Starting phenix.real_space_refine on Tue Mar 3 11:46:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e7d_26587/03_2026/8e7d_26587.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e7d_26587/03_2026/8e7d_26587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e7d_26587/03_2026/8e7d_26587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e7d_26587/03_2026/8e7d_26587.map" model { file = "/net/cci-nas-00/data/ceres_data/8e7d_26587/03_2026/8e7d_26587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e7d_26587/03_2026/8e7d_26587.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 5 5.16 5 C 2285 2.51 5 N 575 2.21 5 O 660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3525 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.48, per 1000 atoms: 0.14 Number of scatterers: 3525 At special positions: 0 Unit cell: (71.02, 83.74, 40.28, 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 5 16.00 O 660 8.00 N 575 7.00 C 2285 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: 0.18 Conformation dependent library (CDL) restraints added in 116.6 milliseconds 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 860 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 51.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16 removed outlier: 6.787A pdb=" N MET B 13 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL D 16 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS B 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET A 13 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 16 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 20 removed outlier: 6.762A pdb=" N ALA B 19 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 19 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 27 removed outlier: 6.414A pdb=" N ALA B 25 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA A 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 30 through 33 removed outlier: 6.270A pdb=" N VAL A 30 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE C 33 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 32 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 30 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N PHE E 33 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 32 " --> pdb=" O PHE E 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 60 through 73 removed outlier: 6.917A pdb=" N GLU B 61 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU D 62 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU B 63 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY B 67 " --> pdb=" O GLU D 66 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE D 68 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU A 61 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU B 62 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU A 63 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY A 67 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 68 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N THR A 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N GLU C 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU A 62 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N VAL C 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 64 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLY C 67 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N GLU A 66 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N TYR C 69 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE A 68 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 71 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE C 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU A 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N THR C 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N GLU E 63 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C 62 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N VAL E 65 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE C 64 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLY E 67 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLU C 66 " --> pdb=" O GLY E 67 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N TYR E 69 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE C 68 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL E 71 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE E 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU C 72 " --> pdb=" O ILE E 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 80 removed outlier: 6.989A pdb=" N SER B 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR D 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N LYS A 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N TRP C 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N LYS C 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N TRP E 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR C 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 99 removed outlier: 6.913A pdb=" N HIS A 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL C 93 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU A 92 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE C 95 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 94 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA C 97 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR A 96 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP C 99 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A 98 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N HIS C 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL E 93 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU C 92 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE E 95 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 94 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA E 97 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR C 96 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ASP E 99 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN C 98 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.612A pdb=" N ARG B 103 " --> pdb=" O ARG D 104 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR D 106 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TYR B 105 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG A 103 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N THR B 106 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR A 105 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 121 removed outlier: 6.795A pdb=" N SER D 115 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER B 115 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER A 115 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR C 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER A 117 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ALA C 120 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR A 119 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER C 115 " --> pdb=" O TYR E 116 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR E 118 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER C 117 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ALA E 120 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR C 119 " --> pdb=" O ALA E 120 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 228 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: 0.35 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1031 1.33 - 1.45: 564 1.45 - 1.57: 2005 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 3610 Sorted by residual: bond pdb=" CA TYR E 116 " pdb=" C TYR E 116 " ideal model delta sigma weight residual 1.520 1.480 0.041 1.17e-02 7.31e+03 1.22e+01 bond pdb=" CA TYR C 116 " pdb=" C TYR C 116 " ideal model delta sigma weight residual 1.520 1.480 0.040 1.17e-02 7.31e+03 1.19e+01 bond pdb=" CA TYR D 116 " pdb=" C TYR D 116 " ideal model delta sigma weight residual 1.520 1.480 0.040 1.17e-02 7.31e+03 1.18e+01 bond pdb=" CA TYR B 116 " pdb=" C TYR B 116 " ideal model delta sigma weight residual 1.520 1.481 0.040 1.17e-02 7.31e+03 1.15e+01 bond pdb=" CA TYR A 116 " pdb=" C TYR A 116 " ideal model delta sigma weight residual 1.520 1.481 0.040 1.17e-02 7.31e+03 1.15e+01 ... (remaining 3605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 4233 0.85 - 1.70: 474 1.70 - 2.55: 142 2.55 - 3.40: 46 3.40 - 4.25: 25 Bond angle restraints: 4920 Sorted by residual: angle pdb=" CA TYR C 114 " pdb=" CB TYR C 114 " pdb=" CG TYR C 114 " ideal model delta sigma weight residual 113.90 118.15 -4.25 1.80e+00 3.09e-01 5.58e+00 angle pdb=" CA TYR B 114 " pdb=" CB TYR B 114 " pdb=" CG TYR B 114 " ideal model delta sigma weight residual 113.90 118.15 -4.25 1.80e+00 3.09e-01 5.58e+00 angle pdb=" CA TYR E 114 " pdb=" CB TYR E 114 " pdb=" CG TYR E 114 " ideal model delta sigma weight