Starting phenix.real_space_refine on Wed Oct 9 14:15:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jey_36203/10_2024/8jey_36203.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jey_36203/10_2024/8jey_36203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jey_36203/10_2024/8jey_36203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jey_36203/10_2024/8jey_36203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jey_36203/10_2024/8jey_36203.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jey_36203/10_2024/8jey_36203.cif" } resolution = 2.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1914 2.51 5 N 528 2.21 5 O 606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 3060 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Time building chain proxies: 2.70, per 1000 atoms: 0.88 Number of scatterers: 3060 At special positions: 0 Unit cell: (75.53, 107.07, 34.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 606 8.00 N 528 7.00 C 1914 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: 0.71 Conformation dependent library (CDL) restraints added in 394.9 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 6.215A pdb=" N VAL A 3 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LYS B 6 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET A 5 " --> pdb=" O LYS B 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.523A pdb=" N ALA A 11 " --> pdb=" O LYS C 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 16 removed outlier: 6.701A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 23 through 29 removed outlier: 9.036A pdb=" N LYS A 23 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N VAL B 26 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A 25 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLU B 28 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 27 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN A 24 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY C 25 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 40 removed outlier: 6.924A pdb=" N GLY B 36 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY A 36 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TYR C 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.586A pdb=" N LYS A 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 52 removed outlier: 5.995A pdb=" N VAL A 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL B 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 66 removed outlier: 8.676A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N THR B 59 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N LYS A 58 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N GLU B 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS A 60 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N VAL B 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASN B 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA C 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU A 57 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 58 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 59 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS C 60 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU A 61 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.490A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.215A pdb=" N VAL D 3 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LYS E 6 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET D 5 " --> pdb=" O LYS E 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.524A pdb=" N ALA D 11 " --> pdb=" O LYS F 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 15 through 16 removed outlier: 6.701A pdb=" N VAL D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 23 through 29 removed outlier: 9.034A pdb=" N LYS D 23 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N VAL E 26 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY D 25 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N GLU E 28 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA D 27 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN D 24 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY F 25 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 35 through 40 removed outlier: 6.924A pdb=" N GLY E 36 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY D 36 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TYR F 39 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.586A pdb=" N LYS D 43 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 49 through 52 removed outlier: 5.994A pdb=" N VAL D 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY D 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 55 through 66 removed outlier: 8.675A pdb=" N ALA D 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N THR E 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N LYS D 58 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N GLU E 61 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS D 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N VAL E 63 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASN E 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA F 56 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU D 57 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS F 58 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR D 59 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS F 60 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU D 61 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 69 through 71 removed outlier: 6.490A pdb=" N ALA D 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 46 hydrogen bonds defined for protein. 