s6f_54626/09_2026/9s6f_54626.cif" } resolution = 3.3 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 7680 2.51 5 N 2464 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12592 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P Time building chain proxies: 1.62, per 1000 atoms: 0.13 Number of scatterers: 12592 At special positions: 0 Unit cell: (107.16, 107.16, 108.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2368 8.00 N 2464 7.00 C 7680 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: 1.00 Conformation dependent library (CDL) restraints added in 570.1 milliseconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 77.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 36 through 46 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA B 86 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 36 through 46 Processing helix chain 'C' and resid 50 through 61 Processing helix chain 'C' and resid 68 through 81 removed outlier: 3.521A pdb=" N GLY C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.867A pdb=" N ALA C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 24 through 28 Processing helix chain 'D' and resid 36 through 46 Processing helix chain 'D' and resid 50 through 61 Processing helix chain 'D' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA D 86 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 12 through 20 Processing helix chain 'E' and resid 24 through 28 Processing helix chain 'E' and resid 36 through 46 Processing helix chain 'E' and resid 50 through 61 Processing helix chain 'E' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA E 86 " --> pdb=" O GLN E 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 12 through 20 Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 36 through 46 Processing helix chain 'F' and resid 50 through 61 Processing helix chain 'F' and resid 68 through 81 removed outlier: 3.521A pdb=" N GLY F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER F 87 " --> pdb=" O ASP F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 11 Processing helix chain 'G' and resid 12 through 20 Processing helix chain 'G' and resid 24 through 28 Processing helix chain 'G' and resid 36 through 46 Processing helix chain 'G' and resid 50 through 61 Processing helix chain 'G' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY G 81 " --> pdb=" O LEU G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER G 87 " --> pdb=" O ASP G 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 11 Processing helix chain 'H' and resid 12 through 20 Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 36 through 46 Processing helix chain 'H' and resid 50 through 61 Processing helix chain 'H' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA H 86 " --> pdb=" O GLN H 82 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER H 87 " --> pdb=" O ASP H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 11 Processing helix chain 'I' and resid 12 through 20 Processing helix chain 'I' and resid 24 through 28 Processing helix chain 'I' and resid 36 through 46 Processing helix chain 'I' and resid 50 through 61 Processing helix chain 'I' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY I 81 " --> pdb=" O LEU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER I 87 " --> pdb=" O ASP I 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 11 Processing helix chain 'J' and resid 12 through 20 Processing helix chain 'J' and resid 24 through 28 Processing helix chain 'J' and resid 36 through 46 Processing helix chain 'J' and resid 50 through 61 Processing helix chain 'J' and resid 68 through 81 removed outlier: 3.521A pdb=" N GLY J 81 " --> pdb=" O LEU J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 95 removed outlier: 3.867A pdb=" N ALA J 86 " --> pdb=" O GLN J 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER J 87 " --> pdb=" O ASP J 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 11 Processing helix chain 'K' and resid 12 through 20 Processing helix chain 'K' and resid 24 through 28 Processing helix chain 'K' and resid 36 through 46 Processing helix chain 'K' and resid 50 through 61 Processing helix chain 'K' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY K 81 " --> pdb=" O LEU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA K 86 " --> pdb=" O GLN K 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER K 87 " --> pdb=" O ASP K 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 11 Processing helix chain 'L' and resid 12 through 20 Processing helix chain 'L' and resid 24 through 28 Processing helix chain 'L' and resid 36 through 46 Processing helix chain 'L' and resid 50 through 61 Processing helix chain 'L' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY L 81 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA L 86 " --> pdb=" O GLN L 