residual 113.90 118.14 -4.24 1.80e+00 3.09e-01 5.54e+00 angle pdb=" CA TYR D 114 " pdb=" CB TYR D 114 " pdb=" CG TYR D 114 " ideal model delta sigma weight residual 113.90 118.12 -4.22 1.80e+00 3.09e-01 5.51e+00 angle pdb=" CA TYR A 114 " pdb=" CB TYR A 114 " pdb=" CG TYR A 114 " ideal model delta sigma weight residual 113.90 118.12 -4.22 1.80e+00 3.09e-01 5.51e+00 ... (remaining 4915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 1755 16.88 - 33.76: 270 33.76 - 50.64: 85 50.64 - 67.52: 10 67.52 - 84.40: 5 Dihedral angle restraints: 2125 sinusoidal: 800 harmonic: 1325 Sorted by residual: dihedral pdb=" CA PHE C 87 " pdb=" C PHE C 87 " pdb=" N HIS C 88 " pdb=" CA HIS C 88 " 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 PHE E 87 " pdb=" C PHE E 87 " pdb=" N HIS E 88 " pdb=" CA HIS E 88 " 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 PHE A 87 " pdb=" C PHE A 87 " pdb=" N HIS A 88 " pdb=" CA HIS A 88 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 364 0.041 - 0.082: 118 0.082 - 0.123: 88 0.123 - 0.164: 10 0.164 - 0.205: 5 Chirality restraints: 585 Sorted by residual: chirality pdb=" CA PRO C 86 " pdb=" N PRO C 86 " pdb=" C PRO C 86 " pdb=" CB PRO C 86 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO A 86 " pdb=" N PRO A 86 " pdb=" C PRO A 86 " pdb=" CB PRO A 86 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO D 86 " pdb=" N PRO D 86 " pdb=" C PRO D 86 " pdb=" CB PRO D 86 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 582 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 101 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO C 102 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 101 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 102 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 101 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 102 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " 0.056 5.00e-02 4.00e+02 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 82 2.67 - 3.23: 3305 3.23 - 3.79: 5427 3.79 - 4.34: 7566 4.34 - 4.90: 13516 Nonbonded interactions: 29896 Sorted by model distance: nonbonded pdb=" O VAL E 28 " pdb=" OH TYR E 69 " model vdw 2.117 3.040 nonbonded pdb=" O VAL C 28 " pdb=" OH TYR C 69 " model vdw 2.117 3.040 nonbonded pdb=" O VAL B 28 " pdb=" OH TYR B 69 " model vdw 2.117 3.040 nonbonded pdb=" O VAL D 28 " pdb=" OH TYR D 69 " model vdw 2.117 3.040 nonbonded pdb=" O VAL A 28 " pdb=" OH TYR A 69 " model vdw 2.118 3.040 ... (remaining 29891 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.080 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.400 Find NCS groups from input model: 0.020 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 : 0.005 0.051 3610 Z= 0.261 Angle : 0.703 4.253 4920 Z= 0.414 Chirality : 0.056 0.205 585 Planarity : 0.010 0.104 605 Dihedral : 18.191 84.395 1265 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.26 % Allowed : 37.40 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.77 (0.27), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.20), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 103 TYR 0.012 0.002 TYR D 105 PHE 0.014 0.003 PHE A 95 TRP 0.012 0.004 TRP E 79 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 3610) covalent geometry : angle 0.70335 ( 4920) hydrogen bonds : bond 0.17909 ( 76) hydrogen bonds : angle 10.07425 ( 228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.127 Fit side-chains REVERT: B 99 ASP cc_start: 0.7719 (t0) cc_final: 0.7469 (t0) REVERT: C 89 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8015 (mm-30) REVERT: C 99 ASP cc_start: 0.7656 (t0) cc_final: 0.7369 (t0) REVERT: D 13 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7696 (tmm) REVERT: D 99 ASP cc_start: 0.6627 (t0) cc_final: 0.6396 (p0) REVERT: D 114 TYR cc_start: 0.8409 (p90) cc_final: 0.5504 (m-10) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.0462 time to fit residues: 6.6504 Evaluate side-chains 73 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 31 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.121622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.102787 restraints weight = 5989.705| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 3.25 r_work: 0.4135 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3610 Z= 0.260 Angle : 0.706 7.944 4920 Z= 0.389 Chirality : 0.053 0.173 585 Planarity : 0.007 0.057 605 Dihedral : 6.307 