Starting phenix.real_space_refine on Fri Aug 22 12:56:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo1_33333/08_2025/7xo1_33333.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo1_33333/08_2025/7xo1_33333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xo1_33333/08_2025/7xo1_33333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo1_33333/08_2025/7xo1_33333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xo1_33333/08_2025/7xo1_33333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo1_33333/08_2025/7xo1_33333.map" } resolution = 3.0 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= 0.004 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 1602 2.51 5 N 444 2.21 5 O 504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2550 Number of models: 1 Model: "" Number of chains: 1 Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Restraints were copied for chains: A, D, B, E, C Time building chain proxies: 0.52, per 1000 atoms: 0.20 Number of scatterers: 2550 At special positions: 0 Unit cell: (128.26, 71.02, 33.92, 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 504 8.00 N 444 7.00 C 1602 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: 0.12 Conformation dependent library (CDL) restraints added in 75.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 37 through 42 removed outlier: 6.508A pdb=" N VAL F 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL D 40 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR F 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER D 42 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY F 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL D 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL E 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 48 through 57 removed outlier: 6.547A pdb=" N VAL F 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLY D 51 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N HIS F 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA D 53 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N VAL F 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.526A pdb=" N VAL D 55 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N THR F 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N GLU D 57 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N ALA F 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL D 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLY E 51 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N HIS D 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA E 53 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N VAL D 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N VAL E 55 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N THR D 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N GLU E 57 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ALA D 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 61 through 66 removed outlier: 6.220A pdb=" N GLU F 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR D 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL F 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL D 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN F 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 69 through 72 Processing sheet with id=AA5, first strand: chain 'F' and resid 75 through 79 Processing sheet with id=AA6, first strand: chain 'F' and resid 82 through 83 removed outlier: 6.261A pdb=" N VAL F 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL D 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 95 through 96 Processing sheet with id=AA8, first strand: chain 'A' and resid 37 through 42 removed outlier: 6.503A pdb=" N VAL A 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL B 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 37 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL C 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER C 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 48 through 57 removed outlier: 6.563A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLY C 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N HIS B 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA C 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL B 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N VAL C 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N THR B 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 10.363A pdb=" N GLU C 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N ALA B 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.231A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU B 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR C 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 69 through 72 Processing sheet with id=AB3, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AB4, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.273A pdb=" N VAL A 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL B 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 95 through 96 32 hydrogen bonds defined for protein. 