Starting phenix.real_space_refine on Fri Dec 27 08:16:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e7d_26587/12_2024/8e7d_26587.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e7d_26587/12_2024/8e7d_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_26587/12_2024/8e7d_26587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e7d_26587/12_2024/8e7d_26587.map" model { file = "/net/cci-nas-00/data/ceres_data/8e7d_26587/12_2024/8e7d_26587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e7d_26587/12_2024/8e7d_26587.cif" } resolution = 3.31 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 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D Time building chain proxies: 2.09, per 1000 atoms: 0.59 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: 0.80 Conformation dependent library (CDL) restraints added in 434.7 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: 0.51 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: 0.94 Time building geometry restraints manager: 0.95 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: 0.00 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.310 Find NCS groups from input model: 0.110 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- 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= 0.351 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 (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: -4.77 (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 TRP 0.012 0.004 TRP E 79 HIS 0.003 0.001 HIS B 88 PHE 0.014 0.003 PHE A 95 TYR 0.012 0.002 TYR D 105 ARG 0.005 0.001 ARG E 103 *********************** 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 : 0.413 Fit side-chains REVERT: B 99 ASP cc_start: 0.7720 (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: 0.1166 time to fit residues: 16.4987 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 : 0.389 ------------------------------------------------------------------------------- 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 37 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 3610 Z= 0.597 Angle : 0.767 8.026 4920 Z= 0.424 Chirality : 0.055 0.178 585 Planarity : 0.007 0.063 605 Dihedral : 6.556 17.926 488 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % 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 (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: -4.18 (0.31), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 79 HIS 0.005 0.002 HIS D 31 PHE 0.025 0.002 PHE A 33 TYR 0.031 0.004 TYR A 114 ARG 0.003 0.000 ARG E 103 *********************** 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 108 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.415 Fit side-chains REVERT: A 13 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7595 (tmm) REVERT: B 13 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7324 (tmm) REVERT: B 89 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 99 ASP cc_start: 0.7599 (t0) cc_final: 0.7192 (t0) REVERT: C 13 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7432 (tmm) REVERT: C 63 GLU cc_start: 0.8188 (mp0) cc_final: 0.7855 (mp0) REVERT: C 89 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7856 (mm-30) REVERT: D 13 MET cc_start: 0.8125 (ttm) cc_final: 0.7739 (tmm) REVERT: D 89 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7832 (mm-30) REVERT: D 115 SER cc_start: 0.8165 (m) cc_final: 0.7899 (t) REVERT: E 103 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.5725 (mmp-170) outliers start: 26 outliers final: 13 residues processed: 97 average time/residue: 0.1270 time to fit residues: 15.7129 Evaluate side-chains 91 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 59 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 28 VAL 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 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 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3610 Z= 0.217 Angle : 0.640 8.505 4920 Z= 0.343 Chirality : 0.052 0.142 585 Planarity : 0.005 0.042 605 Dihedral : 5.848 15.782 485 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 4.94 % Allowed : 30.13 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.01 (0.31), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 79 HIS 0.003 0.001 HIS E 90 PHE 0.018 0.002 PHE E 33 TYR 0.029 0.002 TYR A 114 ARG 0.002 0.000 ARG A 104 *********************** 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 106 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.434 Fit side-chains REVERT: A 13 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7575 (tmm) REVERT: A 103 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7672 (mtt180) REVERT: B 13 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7527 (tmm) REVERT: B 89 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 99 ASP cc_start: 0.7572 (t0) cc_final: 0.7040 (t0) REVERT: C 99 ASP cc_start: 0.7425 (t0) cc_final: 0.7115 (t0) REVERT: C 112 SER cc_start: 0.8911 (p) cc_final: 0.8692 (m) REVERT: D 13 MET cc_start: 0.8034 (ttm) cc_final: 0.7754 (tmm) REVERT: D 74 ASP cc_start: 0.8597 (t0) cc_final: 0.8127 (t0) REVERT: E 88 HIS cc_start: 0.8242 (t-170) cc_final: 0.6738 (p-80) REVERT: E 89 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7908 (mm-30) REVERT: E 95 PHE cc_start: 0.8797 (t80) cc_final: 0.8423 (t80) outliers start: 19 outliers final: 7 residues processed: 97 average time/residue: 0.1276 time to fit residues: 15.8851 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 : 0.391 ------------------------------------------------------------------------------- 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 103 ARG Chi-restraints excluded: chain B residue 13 MET 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 117 SER 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 