17.712 488 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.19 % Allowed : 32.21 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.31), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 104 TYR 0.031 0.003 TYR A 114 PHE 0.026 0.002 PHE A 33 TRP 0.006 0.001 TRP E 79 HIS 0.004 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00597 ( 3610) covalent geometry : angle 0.70556 ( 4920) hydrogen bonds : bond 0.03966 ( 76) hydrogen bonds : angle 7.24488 ( 228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.127 Fit side-chains REVERT: A 13 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7082 (tmm) REVERT: A 112 SER cc_start: 0.9153 (m) cc_final: 0.8610 (p) REVERT: B 13 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6863 (tmm) REVERT: B 89 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 99 ASP cc_start: 0.8158 (t0) cc_final: 0.7789 (t0) REVERT: B 114 TYR cc_start: 0.9183 (p90) cc_final: 0.8968 (p90) REVERT: C 63 GLU cc_start: 0.7782 (mp0) cc_final: 0.7465 (mp0) REVERT: C 75 THR cc_start: 0.8824 (t) cc_final: 0.8536 (p) REVERT: C 89 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7517 (mm-30) REVERT: C 99 ASP cc_start: 0.8009 (t0) cc_final: 0.7505 (t0) REVERT: C 112 SER cc_start: 0.9370 (p) cc_final: 0.8679 (m) REVERT: D 13 MET cc_start: 0.8166 (ttm) cc_final: 0.7512 (tmm) REVERT: D 74 ASP cc_start: 0.8953 (t0) cc_final: 0.8598 (t0) REVERT: D 99 ASP cc_start: 0.6673 (t0) cc_final: 0.6455 (p0) REVERT: E 74 ASP cc_start: 0.8677 (t70) cc_final: 0.7711 (t0) REVERT: E 103 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.5002 (mmp-170) outliers start: 20 outliers final: 8 residues processed: 98 average time/residue: 0.0495 time to fit residues: 6.3359 Evaluate side-chains 89 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 103 ARG Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.250337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.204612 restraints weight = 6569.381| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 1.77 r_work: 0.4395 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.4320 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3610 Z= 0.116 Angle : 0.605 8.340 4920 Z= 0.324 Chirality : 0.052 0.134 585 Planarity : 0.005 0.041 605 Dihedral : 5.710 15.247 485 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.42 % Allowed : 31.17 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 104 TYR 0.027 0.002 TYR A 114 PHE 0.024 0.002 PHE D 33 TRP 0.005 0.001 TRP E 79 HIS 0.003 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 3610) covalent geometry : angle 0.60508 ( 4920) hydrogen bonds : bond 0.03284 ( 76) hydrogen bonds : angle 6.95592 ( 228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7535 (tmm) REVERT: A 112 SER cc_start: 0.9033 (m) cc_final: 0.8513 (p) REVERT: B 13 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7413 (tmm) REVERT: B 89 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7775 (mm-30) REVERT: B 99 ASP cc_start: 0.7868 (t0) cc_final: 0.7226 (t0) REVERT: C 99 ASP cc_start: 0.7542 (t0) cc_final: 0.7324 (t0) REVERT: C 112 SER cc_start: 0.9176 (p) cc_final: 0.8798 (m) REVERT: D 13 MET cc_start: 0.8111 (ttm) cc_final: 0.7806 (tmm) REVERT: D 74 ASP cc_start: 0.8729 (t0) cc_final: 0.8423 (t0) REVERT: D 92 GLU cc_start: 0.8051 (mp0) cc_final: 0.7697 (mp0) REVERT: D 114 TYR cc_start: 0.7960 (p90) cc_final: 0.7750 (p90) REVERT: E 74 ASP cc_start: 0.8675 (t70) cc_final: 0.8065 (t0) REVERT: E 88 HIS cc_start: 0.8340 (t-170) cc_final: 0.6586 (p-80) REVERT: E 89 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8018 (mm-30) REVERT: E 99 ASP cc_start: 0.7776 (t0) cc_final: 0.7523 (t0) REVERT: E 112 SER cc_start: 0.9074 (p) cc_final: 0.8763 (m) outliers start: 17 outliers final: 8 residues processed: 97 average time/residue: 0.0532 time to fit residues: 6.5875 Evaluate side-chains 85 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS E 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.139356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.121313 restraints weight = 5658.321| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 3.07 r_work: 0.4248 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3610 Z= 0.131 Angle : 0.607 8.934 4920 Z= 0.320 Chirality : 0.051 0.130 585 Planarity : 0.004 0.030 605 Dihedral : 5.469 14.594 485 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.19 % Allowed : 31.95 