96 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: 0.20 Time building geometry restraints manager: 0.17 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: 438 1.29 - 1.36: 402 1.36 - 1.42: 102 1.42 - 1.48: 420 1.48 - 1.55: 1200 Bond restraints: 2562 Sorted by residual: bond pdb=" CB LYS F 97 " pdb=" CG LYS F 97 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.59e-01 bond pdb=" CB LYS A 97 " pdb=" CG LYS A 97 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.42e-01 bond pdb=" CB LYS D 97 " pdb=" CG LYS D 97 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.21e-01 bond pdb=" CB LYS E 97 " pdb=" CG LYS E 97 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.18e-01 bond pdb=" CB LYS C 97 " pdb=" CG LYS C 97 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.17e-01 ... (remaining 2557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 3313 0.95 - 1.91: 101 1.91 - 2.86: 24 2.86 - 3.82: 12 3.82 - 4.77: 12 Bond angle restraints: 3462 Sorted by residual: angle pdb=" CA LYS B 97 " pdb=" CB LYS B 97 " pdb=" CG LYS B 97 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.69e+00 angle pdb=" CA LYS E 97 " pdb=" CB LYS E 97 " pdb=" CG LYS E 97 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.69e+00 angle pdb=" CA LYS C 97 " pdb=" CB LYS C 97 " pdb=" CG LYS C 97 " ideal model delta sigma weight residual 114.10 118.86 -4.76 2.00e+00 2.50e-01 5.67e+00 angle pdb=" CA LYS D 97 " pdb=" CB LYS D 97 " pdb=" CG LYS D 97 " ideal model delta sigma weight residual 114.10 118.85 -4.75 2.00e+00 2.50e-01 5.65e+00 angle pdb=" CA LYS A 97 " pdb=" CB LYS A 97 " pdb=" CG LYS A 97 " ideal model delta sigma weight residual 114.10 118.85 -4.75 2.00e+00 2.50e-01 5.64e+00 ... (remaining 3457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 1314 16.18 - 32.36: 132 32.36 - 48.53: 12 48.53 - 64.71: 18 64.71 - 80.89: 12 Dihedral angle restraints: 1488 sinusoidal: 492 harmonic: 996 Sorted by residual: dihedral pdb=" CA LYS D 43 " pdb=" CB LYS D 43 " pdb=" CG LYS D 43 " pdb=" CD LYS D 43 " ideal model delta sinusoidal sigma weight residual -60.00 -111.69 51.69 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA LYS B 43 " pdb=" CB LYS B 43 " pdb=" CG LYS B 43 " pdb=" CD LYS B 43 " ideal model delta sinusoidal sigma weight residual -60.00 -111.69 51.69 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA LYS C 43 " pdb=" CB LYS C 43 " pdb=" CG LYS C 43 " pdb=" CD LYS C 43 " ideal model delta sinusoidal sigma weight residual -60.00 -111.66 51.66 3 1.50e+01 4.44e-03 9.04e+00 ... (remaining 1485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 244 0.027 - 0.053: 89 0.053 - 0.080: 33 0.080 - 0.107: 41 0.107 - 0.133: 49 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA ILE F 88 " pdb=" N ILE F 88 " pdb=" C ILE F 88 " pdb=" CB ILE F 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE D 88 " pdb=" N ILE D 88 " pdb=" C ILE D 88 " pdb=" CB ILE D 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 453 not shown) Planarity restraints: 426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 39 " -0.006 2.00e-02 2.50e+03 7.34e-03 1.08e+00 pdb=" CG TYR F 39 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR F 39 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR F 39 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR F 39 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 39 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 39 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 39 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 39 " 0.006 2.00e-02 2.50e+03 7.34e-03 1.08e+00 pdb=" CG TYR C 39 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 39 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 39 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 39 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 39 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 39 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 39 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 39 " 0.006 2.00e-02 2.50e+03 7.33e-03 1.07e+00 pdb=" CG TYR A 39 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 39 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 39 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 39 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 39 " 0.000 2.00e-02 2.50e+03 ... (remaining 423 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 383 2.79 - 3.32: 2171 3.32 - 3.85: 3983 3.85 - 4.37: 4040 4.37 - 4.90: 8391 Nonbonded interactions: 18968 Sorted by model distance: nonbonded pdb=" OE1 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN A 62 " pdb=" OG1 THR A 64 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.270 3.040 nonbonded pdb=" OE1 GLN D 62 " pdb=" OG1 THR D 64 " model vdw 2.270 3.040 ... (remaining 18963 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: 0.01 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'E' selection = chain 'C' } 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: 2.110 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.340 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:8.