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER L 87 " --> pdb=" O ASP L 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 11 Processing helix chain 'M' and resid 12 through 20 Processing helix chain 'M' and resid 24 through 28 Processing helix chain 'M' and resid 36 through 46 Processing helix chain 'M' and resid 50 through 61 Processing helix chain 'M' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA M 86 " --> pdb=" O GLN M 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER M 87 " --> pdb=" O ASP M 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 11 Processing helix chain 'N' and resid 12 through 20 Processing helix chain 'N' and resid 24 through 28 Processing helix chain 'N' and resid 36 through 46 Processing helix chain 'N' and resid 50 through 61 Processing helix chain 'N' and resid 68 through 81 removed outlier: 3.521A pdb=" N GLY N 81 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA N 86 " --> pdb=" O GLN N 82 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER N 87 " --> pdb=" O ASP N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 11 Processing helix chain 'O' and resid 12 through 20 Processing helix chain 'O' and resid 24 through 28 Processing helix chain 'O' and resid 36 through 46 Processing helix chain 'O' and resid 50 through 61 Processing helix chain 'O' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY O 81 " --> pdb=" O LEU O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA O 86 " --> pdb=" O GLN O 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER O 87 " --> pdb=" O ASP O 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 11 Processing helix chain 'P' and resid 12 through 20 Processing helix chain 'P' and resid 24 through 28 Processing helix chain 'P' and resid 36 through 46 Processing helix chain 'P' and resid 50 through 61 Processing helix chain 'P' and resid 68 through 81 removed outlier: 3.520A pdb=" N GLY P 81 " --> pdb=" O LEU P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 95 removed outlier: 3.866A pdb=" N ALA P 86 " --> pdb=" O GLN P 82 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER P 87 " --> pdb=" O ASP P 83 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4640 1.35 - 1.46: 2256 1.46 - 1.58: 5680 1.58 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 12704 Sorted by residual: bond pdb=" CB ASP L 79 " pdb=" CG ASP L 79 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.84e-01 bond pdb=" CB ASP E 79 " pdb=" CG ASP E 79 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.84e-01 bond pdb=" CB ASP I 79 " pdb=" CG ASP I 79 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.74e-01 bond pdb=" CB ASP B 79 " pdb=" CG ASP B 79 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.74e-01 bond pdb=" CB ASP J 79 " pdb=" CG ASP J 79 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.66e-01 ... (remaining 12699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 15788 0.90 - 1.80: 966 1.80 - 2.70: 174 2.70 - 3.60: 64 3.60 - 4.49: 32 Bond angle restraints: 17024 Sorted by residual: angle pdb=" CA ASP C 79 " pdb=" CB ASP C 79 " pdb=" CG ASP C 79 " ideal model delta sigma weight residual 112.60 114.62 -2.02 1.00e+00 1.00e+00 4.08e+00 angle pdb=" CA ASP J 79 " pdb=" CB ASP J 79 " pdb=" CG ASP J 79 " ideal model delta sigma weight residual 112.60 114.62 -2.02 1.00e+00 1.00e+00 4.08e+00 angle pdb=" CA ASP D 79 " pdb=" CB ASP D 79 " pdb=" CG ASP D 79 " ideal model delta sigma weight residual 112.60 114.62 -2.02 1.00e+00 1.00e+00 4.06e+00 angle pdb=" CA ASP K 79 " pdb=" CB ASP K 79 " pdb=" CG ASP K 79 " ideal model delta sigma weight residual 112.60 114.62 -2.02 1.00e+00 1.00e+00 4.06e+00 angle pdb=" CA ASP P 79 " pdb=" CB ASP P 79 " pdb=" CG ASP P 79 " ideal model delta sigma weight residual 112.60 114.60 -2.00 1.00e+00 1.00e+00 4.00e+00 ... (remaining 17019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.18: 6584 13.18 - 26.36: 696 26.36 - 39.54: 512 39.54 - 52.72: 128 52.72 - 65.90: 96 Dihedral angle restraints: 8016 sinusoidal: 3536 harmonic: 4480 Sorted by residual: dihedral pdb=" N MET H 1 " pdb=" CA MET H 1 " pdb=" CB MET H 1 " pdb=" CG MET H 1 " ideal model delta sinusoidal sigma weight residual -60.00 -116.08 56.08 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" N MET P 1 " pdb=" CA MET P 1 " pdb=" CB MET P 1 " pdb=" CG MET P 1 " ideal model delta sinusoidal sigma weight residual -60.00 -116.08 56.08 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" N MET N 1 " pdb=" CA MET N 1 " pdb=" CB MET N 1 " pdb=" CG MET N 1 " ideal model delta sinusoidal sigma weight residual -60.00 -116.07 56.07 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 8013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1202 0.030 - 0.060: 494 0.060 - 0.091: 128 0.091 - 0.121: 48 0.121 - 0.151: 16 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CA ASP B 79 " pdb=" N ASP B 79 " pdb=" C