Starting phenix.real_space_refine on Wed Mar 4 08:52:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e83_31009/03_2026/7e83_31009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e83_31009/03_2026/7e83_31009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e83_31009/03_2026/7e83_31009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e83_31009/03_2026/7e83_31009.map" model { file = "/net/cci-nas-00/data/ceres_data/7e83_31009/03_2026/7e83_31009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e83_31009/03_2026/7e83_31009.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 64 5.16 5 C 8036 2.51 5 N 2212 2.21 5 O 2392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12704 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1710 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain breaks: 3 Chain: "E" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "A" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1710 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain breaks: 3 Chain: "B" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "D" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1710 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain breaks: 3 Chain: "F" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "G" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1710 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain breaks: 3 Chain: "H" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1466 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Time building chain proxies: 3.11, per 1000 atoms: 0.24 Number of scatterers: 12704 At special positions: 0 Unit cell: (143.323, 143.323, 67.1514, 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 64 16.00 O 2392 8.00 N 2212 7.00 C 8036 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: 0.94 Conformation dependent library (CDL) restraints added in 544.3 milliseconds 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 61.1% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'C' and resid 8 through 16 Processing helix chain 'C' and resid 17 through 20 Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.530A pdb=" N LEU C 59 " --> pdb=" O TRP C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 78 through 81 Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 111 through 123 removed outlier: 3.722A pdb=" N GLU C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 152 Processing helix chain 'C' and resid 419 through 450 Processing helix chain 'C' and resid 473 through 488 removed outlier: 3.902A pdb=" N GLN C 477 " --> pdb=" O SER C 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 64 removed outlier: 3.701A pdb=" N GLU E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.746A pdb=" N GLN E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 99 removed outlier: 3.755A pdb=" N TYR E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 103 removed outlier: 3.900A pdb=" N THR E 103 " --> pdb=" O THR E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 169 through 180 Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 202 through 210 removed outlier: 3.687A pdb=" N MET E 206 " --> pdb=" O ASP E 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 17 through 20 Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.530A pdb=" N LEU A 59 " --> pdb=" O TRP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.722A pdb=" N GLU A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 152 Processing helix chain 'A' and resid 419 through 450 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.902A pdb=" N GLN A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 64 removed outlier: 3.700A pdb=" N GLU B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.746A pdb=" N GLN B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE B 82 " --> pdb=" O TYR B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 99 removed outlier: 3.755A pdb=" N TYR B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 103 removed outlier: 3.900A pdb=" N THR B 103 " --> pdb=" O THR B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 202 through 210 removed outlier: 3.678A pdb=" N MET B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 210 " --> pdb=" O MET B 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 20 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.530A pdb=" N LEU D 59 " --> pdb=" O TRP D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 78 through 81 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.722A pdb=" N GLU D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 152 Processing helix chain 'D' and resid 419 through 450 Processing helix chain 'D' and resid 473 through 488 removed outlier: 3.902A pdb=" N GLN D 477 " --> pdb=" O SER D 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 64 removed outlier: 3.700A pdb=" N GLU F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 82 removed outlier: 3.746A pdb=" N GLN F 80 " --> pdb=" O