Starting phenix.real_space_refine on Mon Feb 10 21:01:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo1_33333/02_2025/7xo1_33333.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo1_33333/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo1_33333/02_2025/7xo1_33333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo1_33333/02_2025/7xo1_33333.map" model { file = "/net/cci-nas-00/data/ceres_data/7xo1_33333/02_2025/7xo1_33333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo1_33333/02_2025/7xo1_33333.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2550 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, F Time building chain proxies: 1.77, per 1000 atoms: 0.69 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: 0.61 Conformation dependent library (CDL) restraints added in 329.5 milliseconds 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: 0.41 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: 0.58 Time building geometry restraints manager: 0.73 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 0.980 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.400 ------------------------------------------------------------------------------- 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= 0.141 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.001 0.000 HIS B 50 PHE 0.001 0.000 PHE B 94 TYR 0.018 0.005 TYR F 39 *********************** 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 : 0.239 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: 0.9267 time to fit residues: 45.8620 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 : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.120215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093646 restraints weight = 2963.251| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.46 r_work: 0.3199 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2562 Z= 0.298 Angle : 0.537 3.505 3462 Z= 0.301 Chirality : 0.053 0.127 456 Planarity : 0.002 0.006 426 Dihedral : 4.774 13.519 372 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.65 % Allowed : 18.60 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS D 50 PHE 0.002 0.000 PHE A 94 TYR 0.014 0.003 TYR C 39 *********************** 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 51 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.259 Fit side-chains REVERT: F 46 GLU cc_start: 0.7756 (tp30) cc_final: 0.7408 (tp30) REVERT: D 43 LYS cc_start: 0.8629 (mttp) cc_final: 0.8129 (mtpp) REVERT: B 43 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8016 (mtpp) REVERT: C 43 LYS cc_start: 0.8896 (mmtp) cc_final: 0.8431 (mtpp) REVERT: C 97 LYS cc_start: 0.6691 (tptt) cc_final: 0.5675 (mtmt) outliers start: 12 outliers final: 6 residues processed: 51 average time/residue: 0.8050 time to fit residues: 42.5500 Evaluate side-chains 45 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100995 restraints weight = 2922.890| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.59 r_work: 0.3326 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2562 Z= 0.124 Angle : 0.426 2.934 3462 Z= 0.242 Chirality : 0.053 0.134 456 Planarity : 0.001 0.006 426 Dihedral : 4.172 11.662 372 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.16 % Allowed : 21.32 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.001 0.000 PHE B 94 TYR 0.015 0.002 TYR A 39 *********************** 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 47 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.289 Fit side-chains REVERT: A 43 LYS cc_start: 0.8473 (mmtp) cc_final: 0.7969 (mtpp) REVERT: D 43 LYS cc_start: 0.8650 (mttp) cc_final: 0.8140 (mtpp) REVERT: B 43 LYS cc_start: 0.8555 (mmtp) cc_final: 0.7989 (mtpp) REVERT: C 43 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8438 (mtpp) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.9133 time to fit residues: 44.3105 Evaluate side-chains 42 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain B residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 0.0020 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.093521 restraints weight = 2980.084| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.38 r_work: 0.3201 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2240 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= 0.343 Angle : 0.538 3.267 3462 Z= 0.306 Chirality : 0.053 0.125 456 Planarity : 0.002 0.007 426 Dihedral : 4.971 14.242 372 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.71 % Allowed : 23.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 50 PHE 0.003 0.001 PHE B 94 TYR 0.017 0.003 TYR C 39 *********************** 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 47 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.258 Fit side-chains REVERT: F 46 GLU cc_start: 0.7804 (tp30) cc_final: 0.7455 (tp30) REVERT: D 43 LYS cc_start: 0.8646 (mttp) cc_final: 0.8172 (mtpp) REVERT: B 43 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8066 (mtpp) REVERT: C 43 LYS cc_start: 0.8919 (mmtp) cc_final: 0.8460 (mtpp) REVERT: C 97 LYS cc_start: 0.6956 (tptt) cc_final: 0.6134 (mmmt) outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 0.8582 time to fit residues: 41.6818 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 : 0.260 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.121751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095170 restraints weight = 2990.131| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.54 r_work: 0.3232 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2562 Z= 0.209 Angle : 0.485 4.389 3462 Z= 0.274 Chirality : 0.053 0.135 456 Planarity : 0.002 0.007 426 Dihedral : 4.676 12.455 372 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.33 % Allowed : 23.26 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.002 0.000 PHE B 94 TYR 0.016 0.002 TYR A 39 *********************** 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 49 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.267 Fit side-chains REVERT: D 43 LYS cc_start: 0.8690 (mttp) cc_final: 0.8133 (mtpp) REVERT: B 43 LYS cc_start: 0.8538 (mmtp) cc_final: 0.8016 (mtpp) REVERT: C 43 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8444 (mtpp) REVERT: C 97 LYS cc_start: 0.6923 (tptt) cc_final: 0.6097 (mmmt) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.6684 time to fit residues: 34.1779 Evaluate side-chains 46 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER 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 32 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.121347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.094705 restraints weight = 2977.766| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.52 r_work: 0.3232 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2562 Z= 0.222 Angle : 0.479 3.608 3462 Z= 0.272 Chirality : 0.053 0.128 456 Planarity : 0.002 0.008 426 Dihedral : 4.661 12.377 372 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.71 % Allowed : 22.09 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS D 50 PHE 0.002 0.000 PHE B 94 TYR 0.019 0.003 TYR C 39 *********************** 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 51 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.307 Fit side-chains REVERT: D 43 LYS cc_start: 0.8696 (mttp) cc_final: 0.8126 (mtpp) REVERT: B 43 LYS cc_start: 0.8522 (mmtp) cc_final: 0.8009 (mtpp) REVERT: E 97 LYS cc_start: 0.6628 (tptt) cc_final: 0.5778 (mtmt) REVERT: C 43 LYS cc_start: 0.8856 (mmtp) cc_final: 0.8434 (mtpp) REVERT: C 97 LYS cc_start: 0.6907 (tptt) cc_final: 0.6100 (mmmt) outliers start: 7 outliers final: 6 residues processed: 50 average time/residue: 0.7720 time to fit residues: 40.0627 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 : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 0.0030 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094496 restraints weight = 2989.498| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.51 r_work: 0.3240 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2562 Z= 0.243 Angle : 0.489 2.975 3462 Z= 0.279 Chirality : 0.053 0.132 456 Planarity : 0.002 0.007 426 Dihedral : 4.765 12.687 372 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 : 3.10 % Allowed : 21.71 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.002 0.000 PHE B 94 TYR 0.018 0.002 TYR A 39 *********************** 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 52 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.340 Fit side-chains REVERT: D 43 LYS cc_start: 0.8689 (mttp) cc_final: 0.8159 (mtpp) REVERT: B 43 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8043 (mtpp) REVERT: E 97 LYS cc_start: 0.6679 (tptt) cc_final: 0.5900 (mtmt) REVERT: C 43 LYS cc_start: 0.8865 (mmtp) cc_final: 0.8447 (mtpp) REVERT: C 97 LYS cc_start: 0.6932 (tptt) cc_final: 0.6177 (mmmt) outliers start: 8 outliers final: 7 residues processed: 51 average time/residue: 0.7881 time to fit residues: 41.6917 Evaluate side-chains 50 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.118956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092748 restraints weight = 2939.267| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.42 r_work: 0.3193 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 2562 Z= 0.382 Angle : 0.578 5.038 3462 Z= 0.327 Chirality : 0.054 0.128 456 Planarity : 0.002 0.007 426 Dihedral : 5.249 13.493 372 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (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 HIS 0.004 0.002 HIS B 50 PHE 0.003 0.001 PHE B 94 TYR 0.017 0.003 TYR A 39 *********************** 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 48 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.296 Fit side-chains REVERT: D 43 LYS cc_start: 0.8635 (mttp) cc_final: 0.8148 (mtpp) REVERT: B 43 LYS cc_start: 0.8655 (mmtp) cc_final: 0.8056 (mtpp) REVERT: E 97 LYS cc_start: 0.6739 (tptt) cc_final: 0.6011 (mtmt) REVERT: C 43 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8441 (mtpp) REVERT: C 97 LYS cc_start: 0.7083 (tptt) cc_final: 0.6158 (mmmt) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.7695 time to fit residues: 38.4243 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 : 0.296 ------------------------------------------------------------------------------- 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 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 35 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.094533 restraints weight = 2920.447| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.33 r_work: 0.3207 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2562 Z= 0.338 Angle : 0.564 4.840 3462 Z= 0.317 Chirality : 0.054 0.134 456 Planarity : 0.002 0.007 426 Dihedral : 5.204 13.067 372 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.71 % Allowed : 23.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.004 0.002 HIS B 50 PHE 0.003 0.000 PHE B 94 TYR 0.018 0.002 TYR A 39 *********************** 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 : 0.296 Fit side-chains REVERT: D 43 LYS cc_start: 0.8713 (mttp) cc_final: 0.8205 (mtpp) REVERT: B 43 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8079 (mtpp) REVERT: E 97 LYS cc_start: 0.6772 (tptt) cc_final: 0.6059 (mtmt) REVERT: C 43 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8454 (mtpp) REVERT: C 97 LYS cc_start: 0.7109 (tptt) cc_final: 0.6178 (mmmt) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.6741 time to fit residues: 35.8018 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 : 0.296 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 30 optimal weight: 0.0030 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.122428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.095846 restraints weight = 2935.907| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.51 r_work: 0.3252 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2308 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= 0.202 Angle : 0.501 4.637 3462 Z= 0.279 Chirality : 0.053 0.131 456 Planarity : 0.002 0.008 426 Dihedral : 4.742 12.455 372 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.33 % Allowed : 24.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.002 0.000 PHE B 94 TYR 0.018 0.003 TYR A 39 ********************** 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 50 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.289 Fit side-chains REVERT: D 43 LYS cc_start: 0.8703 (mttp) cc_final: 0.8142 (mtpp) REVERT: B 43 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8026 (mtpp) REVERT: E 97 LYS cc_start: 0.6665 (tptt) cc_final: 0.5977 (mtmt) REVERT: C 43 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8438 (mtpp) REVERT: C 97 LYS cc_start: 0.6973 (tptt) cc_final: 0.6193 (mmmt) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.7247 time to fit residues: 37.7216 Evaluate side-chains 48 residues out of total 258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain B residue 42 SER 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 4 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 0.0070 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 overall best weight: 2.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094464 restraints weight = 2926.601| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.48 r_work: 0.3232 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2369 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= 0.252 Angle : 0.523 4.452 3462 Z= 0.292 Chirality : 0.053 0.130 456 Planarity : 0.002 0.007 426 Dihedral : 4.867 12.892 372 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.71 % Allowed : 24.81 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.003 0.002 HIS B 50 PHE 0.003 0.000 PHE B 94 TYR 0.017 0.003 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2030.61 seconds wall clock time: 36 minutes 39.41 seconds (2199.41 seconds total)