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.021 0.002 TYR A 114 PHE 0.018 0.002 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3610) covalent geometry : angle 0.60655 ( 4920) hydrogen bonds : bond 0.02955 ( 76) hydrogen bonds : angle 6.61863 ( 228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.092 Fit side-chains REVERT: A 103 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7139 (mtt180) REVERT: A 112 SER cc_start: 0.9157 (m) cc_final: 0.8573 (p) REVERT: B 99 ASP cc_start: 0.7672 (t0) cc_final: 0.7242 (t0) REVERT: B 103 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7158 (mtm180) REVERT: C 99 ASP cc_start: 0.8110 (t0) cc_final: 0.7162 (t0) REVERT: C 112 SER cc_start: 0.9276 (p) cc_final: 0.8811 (m) REVERT: D 13 MET cc_start: 0.8306 (ttm) cc_final: 0.7803 (tmm) REVERT: D 74 ASP cc_start: 0.8821 (t0) cc_final: 0.8518 (t0) REVERT: D 92 GLU cc_start: 0.7642 (mp0) cc_final: 0.7323 (mp0) REVERT: D 114 TYR cc_start: 0.7942 (p90) cc_final: 0.7681 (p90) REVERT: E 66 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7781 (tm-30) REVERT: E 89 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8150 (mm-30) REVERT: E 95 PHE cc_start: 0.8887 (t80) cc_final: 0.8446 (t80) REVERT: E 103 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.5207 (mmp-170) REVERT: E 112 SER cc_start: 0.9246 (p) cc_final: 0.8897 (m) outliers start: 20 outliers final: 9 residues processed: 91 average time/residue: 0.0718 time to fit residues: 7.8655 Evaluate side-chains 83 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 103 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 0.0870 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.131357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.113276 restraints weight = 5811.338| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 3.12 r_work: 0.4245 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 3610 Z= 0.257 Angle : 0.675 8.669 4920 Z= 0.358 Chirality : 0.051 0.134 585 Planarity : 0.004 0.028 605 Dihedral : 5.621 15.690 485 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 6.75 % Allowed : 30.13 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 103 TYR 0.020 0.003 TYR E 114 PHE 0.017 0.002 PHE B 33 TRP 0.003 0.001 TRP B 79 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 3610) covalent geometry : angle 0.67505 ( 4920) hydrogen bonds : bond 0.03312 ( 76) hydrogen bonds : angle 6.36977 ( 228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.241 Fit side-chains REVERT: A 112 SER cc_start: 0.9062 (m) cc_final: 0.8607 (p) REVERT: B 13 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7019 (tmm) REVERT: B 99 ASP cc_start: 0.7585 (t0) cc_final: 0.7287 (t70) REVERT: B 103 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7277 (mtt90) REVERT: C 95 PHE cc_start: 0.8897 (t80) cc_final: 0.8675 (t80) REVERT: C 99 ASP cc_start: 0.8244 (t0) cc_final: 0.7592 (t0) REVERT: C 110 LEU cc_start: 0.9176 (tt) cc_final: 0.8945 (tt) REVERT: C 112 SER cc_start: 0.9283 (p) cc_final: 0.8749 (m) REVERT: D 13 MET cc_start: 0.8321 (ttm) cc_final: 0.7786 (tmm) REVERT: D 92 GLU cc_start: 0.7782 (mp0) cc_final: 0.7538 (mp0) REVERT: D 114 TYR cc_start: 0.8050 (p90) cc_final: 0.7730 (p90) outliers start: 26 outliers final: 17 residues processed: 79 average time/residue: 0.0476 time to fit residues: 4.9501 Evaluate side-chains 84 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.134068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.116463 restraints weight = 5806.353| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.97 r_work: 0.4377 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4275 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3610 Z= 0.194 Angle : 0.659 8.759 4920 Z= 0.348 Chirality : 0.051 0.161 585 Planarity : 0.004 0.031 605 Dihedral : 5.528 16.219 485 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.42 % Allowed : 33.25 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 103 TYR 0.019 0.002 TYR A 114 PHE 0.018 0.002 PHE C 33 TRP 0.003 0.001 TRP B 79 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 3610) covalent geometry : angle 0.65868 ( 4920) hydrogen bonds : bond 0.03031 ( 76) hydrogen bonds : angle 6.30710 ( 228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.097 Fit side-chains REVERT: A 112 SER cc_start: 0.8968 (m) cc_final: 0.8593 (p) REVERT: B 13 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7485 (tmm) REVERT: B 99 ASP cc_start: 0.7531 (t0) cc_final: 0.7131 (t0) REVERT: C 95 PHE cc_start: 0.8971 (t80) cc_final: 0.8583 (t80) REVERT: C 99 ASP cc_start: 0.7947 (t0) cc_final: 0.7500 (t0) REVERT: C 110 LEU cc_start: 0.9333 (tt) cc_final: 0.9088 (tt) REVERT: C 112 SER cc_start: 0.9109 (p) cc_final: 0.8699 (m) REVERT: D 13 MET cc_start: 0.8353 (ttm) cc_final: 0.8005 (tmm) REVERT: E 95 PHE cc_start: 0.8890 (t80) cc_final: 0.8316 (t80) outliers start: 17 outliers final: 11 residues processed: 81 average time/residue: 0.0529 time to fit residues: 5.5435 Evaluate side-chains 76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.129658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.112379 restraints weight = 6077.397| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.95 r_work: 0.4110 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 3610 Z= 0.282 Angle : 0.723 8.640 4920 Z= 0.382 Chirality : 0.053 0.167 585 Planarity : 0.004 0.027 605 Dihedral : 5.679 18.140 485 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.94 % Allowed : 31.69 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 103 TYR 0.018 0.002 TYR E 114 PHE 0.022 0.002 PHE B 33 TRP 0.004 0.001 TRP B 79 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00659 ( 3610) covalent geometry : angle 0.72331 ( 4920) hydrogen bonds : bond 0.03296 ( 76) hydrogen bonds : angle 6.21033 ( 228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.141 Fit side-chains REVERT: A 13 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.6898 (tmm) REVERT: A 112 SER cc_start: 0.9107 (m) cc_final: 0.8713 (p) REVERT: B 13 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.6910 (tmm) REVERT: B 99 ASP cc_start: 0.7717 (t0) cc_final: 0.7218 (t0) REVERT: C 13 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.6995 (tmm) REVERT: C 95 PHE cc_start: 0.8872 (t80) cc_final: 0.8493 (t80) REVERT: C 99 ASP cc_start: 0.8177 (t0) cc_final: 0.7736 (t0) REVERT: C 110 LEU cc_start: 0.9111 (tt) cc_final: 0.8879 (tt) REVERT: C 112 SER cc_start: 0.9314 (p) cc_final: 0.8784 (m) REVERT: D 13 MET cc_start: 0.8539 (ttm) cc_final: 0.7924 (tmm) REVERT: E 95 PHE cc_start: 0.8743 (t80) cc_final: 0.8093 (t80) outliers start: 19 outliers final: 12 residues processed: 75 average time/residue: 0.0438 time to fit residues: 4.5443 Evaluate side-chains 80 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 0.0470 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 0.0270 chunk 34 optimal weight: 3.9990 overall best weight: 1.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.138898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.118257 restraints weight = 6055.039| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 3.06 r_work: 0.4228 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3610 Z= 0.161 Angle : 0.679 8.744 4920 Z= 0.355 Chirality : 0.053 0.136 585 Planarity : 0.004 0.026 605 Dihedral : 5.525 17.458 485 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 4.68 % Allowed : 31.69 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.019 0.002 TYR A 114 PHE 0.021 0.002 PHE B 33 TRP 0.002 0.001 TRP B 79 HIS 0.003 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 3610) covalent geometry : angle 0.67881 ( 4920) hydrogen bonds : bond 0.02866 ( 76) hydrogen bonds : angle 6.22071 ( 228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.164 Fit side-chains REVERT: A 13 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7156 (tmm) REVERT: A 92 GLU cc_start: 0.8011 (mp0) cc_final: 0.7804 (mp0) REVERT: A 112 SER cc_start: 0.9131 (m) cc_final: 0.8640 (p) REVERT: B 13 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7131 (tmm) REVERT: B 99 ASP cc_start: 0.7685 (t0) cc_final: 0.7090 (t0) REVERT: C 13 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7338 (tmm) REVERT: C 95 PHE cc_start: 0.8866 (t80) cc_final: 0.8611 (t80) REVERT: C 99 ASP cc_start: 0.7916 (t0) cc_final: 0.7573 (t0) REVERT: C 112 SER cc_start: 0.9263 (p) cc_final: 0.8824 (m) REVERT: D 13 MET cc_start: 0.8481 (ttm) cc_final: 0.7963 (tmm) REVERT: D 63 GLU cc_start: 0.8506 (mp0) cc_final: 0.8250 (mp0) REVERT: D 114 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7204 (p90) REVERT: E 112 SER cc_start: 0.9310 (p) cc_final: 0.9018 (m) outliers start: 18 outliers final: 10 residues processed: 75 average time/residue: 0.0456 time to fit residues: 4.6856 Evaluate side-chains 74 