GLN F 76 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE F 81 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE F 82 " --> pdb=" O TYR F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 99 removed outlier: 3.755A pdb=" N TYR F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 103 removed outlier: 3.900A pdb=" N THR F 103 " --> pdb=" O THR F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 100 through 103' Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 147 through 157 Processing helix chain 'F' and resid 169 through 180 Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 202 through 210 removed outlier: 3.687A pdb=" N MET F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN F 210 " --> pdb=" O MET F 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 16 Processing helix chain 'G' and resid 17 through 20 Processing helix chain 'G' and resid 55 through 61 removed outlier: 3.530A pdb=" N LEU G 59 " --> pdb=" O TRP G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 78 through 81 Processing helix chain 'G' and resid 91 through 101 Processing helix chain 'G' and resid 111 through 123 removed outlier: 3.722A pdb=" N GLU G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 152 Processing helix chain 'G' and resid 419 through 450 Processing helix chain 'G' and resid 473 through 488 removed outlier: 3.902A pdb=" N GLN G 477 " --> pdb=" O SER G 473 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 64 removed outlier: 3.693A pdb=" N GLU H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.746A pdb=" N GLN H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE H 81 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE H 82 " --> pdb=" O TYR H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.755A pdb=" N TYR H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 103 removed outlier: 3.900A pdb=" N THR H 103 " --> pdb=" O THR H 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 100 through 103' Processing helix chain 'H' and resid 108 through 121 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'H' and resid 147 through 157 Processing helix chain 'H' and resid 169 through 180 Processing helix chain 'H' and resid 192 through 202 Processing helix chain 'H' and resid 202 through 210 removed outlier: 3.687A pdb=" N MET H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN H 210 " --> pdb=" O MET H 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 50 through 54 removed outlier: 3.758A pdb=" N THR C 50 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN C 82 " --> pdb=" O HIS C 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 68 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 54 removed outlier: 3.757A pdb=" N THR A 50 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 82 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AA5, first strand: chain 'D' and resid 50 through 54 removed outlier: 3.757A pdb=" N THR D 50 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 82 " --> pdb=" O HIS D 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 68 through 70 Processing sheet with id=AA7, first strand: chain 'G' and resid 50 through 54 removed outlier: 3.758A pdb=" N THR G 50 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN G 82 " --> pdb=" O HIS G 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 68 through 70 640 hydrogen bonds defined for protein. 1860 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: 1.94 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4240 1.34 - 1.46: 3107 1.46 - 1.58: 5553 1.58 - 1.70: 0 1.70 - 1.81: 104 Bond restraints: 13004 Sorted by residual: bond pdb=" CG1 ILE F 77 " pdb=" CD1 ILE F 77 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CG1 ILE H 77 " pdb=" CD1 ILE H 77 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CG1 ILE B 77 " pdb=" CD1 ILE B 77 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CG1 ILE E 77 " pdb=" CD1 ILE E 77 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.63e+00 bond pdb=" CB MET G 27 " pdb=" CG MET G 27 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 12999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 17376 2.62 - 5.25: 144 5.25 - 7.87: 8 7.87 - 10.50: 4 10.50 - 13.12: 4 Bond angle restraints: 17536 Sorted by residual: angle pdb=" CB MET G 27 " pdb=" CG MET G 27 " pdb=" SD MET G 27 " ideal model delta sigma weight residual 112.70 125.82 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CB MET D 27 " pdb=" CG MET D 27 " pdb=" SD MET D 27 " ideal model delta sigma weight residual 112.70 125.82 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CB MET A 27 " pdb=" CG MET A 27 " pdb=" SD MET A 27 " ideal model delta sigma weight residual 112.70 125.82 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CB MET C 27 " pdb=" CG MET C 27 " pdb=" SD MET C 27 " ideal model delta sigma weight residual 112.70 125.81 -13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CB MET D 445 " pdb=" CG MET D 445 " pdb=" SD MET D 445 " ideal model delta sigma weight residual 112.70 120.65 -7.95 3.00e+00 1.11e-01 7.02e+00 ... (remaining 17531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6892 17.87 - 35.75: 714 35.75 - 53.62: 134 53.62 - 71.49: 32 71.49 - 89.37: 16 Dihedral angle restraints: 7788 sinusoidal: 3244 harmonic: 4544 Sorted by residual: dihedral pdb=" CA HIS G 77 " pdb=" C HIS G 77 " pdb=" N PRO G 78 " pdb=" CA PRO G 78 " ideal model delta harmonic sigma weight residual -180.00 -156.24 -23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA HIS A 77 " pdb=" C HIS A 77 " pdb=" N PRO A 78 " pdb=" CA PRO A 78 " ideal model delta harmonic sigma weight residual -180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA HIS C 77 " pdb=" C HIS C 77 " pdb=" N PRO C 78 " pdb=" CA PRO C 78 " ideal model delta harmonic sigma weight residual -180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 7785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1187 0.030 - 0.060: 393 0.060 - 0.090: 164 0.090 - 0.120: 68 0.120 - 0.151: 8 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CA THR B 170 " pdb=" N THR B 170 " pdb=" C THR B 170 " pdb=" CB THR B 170 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA THR F 170 " pdb=" N THR F 170 " pdb=" C THR F 170 " pdb=" CB THR F 170 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA THR H 170 " pdb=" N THR H 170 " pdb=" C THR H 170 " pdb=" CB THR H 170 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 1817 not shown) Planarity restraints: 2308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 106 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO A 107 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 106 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO G 107 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO G 107 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 107 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 106 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO C 107 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 107 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 107 " 0.028 5.00e-02 4.00e+02 ... (remaining 2305 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 292 2.70 - 3.25: 12875 3.25 - 3.80: 20168 3.80 - 4.35: 26112 4.35 - 4.90: 43430 Nonbonded interactions: 102877 Sorted by model distance: nonbonded pdb=" OG1 THR A 65 " pdb=" OH TYR A 99 " model vdw 2.153 3.040 nonbonded pdb=" OG1 THR C 65 " pdb=" OH TYR C 99 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR D 65 " pdb=" OH TYR D 99 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR G 65 " pdb=" OH TYR G 99 " model vdw 2.154 3.040 nonbonded pdb=" OE2 GLU G 71 " pdb=" OH TYR H 57 " model vdw 2.240 3.040 ... (remaining 102872 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 'C' selection = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'B' selection = chain 'F' selection = chain 'H' } 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: 0.650 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.003 0.050 13004 Z= 0.130 Angle : 0.605 13.120 17536 Z= 0.305 Chirality : 0.039 0.151 1820 Planarity : 0.004 0.050 2308 Dihedral : 15.407 89.368 4836 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.02 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1496 helix: 1.54 (0.18), residues: 844 sheet: -2.49 (0.45), residues: 40 loop : -2.29 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 142 TYR 0.008 0.001 TYR A 134 PHE 0.021 0.001 PHE E 74 TRP 0.002 0.000 TRP G 19 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00309 (13004) covalent geometry : angle 0.60546 (17536) hydrogen bonds : bond 0.12956 ( 640) hydrogen bonds : angle 5.61050 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 492 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6501 (mp0) REVERT: E 132 ASN cc_start: 0.7635 (m110) cc_final: 0.7220 (m-40) REVERT: E 182 MET cc_start: 0.5647 (ptp) cc_final: 0.5159 (ptp) REVERT: A 90 ASP cc_start: 0.7384 (m-30) cc_final: 0.7168 (m-30) REVERT: A 492 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6509 (mp0) REVERT: B 132 ASN cc_start: 0.7643 (m110) cc_final: 0.7230 (m-40) REVERT: B 182 MET cc_start: 0.5694 (ptp) cc_final: 0.5198 (ptp) REVERT: D 90 ASP cc_start: 0.7678 (m-30) cc_final: 0.7458 (m-30) REVERT: D 492 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6497 (mp0) REVERT: F 132 ASN cc_start: 0.7621 (m110) cc_final: 0.7202 (m-40) REVERT: F 182 MET cc_start: 0.5681 (ptp) cc_final: 0.5188 (ptp) REVERT: G 492 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6493 (mp0) REVERT: H 132 ASN cc_start: 0.7622 (m110) cc_final: 0.7204 (m-40) REVERT: H 182 MET cc_start: 0.5600 (ptp) cc_final: 0.5130 (ptp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1521 time to fit residues: 56.5813 Evaluate side-chains 230 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.0370 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 