Starting phenix.real_space_refine on Wed Mar 5 20:35:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e7d_26587/03_2025/8e7d_26587.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e7d_26587/03_2025/8e7d_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_2025/8e7d_26587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e7d_26587/03_2025/8e7d_26587.map" model { file = "/net/cci-nas-00/data/ceres_data/8e7d_26587/03_2025/8e7d_26587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e7d_26587/03_2025/8e7d_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.11, per 1000 atoms: 0.60 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 425.1 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: 0.47 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: 0.85 Time building geometry restraints manager: 0.97 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 1.140 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: 0.030 Set scattering table: 0.050 Process input model: 12.560 Find NCS groups from input model: 0.060 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.800 ------------------------------------------------------------------------------- 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 : 0.404 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: 0.1150 time to fit residues: 16.2207 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 : 0.416 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.125067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.107948 restraints weight = 5973.544| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.94 r_work: 0.4062 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.387 Fit side-chains REVERT: A 13 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7196 (tmm) REVERT: B 13 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.6862 (tmm) REVERT: B 89 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7559 (mm-30) REVERT: B 99 ASP cc_start: 0.7965 (t0) cc_final: 0.7357 (t0) REVERT: C 13 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7032 (tmm) REVERT: C 63 GLU cc_start: 0.7874 (mp0) cc_final: 0.7575 (mp0) REVERT: C 89 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7569 (mm-30) REVERT: C 99 ASP cc_start: 0.8079 (t0) cc_final: 0.7574 (t0) REVERT: D 13 MET cc_start: 0.8238 (ttm) cc_final: 0.7629 (tmm) REVERT: D 89 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7682 (mm-30) REVERT: D 115 SER cc_start: 0.8309 (m) cc_final: 0.7986 (t) REVERT: E 103 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.5125 (mmp-170) outliers start: 26 outliers final: 13 residues processed: 97 average time/residue: 0.1204 time to fit residues: 14.9704 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 : 0.373 ------------------------------------------------------------------------------- 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 27 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 0.0060 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.122024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.103309 restraints weight = 5881.466| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 3.39 r_work: 0.4162 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3610 Z= 0.211 Angle : 0.639 8.490 4920 Z= 0.343 Chirality : 0.052 0.141 585 Planarity : 0.005 0.041 605 Dihedral : 5.844 15.718 485 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % 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 (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 0.005 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 0.001 0.000 ARG D 103 *********************** 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 108 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6829 (tmm) REVERT: B 13 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6779 (tmm) REVERT: B 89 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7193 (mm-30) REVERT: B 99 ASP cc_start: 0.8057 (t0) cc_final: 0.7217 (t0) REVERT: C 63 GLU cc_start: 0.7832 (mp0) cc_final: 0.7595 (mp0) REVERT: C 99 ASP cc_start: 0.7884 (t0) cc_final: 0.7565 (t0) REVERT: C 112 SER cc_start: 0.9430 (p) cc_final: 0.8865 (m) REVERT: D 13 MET cc_start: 0.8166 (ttm) cc_final: 0.7520 (tmm) REVERT: D 74 ASP cc_start: 0.8883 (t0) cc_final: 0.8501 (t0) REVERT: D 114 TYR cc_start: 0.8202 (p90) cc_final: 0.7799 (p90) REVERT: E 63 GLU cc_start: 0.8180 (mp0) cc_final: 0.7905 (mp0) REVERT: E 74 ASP cc_start: 0.8447 (t70) cc_final: 0.8232 (t0) REVERT: E 88 HIS cc_start: 0.8049 (t-170) cc_final: 0.6363 (p-80) REVERT: E 89 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7575 (mm-30) REVERT: E 95 PHE cc_start: 0.8650 (t80) cc_final: 0.7998 (t80) outliers start: 17 outliers final: 7 residues processed: 100 average time/residue: 0.1181 time to fit residues: 15.2966 Evaluate side-chains 88 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 43 optimal weight: 0.0870 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 overall best