ASP B 79 " pdb=" CB ASP B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ASP I 79 " pdb=" N ASP I 79 " pdb=" C ASP I 79 " pdb=" CB ASP I 79 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ASP G 79 " pdb=" N ASP G 79 " pdb=" C ASP G 79 " pdb=" CB ASP G 79 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1885 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG P 36 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO P 37 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO P 37 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO P 37 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 36 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO H 37 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO H 37 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 37 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 36 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO K 37 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO K 37 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO K 37 " -0.015 5.00e-02 4.00e+02 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4418 2.86 - 3.37: 10738 3.37 - 3.88: 18746 3.88 - 4.39: 21222 4.39 - 4.90: 38010 Nonbonded interactions: 93134 Sorted by model distance: nonbonded pdb=" NE ARG O 15 " pdb=" OE1 GLU O 19 " model vdw 2.347 3.120 nonbonded pdb=" NE ARG G 15 " pdb=" OE1 GLU G 19 " model vdw 2.347 3.120 nonbonded pdb=" NE ARG J 15 " pdb=" OE1 GLU J 19 " model vdw 2.347 3.120 nonbonded pdb=" NE ARG C 15 " pdb=" OE1 GLU C 19 " model vdw 2.347 3.120 nonbonded pdb=" NE ARG H 15 " pdb=" OE1 GLU H 19 " model vdw 2.347 3.120 ... (remaining 93129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.020 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.790 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.002 0.025 12704 Z= 0.121 Angle : 0.534 4.494 17024 Z= 0.323 Chirality : 0.038 0.151 1888 Planarity : 0.004 0.026 2288 Dihedral : 17.003 65.904 5072 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.59 % Allowed : 22.94 % Favored : 76.47 % 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 are not related in a simple way. whole: 1.42 (0.24), residues: 1520 helix: 1.54 (0.17), residues: 1056 sheet: None (None), residues: 0 loop : -0.38 (0.33), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 65 PHE 0.007 0.001 PHE N 35 TRP 0.001 0.000 TRP C 26 HIS 0.002 0.001 HIS I 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (12704) covalent geometry : angle 0.53406 / 0.32 (17024) hydrogen bonds : bond 0.22384 / 15.03 ( 720) hydrogen bonds : angle 5.00779 / 3.55 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 270 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6568 (mtm) cc_final: 0.6283 (mtm) REVERT: D 39 MET cc_start: 0.6667 (mtm) cc_final: 0.6292 (mtm) REVERT: E 39 MET cc_start: 0.6561 (mtm) cc_final: 0.6214 (mtm) REVERT: K 39 MET cc_start: 0.6670 (mtm) cc_final: 0.6298 (mtm) REVERT: L 39 MET cc_start: 0.6566 (mtm) cc_final: 0.6216 (mtm) REVERT: M 39 MET cc_start: 0.6576 (mtm) cc_final: 0.6289 (mtm) outliers start: 8 outliers final: 0 residues processed: 278 average time/residue: 0.0762 time to fit residues: 34.4238 Evaluate side-chains 212 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0570 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.178358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.163722 restraints weight = 14213.146| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.62 r_work: 0.3861 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 12704 Z= 0.114 Angle : 0.480 4.419 17024 Z= 0.264 Chirality : 0.039 0.143 1888 Planarity : 0.004 0.034 2288 Dihedral : 2.671 7.900 1776 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 3.24 % Allowed : 21.62 % Favored : 75.15 % 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 are not related in a simple way. whole: 1.92 (0.25), residues: 1520 helix: 1.84 (0.17), residues: 1072 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 PHE 0.007 0.001 PHE P 35 TRP 0.002 0.000 TRP N 26 HIS 0.004 0.002 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (12704) covalent geometry : angle 0.48030 / 0.26 (17024) hydrogen bonds : bond 0.03574 / 2.43 ( 720) hydrogen bonds : angle 3.69107 / 2.64 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 0.535 Fit side-chains REVERT: A 39 MET cc_start: 0.6717 (mtm) cc_final: 0.6301 (mtm) REVERT: C 83 ASP cc_start: 0.7965 (m-30) cc_final: 0.7743 (m-30) REVERT: J 83 ASP cc_start: 0.7975 (m-30) cc_final: 0.7747 (m-30) REVERT: M 39 MET cc_start: 0.6716 (mtm) cc_final: 0.6286 (mtm) outliers start: 44 outliers final: 20 residues processed: 278 average time/residue: 0.1057 time to fit residues: 43.5751 Evaluate side-chains 244 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 21 GLN Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain P residue 67 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 