124 HIS A 77 HIS B 210 GLN D 77 HIS G 77 HIS H 124 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.191021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.131050 restraints weight = 12968.927| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.80 r_work: 0.3106 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13004 Z= 0.132 Angle : 0.559 7.411 17536 Z= 0.294 Chirality : 0.040 0.144 1820 Planarity : 0.004 0.030 2308 Dihedral : 4.260 16.429 1700 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.95 % Favored : 92.78 % Rotamer: Outliers : 0.89 % Allowed : 8.65 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.22), residues: 1496 helix: 1.71 (0.18), residues: 852 sheet: -1.41 (0.61), residues: 40 loop : -2.24 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 108 TYR 0.009 0.001 TYR D 137 PHE 0.014 0.002 PHE B 74 TRP 0.003 0.001 TRP C 19 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00304 (13004) covalent geometry : angle 0.55949 (17536) hydrogen bonds : bond 0.03748 ( 640) hydrogen bonds : angle 4.62289 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 222 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 492 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6542 (mp0) REVERT: A 13 ARG cc_start: 0.8596 (mtt180) cc_final: 0.8389 (mtt180) REVERT: A 492 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6558 (mp0) REVERT: D 13 ARG cc_start: 0.8593 (mtt180) cc_final: 0.8381 (mtt180) REVERT: D 492 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6541 (mp0) REVERT: G 13 ARG cc_start: 0.8599 (mtt180) cc_final: 0.8391 (mtt180) REVERT: G 492 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6520 (mp0) outliers start: 12 outliers final: 5 residues processed: 230 average time/residue: 0.1506 time to fit residues: 45.8600 Evaluate side-chains 217 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 212 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain H residue 66 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 96 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS A 77 HIS D 77 HIS G 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.186013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124807 restraints weight = 13004.968| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.96 r_work: 0.3037 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13004 Z= 0.185 Angle : 0.601 8.037 17536 Z= 0.312 Chirality : 0.043 0.259 1820 Planarity : 0.004 0.032 2308 Dihedral : 4.430 16.373 1700 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.62 % Favored : 91.11 % Rotamer: Outliers : 0.96 % Allowed : 10.80 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.22), residues: 1496 helix: 1.52 (0.18), residues: 876 sheet: -1.00 (0.69), residues: 40 loop : -2.20 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 51 TYR 0.015 0.001 TYR D 137 PHE 0.024 0.002 PHE H 131 TRP 0.005 0.001 TRP D 55 HIS 0.005 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00445 (13004) covalent geometry : angle 0.60060 (17536) hydrogen bonds : bond 0.04098 ( 640) hydrogen bonds : angle 4.57399 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 MET cc_start: 0.3286 (tmm) cc_final: 0.2911 (tmm) REVERT: C 445 MET cc_start: 0.7835 (mmm) cc_final: 0.7603 (mmt) REVERT: C 492 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6502 (mp0) REVERT: A 27 MET cc_start: 0.3273 (tmm) cc_final: 0.2908 (tmm) REVERT: A 445 MET cc_start: 0.7838 (mmm) cc_final: 0.7605 (mmt) REVERT: A 492 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6497 (mp0) REVERT: D 27 MET cc_start: 0.3280 (tmm) cc_final: 0.2909 (tmm) REVERT: D 445 MET cc_start: 0.7832 (mmm) cc_final: 0.7598 (mmt) REVERT: D 492 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6487 (mp0) REVERT: G 27 MET cc_start: 0.3263 (tmm) cc_final: 0.2899 (tmm) REVERT: G 445 MET cc_start: 0.7841 (mmm) cc_final: 0.7607 (mmt) REVERT: G 492 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6502 (mp0) outliers start: 13 outliers final: 5 residues processed: 213 average time/residue: 0.1487 time to fit residues: 42.4828 Evaluate side-chains 197 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 192 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain H residue 66 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 210 GLN A 77 HIS D 77 HIS F 210 GLN G 77 HIS H 210 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.182478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.118346 restraints weight = 13039.130| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.85 r_work: 0.2903 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13004 Z= 0.237 Angle : 0.636 7.368 17536 Z= 0.331 Chirality : 0.045 0.293 1820 Planarity : 0.004 0.032 2308 Dihedral : 4.715 16.952 1700 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.82 % Favored : 91.91 % Rotamer: Outliers : 1.26 % Allowed : 14.13 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1496 helix: 1.33 (0.17), residues: 