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 0.026 2562 Z= 0.105 Angle : 0.528 4.771 3462 Z= 0.288 Chirality : 0.055 0.133 456 Planarity : 0.002 0.008 426 Dihedral : 16.422 80.891 864 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 18.60 % Favored : 81.40 % 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: -2.46 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.005 TYR F 39 PHE 0.001 0.000 PHE B 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 2562) covalent geometry : angle 0.52784 ( 3462) hydrogen bonds : bond 0.14982 ( 32) hydrogen bonds : angle 6.21100 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.060 Fit side-chains REVERT: A 43 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8087 (mtpp) REVERT: B 43 LYS cc_start: 0.8604 (mmtp) cc_final: 0.8074 (mtpp) REVERT: E 43 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8339 (mtpp) REVERT: C 43 LYS cc_start: 0.8745 (mmtp) cc_final: 0.8348 (mtpp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.3058 time to fit residues: 15.1284 Evaluate side-chains 44 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 62 GLN A 62 GLN D 62 GLN D 65 ASN B 62 GLN B 65 ASN E 65 ASN C 65 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.130637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.104023 restraints weight = 2899.511| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.56 r_work: 0.3368 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2562 Z= 0.087 Angle : 0.423 2.798 3462 Z= 0.238 Chirality : 0.053 0.129 456 Planarity : 0.001 0.006 426 Dihedral : 3.783 11.021 372 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.55 % Allowed : 21.32 % Favored : 77.13 % 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: -2.38 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR D 39 PHE 0.001 0.000 PHE A 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 2562) covalent geometry : angle 0.42317 ( 3462) hydrogen bonds : bond 0.02106 ( 32) hydrogen bonds : angle 4.03201 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.098 Fit side-chains REVERT: A 43 LYS cc_start: 0.8565 (mmtp) cc_final: 0.8068 (mtpp) REVERT: D 43 LYS cc_start: 0.8668 (mttp) cc_final: 0.8131 (mtpp) REVERT: B 43 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8030 (mtpp) REVERT: C 43 LYS cc_start: 0.8882 (mmtp) cc_final: 0.8421 (mtpp) outliers start: 4 outliers final: 0 residues processed: 45 average time/residue: 0.4298 time to fit residues: 19.9186 Evaluate side-chains 41 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN E 65 ASN C 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.115781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089511 restraints weight = 3021.615| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.43 r_work: 0.3161 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.032 2562 Z= 0.363 Angle : 0.663 4.189 3462 Z= 0.378 Chirality : 0.056 0.134 456 Planarity : 0.002 0.008 426 Dihedral : 5.505 14.894 372 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.88 % Allowed : 21.32 % Favored : 74.81 % 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: -2.38 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR A 39 PHE 0.004 0.001 PHE B 94 HIS 0.005 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00806 ( 2562) covalent geometry : angle 0.66264 ( 3462) hydrogen bonds : bond 0.03968 ( 32) hydrogen bonds : angle 3.93503 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.105 Fit side-chains REVERT: D 43 LYS cc_start: 0.8631 (mttp) cc_final: 0.8146 (mtpp) REVERT: B 43 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8068 (mtpp) REVERT: B 46 GLU cc_start: 0.8029 (tp30) cc_final: 0.7738 (tp30) REVERT: C 43 LYS cc_start: 0.8938 (mmtp) cc_final: 0.8468 (mtpp) REVERT: C 97 LYS cc_start: 0.7009 (tptt) cc_final: 0.6043 (mmmt) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.4788 time to fit residues: 26.0714 Evaluate side-chains 49 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.122967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096396 restraints weight = 2958.879| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.53 r_work: 0.3254 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2562 Z= 0.135 Angle : 0.486 3.187 3462 Z= 0.272 Chirality : 0.053 0.136 456 Planarity : 0.002 0.013 426 Dihedral : 4.685 12.640 372 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.10 % Allowed : 23.26 % Favored : 73.64 % 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: -2.29 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR A 39 PHE 0.001 0.000 PHE B 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2562) covalent geometry : angle 0.48599 ( 3462) hydrogen bonds : bond 0.02320 ( 