weight: 4.2764 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.114735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.096542 restraints weight = 6278.805| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 3.35 r_work: 0.4051 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 3610 Z= 0.449 Angle : 0.693 9.030 4920 Z= 0.370 Chirality : 0.052 0.144 585 Planarity : 0.005 0.034 605 Dihedral : 5.855 16.116 485 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.97 % Allowed : 30.39 % 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: -3.77 (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 TRP 0.004 0.001 TRP B 79 HIS 0.005 0.001 HIS A 31 PHE 0.020 0.002 PHE B 33 TYR 0.023 0.003 TYR E 114 ARG 0.002 0.000 ARG E 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 97 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.404 Fit side-chains REVERT: A 103 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.6868 (mtt180) REVERT: B 13 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6632 (tmm) REVERT: B 89 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7199 (mm-30) REVERT: B 99 ASP cc_start: 0.7733 (t0) cc_final: 0.7208 (t0) REVERT: B 103 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7068 (mtt180) REVERT: C 13 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.6896 (tmm) REVERT: C 63 GLU cc_start: 0.7913 (mp0) cc_final: 0.7664 (mp0) REVERT: C 99 ASP cc_start: 0.8295 (t0) cc_final: 0.6870 (t0) REVERT: C 103 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7430 (mtm-85) REVERT: C 112 SER cc_start: 0.9358 (p) cc_final: 0.8799 (m) REVERT: D 13 MET cc_start: 0.8442 (ttm) cc_final: 0.7677 (tmm) REVERT: D 114 TYR cc_start: 0.7998 (p90) cc_final: 0.7417 (p90) REVERT: E 63 GLU cc_start: 0.8000 (mp0) cc_final: 0.7772 (mp0) REVERT: E 74 ASP cc_start: 0.8487 (t70) cc_final: 0.7814 (t0) REVERT: E 95 PHE cc_start: 0.8488 (t80) cc_final: 0.7847 (t80) REVERT: E 99 ASP cc_start: 0.7870 (t0) cc_final: 0.7546 (t0) outliers start: 23 outliers final: 13 residues processed: 88 average time/residue: 0.1486 time to fit residues: 16.2194 Evaluate side-chains 86 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG 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 103 ARG 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 C residue 103 ARG 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 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 122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.243803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5184 r_free = 0.5184 target = 0.197378 restraints weight = 6776.079| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 1.71 r_work: 0.4404 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.4328 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3270 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= 0.200 Angle : 0.632 8.532 4920 Z= 0.331 Chirality : 0.052 0.152 585 Planarity : 0.004 0.029 605 Dihedral : 5.563 15.756 485 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.94 % Allowed : 32.47 % 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 (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: -3.82 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 79 HIS 0.001 0.000 HIS C 88 PHE 0.016 0.002 PHE C 33 TYR 0.023 0.002 TYR A 114 ARG 0.002 0.000 ARG A 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 95 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.399 Fit side-chains REVERT: A 13 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7416 (tmm) REVERT: B 13 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7361 (tmm) REVERT: C 95 PHE cc_start: 0.8889 (t80) cc_final: 0.8433 (t80) REVERT: C 99 ASP cc_start: 0.7850 (t0) cc_final: 0.7421 (t0) REVERT: C 103 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7948 (mtm-85) REVERT: C 112 SER cc_start: 0.9194 (p) cc_final: 0.8971 (m) REVERT: D 13 MET cc_start: 0.8207 (ttm) cc_final: 0.7879 (tmm) REVERT: D 74 ASP cc_start: 0.8808 (t0) cc_final: 0.8559 (t0) REVERT: E 95 PHE cc_start: 0.8923 (t80) cc_final: 0.8251 (t80) REVERT: E 112 SER cc_start: 0.9141 (p) cc_final: 0.8927 (m) outliers start: 19 outliers final: 7 residues processed: 89 average time/residue: 0.1395 time to fit residues: 15.4395 Evaluate side-chains 74 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 103 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.130046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.112395 restraints weight = 6018.104| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 3.04 r_work: 0.4364 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4266 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3473 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= 0.366 Angle : 0.691 8.656 4920 Z= 0.364 Chirality : 0.052 0.140 585 Planarity : 0.004 0.028 605 Dihedral : 5.606 18.954 485 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % 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 (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: -3.71 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.004 0.001 HIS A 31 PHE 0.021 0.002 PHE B 33 TYR 0.017 0.002 TYR A 114 ARG 0.002 0.000 ARG B 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 88 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.415 Fit side-chains REVERT: B 13 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7520 (tmm) REVERT: C 13 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7658 (tmm) REVERT: C 95 PHE cc_start: 0.8941 (t80) cc_final: 0.8724 (t80) REVERT: C 99 ASP cc_start: 0.7915 (t0) cc_final: 0.7518 (t0) REVERT: C 112 SER cc_start: 0.9180 (p) cc_final: 0.8849 (m) REVERT: D 13 MET cc_start: 0.8478 (ttm) cc_final: 0.8099 (tmm) REVERT: D 74 ASP cc_start: 0.8864 (t0) cc_final: 0.8233 (t0) REVERT: D 92 GLU cc_start: 0.8195 (mp0) cc_final: 0.7854 (mp0) REVERT: E 66 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7965 (tm-30) outliers start: 18 outliers final: 10 residues processed: 80 average time/residue: 0.1127 time to fit residues: 11.9557 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 : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 75 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 E residue 58 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 0.0770 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 2.4142 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.131755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.114115 restraints weight = 5842.050| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 3.02 r_work: 0.4275 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3610 Z= 0.303 Angle : 0.668 9.002 4920 Z= 0.352 Chirality : 0.051 0.131 585 Planarity : 0.004 0.027 605 Dihedral : 5.548 18.430 485 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % 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 (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: -3.68 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 79 HIS 0.003 0.001 HIS A 31 PHE 0.017 0.002 PHE B 33 TYR 0.018 0.002 TYR A 114 ARG 0.002 0.000 ARG C 103 *********************** 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 90 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7122 (tmm) REVERT: B 13 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7053 (tmm) REVERT: C 95 PHE cc_start: 0.8792 (t80) cc_final: 0.8295 (t80) REVERT: C 99 ASP cc_start: 0.7979 (t0) cc_final: 0.7315 (t0) REVERT: C 112 SER cc_start: 0.9367 (p) cc_final: 0.8959 (m) REVERT: D 13 MET cc_start: 0.8514 (ttm) cc_final: 0.7952 (tmm) REVERT: E 66 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7878 (tm-30) REVERT: E 95 PHE cc_start: 0.8730 (t80) cc_final: 0.8127 (t80) REVERT: E 112 SER cc_start: 0.9232 (p) cc_final: 0.9011 (m) outliers start: 17 outliers final: 8 residues processed: 84 average time/residue: 0.1256 time to fit residues: 13.6672 Evaluate side-chains 77 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 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 58 LEU 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 11 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.132420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.114307 restraints weight = 5897.525| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 3.05 r_work: 0.4227 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3610 Z= 0.292 Angle : 0.685 8.929 4920 Z= 0.356 Chirality : 0.052 0.130 585 Planarity : 0.003 0.025 605 Dihedral : 5.524 18.107 485 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.19 % Allowed : 30.91 % 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 (0.32), 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 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS A 31 PHE 0.020 0.002 PHE C 33 TYR 0.019 0.002 TYR A 114 ARG 0.002 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 92 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 13 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7079 (tmm) REVERT: B 13 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7043 (tmm) REVERT: C 13 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7276 (tmm) REVERT: C 95 PHE cc_start: 0.8815 (t80) cc_final: 0.8305 (t80) REVERT: C 99 ASP cc_start: 0.7902 (t0) cc_final: 0.7450 (t0) REVERT: C 112 SER cc_start: 0.9367 (p) cc_final: 0.8993 (m) REVERT: D 13 MET cc_start: 0.8565 (ttm) cc_final: 0.7974 (tmm) REVERT: D 63 GLU cc_start: 0.8547 (mp0) cc_final: 0.8339 (mp0) REVERT: D 76 LYS cc_start: 0.9018 (mttm) cc_final: 0.8793 (mptt) REVERT: E 66 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7868 (tm-30) REVERT: E 95 PHE cc_start: 0.8763 (t80) cc_final: 0.8118 (t80) REVERT: E 112 SER cc_start: 0.9239 (p) cc_final: 0.9036 (m) outliers start: 20 outliers final: 15 residues processed: 82 average time/residue: 0.1371 time to fit residues: 15.4510 Evaluate side-chains 88 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 A residue 122 VAL 