880 sheet: -0.65 (0.77), residues: 40 loop : -2.34 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 51 TYR 0.011 0.002 TYR D 137 PHE 0.022 0.003 PHE B 178 TRP 0.004 0.001 TRP D 19 HIS 0.006 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00579 (13004) covalent geometry : angle 0.63599 (17536) hydrogen bonds : bond 0.04342 ( 640) hydrogen bonds : angle 4.64860 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 475 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: A 475 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: D 141 ARG cc_start: 0.8330 (ttt-90) cc_final: 0.8106 (ttt180) REVERT: D 475 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: G 475 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7798 (mt-10) outliers start: 17 outliers final: 9 residues processed: 212 average time/residue: 0.1442 time to fit residues: 40.6699 Evaluate side-chains 194 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain H residue 66 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 210 GLN A 77 HIS B 210 GLN D 77 HIS F 210 GLN G 77 HIS H 210 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.185452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.123027 restraints weight = 13133.706| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.85 r_work: 0.2955 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13004 Z= 0.146 Angle : 0.582 9.742 17536 Z= 0.299 Chirality : 0.042 0.294 1820 Planarity : 0.004 0.037 2308 Dihedral : 4.556 17.071 1700 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.55 % Favored : 92.18 % Rotamer: Outliers : 1.48 % Allowed : 16.42 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.22), residues: 1496 helix: 1.51 (0.18), residues: 880 sheet: -0.29 (0.79), residues: 40 loop : -2.22 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 51 TYR 0.008 0.001 TYR D 137 PHE 0.013 0.002 PHE B 178 TRP 0.003 0.001 TRP D 19 HIS 0.005 0.001 HIS G 94 Details of bonding type rmsd covalent geometry : bond 0.00351 (13004) covalent geometry : angle 0.58158 (17536) hydrogen bonds : bond 0.03609 ( 640) hydrogen bonds : angle 4.46190 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8335 (m) REVERT: C 141 ARG cc_start: 0.8224 (ttt-90) cc_final: 0.8015 (ttt180) REVERT: C 475 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: C 492 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6805 (mp0) REVERT: A 69 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8319 (m) REVERT: A 475 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: A 492 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6765 (mp0) REVERT: D 141 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.8070 (ttt180) REVERT: D 475 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: D 492 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6772 (mp0) REVERT: G 69 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8322 (m) REVERT: G 475 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: G 492 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6800 (mp0) outliers start: 20 outliers final: 9 residues processed: 204 average time/residue: 0.1400 time to fit residues: 38.7095 Evaluate side-chains 192 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain H residue 64 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 34 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 210 GLN A 77 HIS D 77 HIS F 210 GLN G 77 HIS H 210 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.185074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.122118 restraints weight = 13044.298| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.87 r_work: 0.3038 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13004 Z= 0.148 Angle : 0.581 8.114 17536 Z= 0.299 Chirality : 0.042 0.314 1820 Planarity : 0.004 0.045 2308 Dihedral : 4.500 17.180 1700 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.49 % Favored : 92.25 % Rotamer: Outliers : 2.44 % Allowed : 17.01 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.22), residues: 1496 helix: 1.52 (0.18), residues: 880 sheet: -0.20 (0.81), residues: 40 loop : -2.16 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 51 TYR 0.007 0.001 TYR D 137 PHE 0.028 0.002 PHE F 178 TRP 0.003 0.001 TRP D 19 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00358 (13004) covalent geometry : angle 0.58141 (17536) hydrogen bonds : bond 0.03582 ( 640) hydrogen bonds : angle 4.43453 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.8260 (m) REVERT: C 90 ASP cc_start: 0.8281 (m-30) cc_final: 0.8018 (m-30) REVERT: C 141 ARG cc_start: 0.8106 (ttt-90) cc_final: 0.7899 (ttt180) REVERT: C 475 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: C 492 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6786 (mp0) REVERT: A 69 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8252 (m) REVERT: A 90 ASP cc_start: 0.8271 (m-30) cc_final: 0.7993 (m-30) REVERT: A 475 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: A 492 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6769 (mp0) REVERT: D 69 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8277 (m) REVERT: D 90 ASP cc_start: 0.8294 (m-30) cc_final: 0.8019 (m-30) REVERT: D 475 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: D 492 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6775 (mp0) REVERT: G 69 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8282 (m) REVERT: G 475 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: G 492 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6781 (mp0) outliers start: 33 outliers final: 13 residues processed: 212 average time/residue: 0.1449 time to fit residues: 41.2096 Evaluate side-chains 200 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain H residue 64 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 101 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 113 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 30 optimal weight: 0.0980 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 210 GLN A 77 HIS B 210 GLN D 77 HIS F 210 GLN G 77 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.190255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130751 restraints weight = 13129.716| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.00 r_work: 0.3089 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13004 Z= 0.115 Angle : 0.559 11.559 17536 Z= 0.285 Chirality : 0.040 0.296 1820 Planarity : 0.004 0.043 2308 Dihedral : 4.278 16.990 1700 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.95 % Favored : 92.78 % Rotamer: Outliers : 1.63 % Allowed : 17.83 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.22), residues: 1496 helix: 1.80 (0.18), residues: 856 sheet: -0.10 (0.82), residues: 40 loop : -2.18 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 51 TYR 0.006 0.001 TYR C 137 PHE 0.037 0.002 PHE B 178 TRP 0.005 0.001 TRP C 55 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00275 (13004) covalent geometry : angle 0.55859 (17536) hydrogen bonds : bond 0.03092 ( 640) hydrogen bonds : angle 4.30614 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8362 (mt) REVERT: C 492 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6835 (mp0) REVERT: A 45 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8361 (mt) REVERT: A 492 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6812 (mp0) REVERT: D 45 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8372 (mt) REVERT: D 445 MET cc_start: 0.7754 (mmm) cc_final: 0.7325 (mmt) REVERT: D 492 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6821 (mp0) REVERT: G 45 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8379 (mt) REVERT: G 492 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6835 (mp0) outliers start: 22 outliers final: 8 residues processed: 204 average time/residue: 0.1339 time to fit residues: 37.2469 Evaluate side-chains 195 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain H residue 64 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 109 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 86 optimal weight: 0.2980 chunk 114 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 210 GLN A 77 HIS B 210 GLN D 77 HIS F 210 GLN G 77 HIS H 210 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.186568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.123861 restraints weight = 12985.654| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.86 r_work: 0.2968 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13004 Z= 0.148 Angle : 0.576 9.379 17536 Z= 0.294 Chirality : 0.042 0.287 1820 Planarity : 0.004 0.051 2308 Dihedral : 4.315 16.608 1700 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.49 % Favored : 92.25 % Rotamer: Outliers : 2.29 % Allowed : 17.31 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.22), residues: 1496 helix: 1.86 (0.18), residues: 856 sheet: 0.07 (0.83), residues: 40 loop : -2.17 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 51 TYR 0.007 0.001 TYR H 57 PHE 0.029 0.002 PHE B 178 TRP 0.003 0.001 TRP D 19 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00361 (13004) covalent geometry : angle 0.57574 (17536) hydrogen bonds : bond 0.03438 ( 640) hydrogen bonds : angle 4.33543 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8324 (m) REVERT: C 492 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6876 (mp0) REVERT: E 131 PHE cc_start: 0.8409 (t80) cc_final: 0.8209 (t80) REVERT: A 69 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8319 (m) REVERT: A 492 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6808 (mp0) REVERT: D 492 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6832 (mp0) REVERT: F 131 PHE cc_start: 0.8403 (t80) cc_final: 0.8201 (t80) REVERT: G 69 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8326 (m) REVERT: G 492 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6840 (mp0) REVERT: H 131 PHE cc_start: 0.8400 (t80) cc_final: 0.8198 (t80) outliers start: 31 outliers final: 16 residues processed: 218 average time/residue: 0.1277 time to fit residues: 38.0790 Evaluate side-chains 208 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 66 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 210 GLN A 77 HIS B 210 GLN D 77 HIS F 210 GLN G 77 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.189913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129350 restraints weight = 13013.955| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.82 r_work: 0.3144 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13004 Z= 0.118 Angle : 0.575 10.428 17536 Z= 0.290 Chirality : 0.041 0.260 1820 Planarity : 0.004 0.064 2308 Dihedral : 4.251 16.826 1700 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.22 % Favored : 92.51 % Rotamer: Outliers : 1.41 % Allowed : 18.42 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.22), residues: 1496 helix: 1.92 (0.18), residues: 856 sheet: 0.08 (0.84), residues: 40 loop : -2.11 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 51 TYR 0.006 0.001 TYR G 106 PHE 0.025 0.002 PHE F 178 TRP 0.004 0.001 TRP D 55 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00283 (13004) covalent geometry : angle 0.57524 (17536) hydrogen bonds : bond 0.03137 ( 640) hydrogen bonds : angle 4.27030 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 146 GLU cc_start: 0.6244 (mt-10) cc_final: 0.5990 (mt-10) REVERT: C 492 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6771 (mp0) REVERT: A 492 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6752 (mp0) REVERT: D 492 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6764 (mp0) REVERT: G 492 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6775 (mp0) outliers start: 19 outliers final: 12 residues processed: 201 average time/residue: 0.1310 time to fit residues: 36.2489 Evaluate side-chains 192 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 210 GLN A 77 HIS B 210 GLN D 77 HIS F 210 GLN G 77 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.189147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126838 restraints weight = 13088.021| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.87 r_work: 0.3052 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13004 Z= 0.134 Angle : 0.598 10.960 17536 Z= 0.300 Chirality : 0.041 0.226 1820 Planarity : 0.004 0.061 2308 Dihedral : 4.233 16.352 1700 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.75 % Favored : 91.98 % Rotamer: Outliers : 1.48 % Allowed : 17.97 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1496 helix: 1.84 (0.18), residues: 868 sheet: 0.16 (0.85), residues: 40 loop : -2.16 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 51 TYR 0.006 0.001 TYR H 57 PHE 0.032 0.002 PHE B 131 TRP 0.003 0.001 TRP A 19 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00327 (13004) covalent geometry : angle 0.59844 (17536) hydrogen bonds : bond 0.03259 ( 640) hydrogen bonds : angle 4.28959 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 492 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6760 (mp0) REVERT: A 492 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6736 (mp0) REVERT: D 492 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6744 (mp0) REVERT: G 492 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6768 (mp0) outliers start: 20 outliers final: 12 residues processed: 193 average time/residue: 0.1340 time to fit residues: 35.3658 Evaluate side-chains 192 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 64 CYS Chi-restraints excluded: chain H residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 140 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 106 optimal weight: 0.0570 chunk 83 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 210 GLN A 77 HIS B 210 GLN D 77 HIS F 210 GLN G 77 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.190382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130610 restraints weight = 12938.909| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.20 r_work: 0.3079 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13004 Z= 0.123 Angle : 0.588 10.548 17536 Z= 0.298 Chirality : 0.041 0.181 1820 Planarity : 0.004 0.060 2308 Dihedral : 4.208 16.255 1700 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.62 % Favored : 92.11 % Rotamer: Outliers : 1.18 % Allowed : 18.57 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1496 helix: 1.86 (0.18), residues: 868 sheet: 0.22 (0.85), residues: 40 loop : -2.12 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 51 TYR 0.006 0.001 TYR G 106 PHE 0.033 0.002 PHE F 131 TRP 0.003 0.001 TRP D 8 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00295 (13004) covalent geometry : angle 0.58815 (17536) hydrogen bonds : bond 0.03119 ( 640) hydrogen bonds : angle 4.27191 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3075.91 seconds wall clock time: 53 minutes 19.22 seconds (3199.22 seconds total)