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.133664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.116293 restraints weight = 5909.376| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.95 r_work: 0.4204 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3610 Z= 0.229 Angle : 0.733 8.810 4920 Z= 0.377 Chirality : 0.053 0.167 585 Planarity : 0.004 0.026 605 Dihedral : 5.625 21.359 485 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 4.42 % Allowed : 31.95 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 103 TYR 0.017 0.002 TYR A 114 PHE 0.022 0.002 PHE B 33 TRP 0.003 0.001 TRP C 79 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 3610) covalent geometry : angle 0.73335 ( 4920) hydrogen bonds : bond 0.03047 ( 76) hydrogen bonds : angle 6.10641 ( 228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.130 Fit side-chains REVERT: A 13 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7159 (tmm) REVERT: A 112 SER cc_start: 0.9081 (m) cc_final: 0.8606 (p) REVERT: B 13 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7167 (tmm) REVERT: B 99 ASP cc_start: 0.7719 (t0) cc_final: 0.7333 (t0) REVERT: C 13 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7347 (tmm) REVERT: C 99 ASP cc_start: 0.7890 (t0) cc_final: 0.7537 (t0) REVERT: C 112 SER cc_start: 0.9315 (p) cc_final: 0.8888 (m) REVERT: D 13 MET cc_start: 0.8492 (ttm) cc_final: 0.7973 (tmm) REVERT: D 114 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7149 (p90) REVERT: E 112 SER cc_start: 0.9277 (p) cc_final: 0.9072 (m) outliers start: 17 outliers final: 11 residues processed: 73 average time/residue: 0.0467 time to fit residues: 4.5576 Evaluate side-chains 78 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.128851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.110875 restraints weight = 6093.423| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 3.09 r_work: 0.4179 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 3610 Z= 0.296 Angle : 0.799 9.255 4920 Z= 0.414 Chirality : 0.055 0.187 585 Planarity : 0.004 0.026 605 Dihedral : 5.831 21.413 485 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 4.68 % Allowed : 31.95 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 103 TYR 0.019 0.003 TYR E 114 PHE 0.022 0.002 PHE B 33 TRP 0.005 0.001 TRP C 79 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00703 ( 3610) covalent geometry : angle 0.79899 ( 4920) hydrogen bonds : bond 0.03281 ( 76) hydrogen bonds : angle 6.06154 ( 228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.164 Fit side-chains REVERT: A 13 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7042 (tmm) REVERT: A 112 SER cc_start: 0.9074 (m) cc_final: 0.8667 (p) REVERT: B 13 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7161 (tmm) REVERT: B 99 ASP cc_start: 0.7779 (t0) cc_final: 0.7188 (t0) REVERT: C 13 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7295 (tmm) REVERT: C 99 ASP cc_start: 0.7947 (t0) cc_final: 0.7641 (t0) REVERT: C 112 SER cc_start: 0.9366 (p) cc_final: 0.8872 (m) REVERT: D 13 MET cc_start: 0.8520 (ttm) cc_final: 0.8025 (tmm) REVERT: D 76 LYS cc_start: 0.8983 (mptt) cc_final: 0.8730 (mptt) REVERT: D 114 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7180 (p90) REVERT: E 63 GLU cc_start: 0.8370 (mp0) cc_final: 0.8072 (pm20) REVERT: E 95 PHE cc_start: 0.9038 (t80) cc_final: 0.8556 (t80) outliers start: 18 outliers final: 13 residues processed: 73 average time/residue: 0.0459 time to fit residues: 4.4442 Evaluate side-chains 80 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.139199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.118697 restraints weight = 6083.240| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 3.05 r_work: 0.4239 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3610 Z= 0.173 Angle : 0.746 9.114 4920 Z= 0.382 Chirality : 0.054 0.169 585 Planarity : 0.003 0.025 605 Dihedral : 5.610 20.422 485 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.68 % Allowed : 31.95 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.019 0.002 TYR A 114 PHE 0.022 0.002 PHE B 33 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 3610) covalent geometry : angle 0.74641 ( 4920) hydrogen bonds : bond 0.02923 ( 76) hydrogen bonds : angle 6.11923 ( 228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 881.20 seconds wall clock time: 15 minutes 48.38 seconds (948.38 seconds total)