4 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.0470 chunk 43 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3610 Z= 0.261 Angle : 0.642 8.864 4920 Z= 0.339 Chirality : 0.051 0.135 585 Planarity : 0.004 0.032 605 Dihedral : 5.633 15.392 485 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 6.75 % Allowed : 29.61 % 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 (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: -3.86 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.003 0.001 HIS A 31 PHE 0.019 0.002 PHE B 33 TYR 0.022 0.002 TYR A 114 ARG 0.001 0.000 ARG B 103 *********************** 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 103 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.411 Fit side-chains REVERT: A 13 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7536 (tmm) REVERT: B 13 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7432 (tmm) REVERT: B 89 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7921 (mm-30) REVERT: B 99 ASP cc_start: 0.7536 (t0) cc_final: 0.7280 (t70) REVERT: C 99 ASP cc_start: 0.7509 (t0) cc_final: 0.7017 (t0) REVERT: D 13 MET cc_start: 0.8082 (ttm) cc_final: 0.7795 (tmm) REVERT: D 74 ASP cc_start: 0.8645 (t0) cc_final: 0.8122 (t0) outliers start: 26 outliers final: 11 residues processed: 91 average time/residue: 0.1606 time to fit residues: 17.7829 Evaluate side-chains 84 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 E residue 28 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.0670 chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 HIS ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3534 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= 0.188 Angle : 0.632 8.204 4920 Z= 0.331 Chirality : 0.052 0.128 585 Planarity : 0.004 0.027 605 Dihedral : 5.433 15.269 485 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.16 % Allowed : 30.91 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.80 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 79 HIS 0.001 0.000 HIS B 90 PHE 0.017 0.002 PHE B 33 TYR 0.020 0.001 TYR A 114 ARG 0.002 0.000 ARG C 103 *********************** 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 96 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.442 Fit side-chains REVERT: A 13 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7496 (tmm) REVERT: B 13 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7475 (tmm) REVERT: B 89 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7805 (mm-30) REVERT: C 95 PHE cc_start: 0.8817 (t80) cc_final: 0.8590 (t80) REVERT: D 13 MET cc_start: 0.8155 (ttm) cc_final: 0.7873 (tmm) REVERT: D 74 ASP cc_start: 0.8522 (t0) cc_final: 0.8296 (t0) REVERT: E 66 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7991 (tm-30) REVERT: E 76 LYS cc_start: 0.8395 (mttm) cc_final: 0.7346 (mmmt) outliers start: 16 outliers final: 7 residues processed: 88 average time/residue: 0.1495 time to fit residues: 16.3480 Evaluate side-chains 78 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 76 LYS Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 0.0020 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 3610 Z= 0.491 Angle : 0.729 9.388 4920 Z= 0.385 Chirality : 0.052 0.140 585 Planarity : 0.004 0.027 605 Dihedral : 5.664 17.939 485 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.71 % Allowed : 30.39 % Favored : 63.90 % 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: -3.65 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 79 HIS 0.004 0.001 HIS E 31 PHE 0.014 0.002 PHE B 33 TYR 0.021 0.003 TYR E 114 ARG 0.004 0.001 ARG C 103 *********************** 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: 22 poor density : 68 time to evaluate : 0.355 Fit side-chains REVERT: A 13 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7500 (tmm) REVERT: B 13 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7450 (tmm) REVERT: B 89 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7873 (mm-30) REVERT: B 99 ASP cc_start: 0.7515 (t70) cc_final: 0.7258 (t0) REVERT: C 95 PHE cc_start: 0.8867 (t80) cc_final: 0.8656 (t80) REVERT: D 13 MET cc_start: 0.8370 (ttm) cc_final: 0.8021 (tmm) REVERT: E 62 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8048 (pt0) REVERT: E 76 LYS cc_start: 0.8637 (mttm) cc_final: 0.7501 (mmmt) outliers start: 22 outliers final: 14 residues processed: 75 average time/residue: 0.1154 time to fit residues: 11.5645 Evaluate side-chains 79 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 59 THR 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 75 THR 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 62 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 63 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3610 Z= 0.352 Angle : 0.696 9.349 4920 Z= 0.365 Chirality : 0.052 0.132 585 Planarity : 0.004 0.024 605 Dihedral : 5.630 17.281 485 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.16 % Allowed : 32.47 % 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 (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: -3.64 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.003 0.001 HIS E 31 PHE 0.021 0.002 PHE B 33 TYR 0.024 0.002 TYR A 114 ARG 0.003 0.000 ARG A 34 *********************** 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 84 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7509 (tmm) REVERT: B 13 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7461 (tmm) REVERT: B 89 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7840 (mm-30) REVERT: B 99 ASP cc_start: 0.7518 (t70) cc_final: 0.7225 (t0) REVERT: C 95 PHE cc_start: 0.8859 (t80) cc_final: 0.8486 (t80) REVERT: D 13 MET cc_start: 0.8351 (ttm) cc_final: 0.8022 (tmm) REVERT: E 76 LYS cc_start: 0.8611 (mttm) cc_final: 0.7538 (mmmt) REVERT: E 95 PHE cc_start: 0.8772 (t80) cc_final: 0.8449 (t80) outliers start: 16 outliers final: 10 residues processed: 76 average time/residue: 0.1344 time to fit residues: 13.4000 Evaluate side-chains 79 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 62 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 34 optimal weight: 0.0070 chunk 39 optimal weight: 0.0270 chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.8060 ------------------------------------------------------------------------------- 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** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3610 Z= 0.344 Angle : 0.715 9.340 4920 Z= 0.373 Chirality : 0.052 0.138 585 Planarity : 0.004 0.023 605 Dihedral : 5.629 17.781 485 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 4.42 % Allowed : 31.43 % Favored : 64.16 % 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: -3.59 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS E 31 PHE 0.020 0.002 PHE B 33 TYR 0.022 0.002 TYR A 114 ARG 0.003 0.000 ARG C 103 *********************** 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: 17 poor density : 68 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7525 (tmm) REVERT: B 13 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7489 (tmm) REVERT: B 89 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7822 (mm-30) REVERT: C 13 MET cc_start: 0.8189 (tmm) cc_final: 0.7909 (tmm) REVERT: C 95 PHE cc_start: 0.8869 (t80) cc_final: 0.8483 (t80) REVERT: D 13 MET cc_start: 0.8347 (ttm) cc_final: 0.8026 (tmm) REVERT: E 76 LYS cc_start: 0.8614 (mttm) cc_final: 0.7541 (mmmt) REVERT: E 95 PHE cc_start: 0.8746 (t80) cc_final: 0.8389 (t80) outliers start: 17 outliers final: 11 residues processed: 76 average time/residue: 0.1130 time to fit residues: 11.2656 Evaluate side-chains 76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 122 VAL Chi-restraints excluded: chain B 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 62 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 3610 Z= 0.549 Angle : 0.803 9.348 4920 Z= 0.422 Chirality : 0.055 0.177 585 Planarity : 0.004 0.024 605 Dihedral : 5.870 18.663 485 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 : 3.64 % Allowed : 31.95 % 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 (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: -3.58 (0.32), 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 TRP 0.005 0.002 TRP C 79 HIS 0.006 0.001 HIS E 31 PHE 0.026 0.003 PHE D 33 TYR 0.023 0.003 TYR E 114 ARG 0.005 0.001 ARG C 103 *********************** 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 76 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.382 Fit side-chains REVERT: A 13 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7424 (tmm) REVERT: B 13 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7526 (tmm) REVERT: D 13 MET cc_start: 0.8366 (ttm) cc_final: 0.8048 (tmm) REVERT: E 62 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8143 (pt0) REVERT: E 76 LYS cc_start: 0.8672 (mttm) cc_final: 0.7606 (mmmt) REVERT: E 112 SER cc_start: 0.8841 (m) cc_final: 0.8490 (p) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 0.1192 time to fit residues: 11.0352 Evaluate side-chains 71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 75 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 62 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.0060 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- 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** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3610 Z= 0.240 Angle : 0.724 9.616 4920 Z= 0.372 Chirality : 0.053 0.154 585 Planarity : 0.003 0.027 605 Dihedral : 5.531 18.012 485 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.34 % Allowed : 32.99 % Favored : 64.68 % 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: -3.58 (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 TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS B 31 PHE 0.022 0.002 PHE B 33 TYR 0.024 0.002 TYR A 114 ARG 0.002 0.000 ARG C 103 ********************** 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 85 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7310 (tmm) REVERT: B 13 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7541 (tmm) REVERT: B 100 SER cc_start: 0.8280 (p) cc_final: 0.8025 (m) REVERT: C 95 PHE cc_start: 0.8843 (t80) cc_final: 0.8575 (t80) REVERT: D 13 MET cc_start: 0.8286 (ttm) cc_final: 0.8037 (tmm) REVERT: D 89 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7586 (mm-30) REVERT: E 66 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8098 (tm-30) REVERT: E 76 LYS cc_start: 0.8584 (mttm) cc_final: 0.7556 (mmmt) REVERT: E 112 SER cc_start: 0.8470 (m) cc_final: 0.7979 (p) outliers start: 9 outliers final: 4 residues processed: 80 average time/residue: 0.1219 time to fit residues: 12.7110 Evaluate side-chains 72 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.132143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.114133 restraints weight = 6138.755| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 3.02 r_work: 0.4147 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 3610 Z= 0.490 Angle : 0.839 13.142 4920 Z= 0.429 Chirality : 0.055 0.172 585 Planarity : 0.004 0.023 605 Dihedral : 5.749 21.805 485 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 2.86 % Allowed : 32.99 % Favored : 64.16 % 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: -3.49 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 79 HIS 0.004 0.001 HIS E 31 PHE 0.024 0.003 PHE D 33 TYR 0.024 0.003 TYR E 114 ARG 0.005 0.000 ARG C 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1157.32 seconds wall clock time: 21 minutes 46.87 seconds (1306.87 seconds total)