113 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 139 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.177071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.162285 restraints weight = 14221.469| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.62 r_work: 0.3842 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 12704 Z= 0.100 Angle : 0.444 4.415 17024 Z= 0.241 Chirality : 0.038 0.136 1888 Planarity : 0.004 0.033 2288 Dihedral : 2.675 9.058 1776 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.94 % Allowed : 22.35 % Favored : 74.71 % 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 are not related in a simple way. whole: 1.90 (0.25), residues: 1520 helix: 1.93 (0.17), residues: 1072 sheet: None (None), residues: 0 loop : -0.32 (0.38), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 36 PHE 0.006 0.001 PHE P 35 TRP 0.002 0.001 TRP B 26 HIS 0.003 0.002 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (12704) covalent geometry : angle 0.44371 / 0.24 (17024) hydrogen bonds : bond 0.03195 / 2.16 ( 720) hydrogen bonds : angle 3.67036 / 2.63 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6696 (mtm) cc_final: 0.6245 (mtm) REVERT: M 39 MET cc_start: 0.6713 (mtm) cc_final: 0.6239 (mtm) outliers start: 40 outliers final: 20 residues processed: 256 average time/residue: 0.0883 time to fit residues: 35.5225 Evaluate side-chains 240 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain N residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 57 optimal weight: 0.0060 chunk 71 optimal weight: 0.3980 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.177910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.162656 restraints weight = 14271.155| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.69 r_work: 0.3851 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12704 Z= 0.094 Angle : 0.445 4.598 17024 Z= 0.239 Chirality : 0.038 0.132 1888 Planarity : 0.003 0.030 2288 Dihedral : 2.603 9.404 1776 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.50 % Allowed : 23.68 % Favored : 73.82 % 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 are not related in a simple way. whole: 1.91 (0.24), residues: 1520 helix: 1.99 (0.17), residues: 1072 sheet: None (None), residues: 0 loop : -0.48 (0.36), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 65 PHE 0.004 0.001 PHE G 73 TRP 0.003 0.001 TRP F 26 HIS 0.003 0.001 HIS K 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (12704) covalent geometry : angle 0.44524 / 0.24 (17024) hydrogen bonds : bond 0.02734 / 1.84 ( 720) hydrogen bonds : angle 3.65110 / 2.62 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6794 (mtm) cc_final: 0.6272 (mtm) REVERT: C 79 ASP cc_start: 0.7343 (p0) cc_final: 0.7129 (p0) REVERT: J 79 ASP cc_start: 0.7324 (p0) cc_final: 0.7116 (p0) REVERT: M 39 MET cc_start: 0.6802 (mtm) cc_final: 0.6250 (mtm) outliers start: 34 outliers final: 24 residues processed: 252 average time/residue: 0.0845 time to fit residues: 34.3804 Evaluate side-chains 256 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 84 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 74 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 106 optimal weight: 0.0470 chunk 55 optimal weight: 2.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.178298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.163763 restraints weight = 14235.002| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.59 r_work: 0.3872 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12704 Z= 0.093 Angle : 0.449 6.904 17024 Z= 0.238 Chirality : 0.037 0.131 1888 Planarity : 0.003 0.029 2288 Dihedral : 2.568 9.291 1776 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.62 % Allowed : 24.26 % Favored : 74.12 % 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 are not related in a simple way. whole: 1.97 (0.24), residues: 1520 helix: 2.05 (0.17), residues: 1072 sheet: None (None), residues: 0 loop : -0.52 (0.36), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 36 PHE 0.004 0.001 PHE J 88 TRP 0.003 0.001 TRP F 26 HIS 0.003 0.002 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (12704) covalent geometry : angle 0.44928 / 0.24 (17024) hydrogen bonds : bond 0.02582 / 1.74 ( 720) hydrogen bonds : angle 3.66290 / 2.62 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8437 (mm-40) REVERT: B 59 ILE cc_start: 0.8756 (mp) cc_final: 0.8507 (mp) REVERT: B 83 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: E 83 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: I 59 ILE cc_start: 0.8752 (mp) cc_final: 0.8500 (mp) REVERT: I 83 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8330 (m-30) REVERT: L 83 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: M 57 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8433 (mm-40) outliers start: 22 outliers final: 