138 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: 0.68 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1002 1.34 - 1.46: 335 1.46 - 1.57: 1711 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 3072 Sorted by residual: bond pdb=" N VAL A 26 " pdb=" CA VAL A 26 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.48e+00 bond pdb=" N VAL E 26 " pdb=" CA VAL E 26 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.06e+00 bond pdb=" N VAL D 26 " pdb=" CA VAL D 26 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.06e+00 bond pdb=" N VAL C 26 " pdb=" CA VAL C 26 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.89e+00 bond pdb=" N VAL B 26 " pdb=" CA VAL B 26 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.88e+00 ... (remaining 3067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 3573 0.97 - 1.94: 403 1.94 - 2.91: 92 2.91 - 3.88: 24 3.88 - 4.84: 18 Bond angle restraints: 4110 Sorted by residual: angle pdb=" N GLU E 13 " pdb=" CA GLU E 13 " pdb=" C GLU E 13 " ideal model delta sigma weight residual 112.58 108.44 4.14 1.22e+00 6.72e-01 1.15e+01 angle pdb=" N GLU D 13 " pdb=" CA GLU D 13 " pdb=" C GLU D 13 " ideal model delta sigma weight residual 112.58 108.45 4.13 1.22e+00 6.72e-01 1.15e+01 angle pdb=" N GLU B 13 " pdb=" CA GLU B 13 " pdb=" C GLU B 13 " ideal model delta sigma weight residual 112.58 108.46 4.12 1.22e+00 6.72e-01 1.14e+01 angle pdb=" N GLU A 13 " pdb=" CA GLU A 13 " pdb=" C GLU A 13 " ideal model delta sigma weight residual 112.58 108.47 4.11 1.22e+00 6.72e-01 1.14e+01 angle pdb=" N GLU F 13 " pdb=" CA GLU F 13 " pdb=" C GLU F 13 " ideal model delta sigma weight residual 112.58 108.51 4.07 1.22e+00 6.72e-01 1.11e+01 ... (remaining 4105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.63: 1508 9.63 - 19.26: 244 19.26 - 28.89: 60 28.89 - 38.52: 36 38.52 - 48.15: 12 Dihedral angle restraints: 1860 sinusoidal: 684 harmonic: 1176 Sorted by residual: dihedral pdb=" CA LYS C 58 " pdb=" C LYS C 58 " pdb=" N THR C 59 " pdb=" CA THR C 59 " ideal model delta harmonic sigma weight residual -180.00 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA LYS F 58 " pdb=" C LYS F 58 " pdb=" N THR F 59 " pdb=" CA THR F 59 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA LYS D 58 " pdb=" C LYS D 58 " pdb=" N THR D 59 " pdb=" CA THR D 59 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 1857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 315 0.038 - 0.076: 82 0.076 - 0.114: 93 0.114 - 0.152: 11 0.152 - 0.190: 9 Chirality restraints: 510 Sorted by residual: chirality pdb=" CA GLU D 20 " pdb=" N GLU D 20 " pdb=" C GLU D 20 " pdb=" CB GLU D 20 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA GLU E 20 " pdb=" N GLU E 20 " pdb=" C GLU E 20 " pdb=" CB GLU E 20 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA GLU A 20 " pdb=" N GLU A 20 " pdb=" C GLU A 20 " pdb=" CB GLU A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 507 not shown) Planarity restraints: 510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 8 " 0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C LEU F 8 " -0.017 2.00e-02 2.50e+03 pdb=" O LEU F 8 " 0.006 2.00e-02 2.50e+03 pdb=" N SER F 9 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 8 " -0.005 2.00e-02 2.50e+03 9.97e-03 9.94e-01 pdb=" C LEU C 8 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU C 8 " -0.006 2.00e-02 2.50e+03 pdb=" N SER C 9 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 8 " -0.005 2.00e-02 2.50e+03 9.73e-03 9.48e-01 pdb=" C LEU A 8 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A 8 " -0.006 2.00e-02 2.50e+03 pdb=" N SER A 9 " -0.006 2.00e-02 2.50e+03 ... (remaining 507 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 935 2.85 - 3.36: 2546 3.36 - 3.88: 4675 3.88 - 4.39: 4989 4.39 - 4.90: 10500 Nonbonded interactions: 23645 Sorted by model distance: nonbonded pdb=" NZ LYS B 6 " pdb=" OE2 GLU B 20 " model vdw 2.339 3.120 nonbonded pdb=" NZ LYS F 6 " pdb=" OE2 GLU F 20 " model vdw 2.339 3.120 nonbonded pdb=" NZ LYS E 6 " pdb=" OE2 GLU E 20 " model vdw 2.340 3.120 nonbonded pdb=" NZ LYS A 6 " pdb=" OE2 GLU A 20 " model vdw 2.340 3.120 nonbonded pdb=" NZ LYS C 6 " pdb=" OE2 GLU C 20 " model vdw 2.340 3.120 ... (remaining 23640 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.440 Find NCS groups from input model: 0.100 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:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.004 0.035 3072 Z= 0.271 Angle : 0.746 4.845 4110 Z= 0.464 Chirality : 0.058 0.190 510 Planarity : 0.002 0.010 510 Dihedral : 11.672 48.153 1116 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.60 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 50 PHE 0.007 0.002 PHE E 4 TYR 0.008 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.366 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.3996 time to fit residues: 81.8186 Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 0.0980 chunk 17 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3072 Z= 0.123 Angle : 0.463 5.078 4110 Z= 0.255 Chirality : 0.050 0.123 510 Planarity : 0.002 0.008 510 Dihedral : 4.632 16.948 432 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.43 % Favored : 93.33 % Rotamer: Outliers : 3.21 % Allowed : 8.65 % Favored : 88.14 % 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: -4.12 (0.27), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.004 0.001 PHE A 4 TYR 0.008 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.325 Fit side-chains outliers start: 10 outliers final: 0 residues processed: 61 average time/residue: 1.3216 time to fit residues: 82.7584 Evaluate side-chains 49 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS F 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3072 Z= 0.366 Angle : 0.589 6.543 4110 Z= 0.319 Chirality : 0.052 0.133 510 Planarity : 0.003 0.008 510 Dihedral : 5.493 16.297 432 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.88 % Allowed : 10.26 % Favored : 86.86 % 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: -3.84 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.008 0.003 PHE F 4 TYR 0.017 0.004 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.329 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 57 average time/residue: 1.5775 time to fit residues: 92.1563 Evaluate side-chains 60 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3072 Z= 0.250 Angle : 0.535 5.990 4110 Z= 0.282 Chirality : 0.052 0.141 510 Planarity : 0.002 0.009 510 Dihedral : 5.315 15.934 432 