32) hydrogen bonds : angle 3.68571 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.105 Fit side-chains REVERT: A 43 LYS cc_start: 0.8479 (mmtp) cc_final: 0.7969 (mtpp) REVERT: D 43 LYS cc_start: 0.8708 (mttp) cc_final: 0.8155 (mtpp) REVERT: B 43 LYS cc_start: 0.8550 (mmtp) cc_final: 0.8000 (mtpp) REVERT: C 43 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8437 (mtpp) REVERT: C 97 LYS cc_start: 0.6874 (tptt) cc_final: 0.6036 (mmmt) outliers start: 8 outliers final: 7 residues processed: 51 average time/residue: 0.3530 time to fit residues: 18.6737 Evaluate side-chains 45 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.4980 chunk 12 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.119981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093343 restraints weight = 2926.012| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.49 r_work: 0.3203 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2562 Z= 0.193 Angle : 0.520 3.441 3462 Z= 0.293 Chirality : 0.053 0.126 456 Planarity : 0.002 0.011 426 Dihedral : 4.891 14.138 372 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.71 % Allowed : 24.03 % Favored : 73.26 % 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: -2.25 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR A 39 PHE 0.002 0.000 PHE B 94 HIS 0.003 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 2562) covalent geometry : angle 0.52026 ( 3462) hydrogen bonds : bond 0.02701 ( 32) hydrogen bonds : angle 3.77533 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.106 Fit side-chains REVERT: D 43 LYS cc_start: 0.8624 (mttp) cc_final: 0.8119 (mtpp) REVERT: B 43 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8009 (mtpp) REVERT: C 43 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8434 (mtpp) REVERT: C 97 LYS cc_start: 0.6952 (tptt) cc_final: 0.6101 (mmmt) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.3911 time to fit residues: 19.4021 Evaluate side-chains 47 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.119922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093211 restraints weight = 3003.572| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.52 r_work: 0.3218 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2562 Z= 0.199 Angle : 0.539 4.568 3462 Z= 0.302 Chirality : 0.053 0.133 456 Planarity : 0.002 0.011 426 Dihedral : 4.988 14.097 372 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.71 % Allowed : 24.42 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.22 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR A 39 PHE 0.003 0.000 PHE B 94 HIS 0.003 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 2562) covalent geometry : angle 0.53900 ( 3462) hydrogen bonds : bond 0.02703 ( 32) hydrogen bonds : angle 3.77125 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.093 Fit side-chains REVERT: D 43 LYS cc_start: 0.8708 (mttp) cc_final: 0.8183 (mtpp) REVERT: B 43 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8060 (mtpp) REVERT: E 97 LYS cc_start: 0.6823 (tptt) cc_final: 0.5917 (mtmt) REVERT: C 43 LYS cc_start: 0.8867 (mmtp) cc_final: 0.8460 (mtpp) REVERT: C 97 LYS cc_start: 0.7032 (tptt) cc_final: 0.6190 (mmmt) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.3801 time to fit residues: 18.8904 Evaluate side-chains 46 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 0.3980 chunk 13 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092857 restraints weight = 2920.510| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.37 r_work: 0.3207 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 2562 Z= 0.228 Angle : 0.556 3.896 3462 Z= 0.313 Chirality : 0.053 0.129 456 Planarity : 0.002 0.010 426 Dihedral : 5.153 14.602 372 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.71 % Allowed : 25.19 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.19 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR A 39 PHE 0.003 0.000 PHE B 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 2562) covalent geometry : angle 0.55618 ( 3462) hydrogen bonds : bond 0.02880 ( 32) hydrogen bonds : angle 3.83163 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.131 Fit side-chains REVERT: D 43 LYS cc_start: 0.8652 (mttp) cc_final: 0.8190 (mtpp) REVERT: B 43 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8083 (mtpp) REVERT: E 97 LYS cc_start: 0.6887 (tptt) cc_final: 0.6096 (mtmt) REVERT: C 43 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8462 (mtpp) REVERT: C 97 LYS cc_start: 0.7081 (tptt) cc_final: 0.6254 (mmmt) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.4302 time to fit residues: 21.7457 Evaluate side-chains 48 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.124059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097303 restraints weight = 2942.497| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.53 r_work: 0.3265 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2562 Z= 0.130 Angle : 0.487 4.196 3462 Z= 0.271 Chirality : 0.053 