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 D residue 122 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 75 THR 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 18 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.142738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.120974 restraints weight = 5985.396| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 3.05 r_work: 0.4273 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3610 Z= 0.252 Angle : 0.693 8.887 4920 Z= 0.356 Chirality : 0.052 0.126 585 Planarity : 0.003 0.024 605 Dihedral : 5.420 17.481 485 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.64 % Allowed : 32.47 % 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: -3.61 (0.32), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 79 HIS 0.001 0.000 HIS E 31 PHE 0.024 0.002 PHE D 33 TYR 0.018 0.001 TYR A 114 ARG 0.002 0.000 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 89 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.369 Fit side-chains REVERT: A 13 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.6971 (tmm) REVERT: A 112 SER cc_start: 0.9241 (p) cc_final: 0.8982 (m) REVERT: B 13 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7207 (tmm) REVERT: C 95 PHE cc_start: 0.8825 (t80) cc_final: 0.8279 (t80) REVERT: C 99 ASP cc_start: 0.7870 (t0) cc_final: 0.7521 (t0) REVERT: C 112 SER cc_start: 0.9306 (p) cc_final: 0.8991 (m) REVERT: D 13 MET cc_start: 0.8467 (ttm) cc_final: 0.8037 (tmm) REVERT: D 89 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7541 (mm-30) REVERT: E 66 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7948 (tm-30) REVERT: E 95 PHE cc_start: 0.8890 (t80) cc_final: 0.8338 (t80) REVERT: E 112 SER cc_start: 0.9243 (p) cc_final: 0.9035 (m) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.1012 time to fit residues: 11.4155 Evaluate side-chains 80 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 61 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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** A 88 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.136234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.117932 restraints weight = 5980.534| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 3.00 r_work: 0.4230 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3610 Z= 0.331 Angle : 0.734 9.534 4920 Z= 0.379 Chirality : 0.053 0.134 585 Planarity : 0.003 0.023 605 Dihedral : 5.482 17.600 485 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.16 % Allowed : 31.95 % 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: -3.53 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.003 0.001 HIS A 31 PHE 0.020 0.002 PHE D 33 TYR 0.023 0.002 TYR A 114 ARG 0.003 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 88 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.390 Fit side-chains REVERT: A 13 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.6883 (tmm) REVERT: B 13 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7165 (tmm) REVERT: B 100 SER cc_start: 0.8461 (p) cc_final: 0.8067 (m) REVERT: C 13 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7361 (tmm) REVERT: C 95 PHE cc_start: 0.8832 (t80) cc_final: 0.8338 (t80) REVERT: C 99 ASP cc_start: 0.7934 (t0) cc_final: 0.7663 (t0) REVERT: C 112 SER cc_start: 0.9261 (p) cc_final: 0.8926 (m) REVERT: D 13 MET cc_start: 0.8504 (ttm) cc_final: 0.8009 (tmm) REVERT: D 114 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6646 (p90) REVERT: E 66 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7956 (tm-30) REVERT: E 95 PHE cc_start: 0.8878 (t80) cc_final: 0.8307 (t80) REVERT: E 112 SER cc_start: 0.9286 (p) cc_final: 0.9016 (m) outliers start: 16 outliers final: 9 residues processed: 83 average time/residue: 0.1070 time to fit residues: 11.8239 Evaluate side-chains 83 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 122 VAL Chi-restraints excluded: chain B residue 13 MET 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 D residue 114 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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** A 88 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.132678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.114486 restraints weight = 6159.682| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 3.05 r_work: 0.4149 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3610 Z= 0.438 Angle : 0.776 9.304 4920 Z= 0.404 Chirality : 0.054 0.184 585 Planarity : 0.004 0.022 605 Dihedral : 5.702 18.855 485 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 3.64 % Allowed : 32.73 % 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: -3.52 (0.33), residues: 430 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 79 HIS 0.004 0.001 HIS A 31 PHE 0.024 0.003 PHE D 33 TYR 0.023 0.003 TYR A 114 ARG 0.003 0.000 ARG C 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.09 seconds wall clock time: 32 minutes 34.38 seconds (1954.38 seconds total)