12 residues processed: 234 average time/residue: 0.0815 time to fit residues: 31.1293 Evaluate side-chains 234 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain O residue 84 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 3 optimal weight: 0.0010 chunk 53 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.177114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.163016 restraints weight = 14203.347| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.53 r_work: 0.3872 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12704 Z= 0.099 Angle : 0.460 5.921 17024 Z= 0.247 Chirality : 0.038 0.160 1888 Planarity : 0.003 0.028 2288 Dihedral : 2.586 9.238 1776 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.91 % Allowed : 25.15 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.24), residues: 1520 helix: 2.08 (0.17), residues: 1072 sheet: None (None), residues: 0 loop : -0.52 (0.36), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 32 PHE 0.004 0.001 PHE K 88 TRP 0.003 0.001 TRP B 26 HIS 0.004 0.002 HIS M 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (12704) covalent geometry : angle 0.45953 / 0.25 (17024) hydrogen bonds : bond 0.02739 / 1.85 ( 720) hydrogen bonds : angle 3.66636 / 2.61 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6483 (mtm) cc_final: 0.6281 (mtm) REVERT: A 57 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8464 (mm-40) REVERT: B 59 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8448 (mp) REVERT: B 83 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: E 83 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8180 (m-30) REVERT: I 59 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8437 (mp) REVERT: I 83 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8247 (m-30) REVERT: L 83 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: M 39 MET cc_start: 0.6508 (mtm) cc_final: 0.6288 (mtm) REVERT: M 57 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8463 (mm-40) outliers start: 26 outliers final: 18 residues processed: 238 average time/residue: 0.0856 time to fit residues: 32.6325 Evaluate side-chains 242 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 0.0970 chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 0.0670 chunk 94 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.162793 restraints weight = 14111.680| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.66 r_work: 0.3866 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12704 Z= 0.096 Angle : 0.457 6.924 17024 Z= 0.247 Chirality : 0.038 0.155 1888 Planarity : 0.003 0.028 2288 Dihedral : 2.563 9.026 1776 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.21 % Allowed : 26.03 % Favored : 71.76 % 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 are not related in a simple way. whole: 2.00 (0.24), residues: 1520 helix: 2.13 (0.17), residues: 1072 sheet: None (None), residues: 0 loop : -0.67 (0.35), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 90 PHE 0.005 0.001 PHE J 88 TRP 0.003 0.001 TRP E 26 HIS 0.003 0.002 HIS P 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (12704) covalent geometry : angle 0.45744 / 0.25 (17024) hydrogen bonds : bond 0.02576 / 1.74 ( 720) hydrogen bonds : angle 3.67832 / 2.62 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8499 (mm-40) REVERT: B 59 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8446 (mp) REVERT: I 59 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8437 (mp) REVERT: M 57 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8494 (mm-40) outliers start: 30 outliers final: 18 residues processed: 232 average time/residue: 0.0810 time to fit residues: 30.4912 Evaluate side-chains 238 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 70 optimal weight: 0.0370 chunk 32 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.176162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.160962 restraints weight = 14139.940| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.66 r_work: 0.3842 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12704 Z= 0.104 Angle : 0.475 7.289 17024 Z= 0.256 Chirality : 0.039 0.149 1888 Planarity : 0.003 0.028 2288 Dihedral : 2.624 9.146 1776 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.62 % Allowed : 27.06 % Favored : 71.32 % 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 are not related in a simple way. whole: 2.03 (0.24), residues: 1520 helix: 2.13 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -0.60 (0.36), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 32 PHE 0.006 0.001 PHE J 88 TRP 0.003 0.001 TRP E 26 HIS 0.003 0.002 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 (12704) covalent geometry : angle 0.47510 / 0.26 (17024) hydrogen bonds : bond 0.02844 / 1.92 ( 720) hydrogen bonds : angle 3.67657 / 2.61 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8512 (mm-40) REVERT: G 33 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7781 (mm-30) REVERT: M 57 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8504 (mm-40) REVERT: O 33 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7775 (mm-30) outliers start: 22 outliers final: 18 residues processed: 232 average time/residue: 0.0807 time to fit residues: 30.6068 Evaluate side-chains 240 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 111 optimal weight: 0.0010 chunk 34 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.177753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.164091 restraints weight = 14270.705| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.47 r_work: 0.3879 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12704 Z= 0.100 Angle : 0.479 7.635 17024 Z= 0.257 Chirality : 0.038 0.146 1888 Planarity : 0.003 0.029 2288 Dihedral : 2.568 8.991 1776 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.32 % Allowed : 27.21 % Favored : 71.47 % 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 are not related in a simple way. whole: 2.02 (0.24), residues: 1520 helix: 2.03 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 13 PHE 0.004 0.001 PHE J 88 TRP 0.004 0.001 TRP H 26 HIS 0.003 0.002 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (12704) covalent geometry : angle 0.47861 / 0.26 (17024) hydrogen bonds : bond 0.02599 / 1.76 ( 720) hydrogen bonds : angle 3.69000 / 2.63 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8448 (mm-40) REVERT: G 33 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7784 (mm-30) REVERT: M 57 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8446 (mm-40) REVERT: O 33 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7783 (mm-30) outliers start: 18 outliers final: 14 residues processed: 232 average time/residue: 0.0809 time to fit residues: 30.4644 Evaluate side-chains 232 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 87 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 0.0270 chunk 88 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 47 optimal weight: 0.0050 overall best weight: 0.3852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.178839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.165234 restraints weight = 14263.911| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.46 r_work: 0.3899 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12704 Z= 0.099 Angle : 0.479 7.958 17024 Z= 0.258 Chirality : 0.038 0.152 1888 Planarity : 0.003 0.028 2288 Dihedral : 2.532 8.791 1776 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.03 % Allowed : 27.50 % Favored : 71.47 % 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 are not related in a simple way. whole: 2.05 (0.24), residues: 1520 helix: 2.05 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -0.42 (0.36), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 36 PHE 0.004 0.001 PHE B 35 TRP 0.004 0.001 TRP B 26 HIS 0.003 0.001 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (12704) covalent geometry : angle 0.47865 / 0.26 (17024) hydrogen bonds : bond 0.02418 / 1.62 ( 720) hydrogen bonds : angle 3.67651 / 2.62 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8458 (mm-40) REVERT: A 83 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: G 33 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7785 (mm-30) REVERT: M 57 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8457 (mm-40) REVERT: M 83 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: O 33 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7800 (mm-30) outliers start: 14 outliers final: 12 residues processed: 226 average time/residue: 0.0832 time to fit residues: 30.5890 Evaluate side-chains 230 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.175605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.160318 restraints weight = 14331.605| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.67 r_work: 0.3833 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12704 Z= 0.115 Angle : 0.510 8.093 17024 Z= 0.272 Chirality : 0.040 0.161 1888 Planarity : 0.003 0.028 2288 Dihedral : 2.696 9.271 1776 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.18 % Allowed : 27.21 % Favored : 71.62 % 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 are not related in a simple way. whole: 2.07 (0.24), residues: 1520 helix: 2.01 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -0.25 (0.38), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 36 PHE 0.007 0.001 PHE J 88 TRP 0.004 0.001 TRP K 26 HIS 0.004 0.002 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12704) covalent geometry : angle 0.51023 / 0.27 (17024) hydrogen bonds : bond 0.03097 / 2.09 ( 720) hydrogen bonds : angle 3.69803 / 2.62 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2802.35 seconds wall clock time: 48 minutes 39.76 seconds (2919.76 seconds total)