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.24 % Allowed : 12.18 % Favored : 85.58 % 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: -3.72 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.005 0.002 PHE A 4 TYR 0.012 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.372 Fit side-chains REVERT: C 5 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6864 (ttt) REVERT: E 5 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.6997 (ttt) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 1.2740 time to fit residues: 75.8582 Evaluate side-chains 57 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 3072 Z= 0.249 Angle : 0.545 6.751 4110 Z= 0.284 Chirality : 0.052 0.145 510 Planarity : 0.002 0.011 510 Dihedral : 5.358 17.242 432 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.56 % Allowed : 12.82 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.63 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.004 0.002 PHE B 4 TYR 0.012 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.356 Fit side-chains REVERT: C 5 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6892 (ttt) REVERT: E 5 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7014 (ttt) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 1.3647 time to fit residues: 82.5474 Evaluate side-chains 62 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 0.0370 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 overall best weight: 1.4460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 3072 Z= 0.181 Angle : 0.527 8.330 4110 Z= 0.266 Chirality : 0.051 0.140 510 Planarity : 0.002 0.013 510 Dihedral : 5.091 17.024 432 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.21 % Allowed : 13.14 % Favored : 83.65 % 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: -3.55 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.003 0.001 PHE F 4 TYR 0.009 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.363 Fit side-chains REVERT: C 5 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6809 (ttt) outliers start: 10 outliers final: 5 residues processed: 59 average time/residue: 1.3317 time to fit residues: 80.6150 Evaluate side-chains 61 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3072 Z= 0.287 Angle : 0.575 7.603 4110 Z= 0.297 Chirality : 0.053 0.160 510 Planarity : 0.002 0.016 510 Dihedral : 5.440 17.857 432 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.56 % Allowed : 13.46 % Favored : 83.97 % 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: -3.51 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.007 0.002 PHE F 4 TYR 0.014 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.371 Fit side-chains REVERT: C 5 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6879 (ttt) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 1.4078 time to fit residues: 85.2765 Evaluate side-chains 64 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3072 Z= 0.145 Angle : 0.522 9.541 4110 Z= 0.258 Chirality : 0.051 0.140 510 Planarity : 0.002 0.016 510 Dihedral : 4.965 17.062 432 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.56 % Allowed : 14.74 % Favored : 82.69 % 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: -3.44 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.003 0.001 PHE F 4 TYR 0.008 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.369 Fit side-chains REVERT: C 5 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6762 (ttt) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 1.3757 time to fit residues: 86.5125 Evaluate side-chains 60 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3072 Z= 0.354 Angle : 0.621 8.850 4110 Z= 0.320 Chirality : 0.053 0.183 510 Planarity : 0.003 0.018 510 Dihedral : 5.579 17.870 432 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.24 % Allowed : 15.06 % Favored : 82.69 % 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: -3.44 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.009 0.003 PHE F 4 TYR 0.017 0.004 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.382 Fit side-chains REVERT: C 5 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6903 (ttt) REVERT: D 5 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6853 (ttt) outliers start: 7 outliers final: 5 residues processed: 59 average time/residue: 1.2948 time to fit residues: 78.7255 Evaluate side-chains 65 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3072 Z= 0.285 Angle : 0.593 9.774 4110 Z= 0.301 Chirality : 0.053 0.184 510 Planarity : 0.002 0.018 510 Dihedral : 5.506 17.354 432 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.56 % Allowed : 14.10 % Favored : 83.33 % 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: -3.43 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.007 0.002 PHE F 4 TYR 0.013 0.003 TYR F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.371 Fit side-chains REVERT: C 5 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6870 (ttt) REVERT: D 5 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6854 (ttt) REVERT: E 5 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7001 (ttt) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 1.3581 time to fit residues: 83.6627 Evaluate side-chains 66 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 8 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.169080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.155458 restraints weight = 3414.009| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 1.61 r_work: 0.4158 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4059 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3072 Z= 0.258 Angle : 0.584 10.171 4110 Z= 0.294 Chirality : 0.053 0.199 510 Planarity : 0.002 0.020 510 Dihedral : 5.406 17.198 432 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.56 % Allowed : 14.10 % Favored : 83.33 % 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: -3.40 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.007 0.002 PHE F 4 TYR 0.012 0.003 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.06 seconds wall clock time: 37 minutes 19.69 seconds (2239.69 seconds total)