0.135 456 Planarity : 0.002 0.015 426 Dihedral : 4.594 12.170 372 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.71 % Allowed : 25.19 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.10 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.003 TYR C 39 PHE 0.002 0.000 PHE B 94 HIS 0.003 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 2562) covalent geometry : angle 0.48711 ( 3462) hydrogen bonds : bond 0.02007 ( 32) hydrogen bonds : angle 3.65217 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.130 Fit side-chains REVERT: F 46 GLU cc_start: 0.7935 (tp30) cc_final: 0.7542 (tp30) REVERT: D 43 LYS cc_start: 0.8694 (mttp) cc_final: 0.8150 (mtpp) REVERT: B 43 LYS cc_start: 0.8574 (mmtp) cc_final: 0.8061 (mtpp) REVERT: E 97 LYS cc_start: 0.6600 (tptt) cc_final: 0.5811 (mtmt) REVERT: C 43 LYS cc_start: 0.8859 (mmtp) cc_final: 0.8431 (mtpp) REVERT: C 97 LYS cc_start: 0.6955 (tptt) cc_final: 0.6184 (mmmt) outliers start: 7 outliers final: 6 residues processed: 53 average time/residue: 0.4035 time to fit residues: 22.1234 Evaluate side-chains 50 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 29 optimal weight: 0.0470 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.122434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095596 restraints weight = 2983.243| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.52 r_work: 0.3246 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2562 Z= 0.143 Angle : 0.494 4.199 3462 Z= 0.275 Chirality : 0.053 0.128 456 Planarity : 0.002 0.014 426 Dihedral : 4.606 12.525 372 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.71 % Allowed : 25.97 % 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 aren not related in a simple way. whole: -2.08 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.003 TYR A 39 PHE 0.002 0.000 PHE B 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 2562) covalent geometry : angle 0.49402 ( 3462) hydrogen bonds : bond 0.02204 ( 32) hydrogen bonds : angle 3.67447 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.121 Fit side-chains REVERT: F 46 GLU cc_start: 0.7896 (tp30) cc_final: 0.7519 (tp30) REVERT: D 43 LYS cc_start: 0.8709 (mttp) cc_final: 0.8134 (mtpp) REVERT: B 43 LYS cc_start: 0.8655 (mmtp) cc_final: 0.8051 (mtpp) REVERT: E 97 LYS cc_start: 0.6621 (tptt) cc_final: 0.5897 (mtmt) REVERT: C 43 LYS cc_start: 0.8860 (mmtp) cc_final: 0.8432 (mtpp) REVERT: C 97 LYS cc_start: 0.6960 (tptt) cc_final: 0.6185 (mmmt) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.4071 time to fit residues: 21.4579 Evaluate side-chains 50 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.119367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092808 restraints weight = 3012.329| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.48 r_work: 0.3201 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2562 Z= 0.244 Angle : 0.568 4.232 3462 Z= 0.321 Chirality : 0.054 0.131 456 Planarity : 0.002 0.015 426 Dihedral : 5.153 13.401 372 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.71 % Allowed : 25.58 % Favored : 71.71 % 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 aren not related in a simple way. whole: -2.11 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.003 TYR A 39 PHE 0.003 0.001 PHE B 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 2562) covalent geometry : angle 0.56801 ( 3462) hydrogen bonds : bond 0.03036 ( 32) hydrogen bonds : angle 3.82021 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.113 Fit side-chains REVERT: D 43 LYS cc_start: 0.8710 (mttp) cc_final: 0.8194 (mtpp) REVERT: B 43 LYS cc_start: 0.8686 (mmtp) cc_final: 0.8082 (mtpp) REVERT: E 97 LYS cc_start: 0.6856 (tptt) cc_final: 0.6140 (mtmt) REVERT: C 43 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8466 (mtpp) REVERT: C 97 LYS cc_start: 0.7082 (tptt) cc_final: 0.6160 (mmmt) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.4050 time to fit residues: 21.3703 Evaluate side-chains 49 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.121399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094620 restraints weight = 2975.223| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.51 r_work: 0.3241 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2562 Z= 0.171 Angle : 0.520 4.392 3462 Z= 0.291 Chirality : 0.053 0.131 456 Planarity : 0.002 0.017 426 Dihedral : 4.881 12.878 372 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.71 % Allowed : 25.58 % Favored : 71.71 % 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 aren not related in a simple way. whole: -2.09 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR A 39 PHE 0.002 0.000 PHE B 94 HIS 0.003 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 2562) covalent geometry : angle 0.52018 ( 3462) hydrogen bonds : bond 0.02483 ( 32) hydrogen bonds : angle 3.72948 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1076.66 seconds wall clock time: 19 minutes 12.87 seconds (1152.87 seconds total)