Starting phenix.real_space_refine on Wed Jul 30 11:46:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e83_31009/07_2025/7e83_31009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e83_31009/07_2025/7e83_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_31009/07_2025/7e83_31009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e83_31009/07_2025/7e83_31009.map" model { file = "/net/cci-nas-00/data/ceres_data/7e83_31009/07_2025/7e83_31009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e83_31009/07_2025/7e83_31009.cif" } resolution = 3.1 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= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.43, per 1000 atoms: 0.58 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: 3.20 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.15 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: 3.36 Time building geometry restraints manager: 3.60 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: 0.11 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'G' } 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: 0.770 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.260 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.250 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.002 0.000 TRP G 19 HIS 0.006 0.001 HIS C 94 PHE 0.021 0.001 PHE E 74 TYR 0.008 0.001 TYR A 134 ARG 0.006 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.12956 ( 640) hydrogen bonds : angle 5.61050 ( 1860) covalent geometry : bond 0.00309 (13004) covalent geometry : angle 0.60546 (17536) *********************** 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 : 1.308 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: 0.6510 (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: 0.3518 time to fit residues: 129.7471 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 : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 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 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 = 0.4021 r_free = 0.4021 target = 0.187839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.125944 restraints weight = 12947.731| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.83 r_work: 0.3027 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1454 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= 0.157 Angle : 0.576 7.418 17536 Z= 0.303 Chirality : 0.041 0.145 1820 Planarity : 0.004 0.031 2308 Dihedral : 4.330 17.117 1700 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.75 % Favored : 91.98 % Rotamer: Outliers : 0.89 % Allowed : 8.06 % Favored : 91.05 % 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: 0.15 (0.22), residues: 1496 helix: 1.68 (0.18), residues: 852 sheet: -1.34 (0.62), residues: 40 loop : -2.27 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 55 HIS 0.006 0.001 HIS C 94 PHE 0.015 0.002 PHE B 74 TYR 0.011 0.001 TYR C 137 ARG 0.003 0.000 ARG C 108 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 640) hydrogen bonds : angle 4.65069 ( 1860) covalent geometry : bond 0.00370 (13004) covalent geometry : angle 0.57637 (17536) *********************** 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 228 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 445 MET cc_start: 0.7728 (mmm) cc_final: 0.7450 (mmt) REVERT: C 492 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6454 (mp0) REVERT: E 132 ASN cc_start: 0.7587 (m110) cc_final: 0.7057 (m-40) REVERT: A 445 MET cc_start: 0.7744 (mmm) cc_final: 0.7465 (mmt) REVERT: A 492 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6461 (mp0) REVERT: B 132 ASN cc_start: 0.7588 (m110) cc_final: 0.7057 (m-40) REVERT: D 13 ARG cc_start: 0.8707 (mtt180) cc_final: 0.8487 (mtt180) REVERT: D 445 MET cc_start: 0.7732 (mmm) cc_final: 0.7452 (mmt) REVERT: D 492 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6445 (mp0) REVERT: F 132 ASN cc_start: 0.7598 (m110) cc_final: 0.7066 (m-40) REVERT: G 445 MET cc_start: 0.7712 (mmm) cc_final: 0.7432 (mmt) REVERT: G 492 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6437 (mp0) REVERT: H 132 ASN cc_start: 0.7601 (m110) cc_final: 0.7077 (m-40) outliers start: 12 outliers final: 5 residues processed: 224 average time/residue: 0.4794 time to fit residues: 141.3820 Evaluate side-chains 205 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 200 time to evaluate : 1.890 ------------------------------------------------------------------------------- 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 53 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 110 optimal weight: 0.0770 chunk 67 optimal weight: 0.9980 chunk 69 optimal weight: 0.0270 chunk 116 optimal weight: 4.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.193262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.134559 restraints weight = 12979.722| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.84 r_work: 0.3134 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13004 Z= 0.110 Angle : 0.523 7.909 17536 Z= 0.273 Chirality : 0.039 0.229 1820 Planarity : 0.003 0.031 2308 Dihedral : 4.164 16.500 1700 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.42 % Favored : 92.31 % Rotamer: Outliers : 1.18 % Allowed : 9.69 % Favored : 89.13 % 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: 0.23 (0.22), residues: 1496 helix: 1.75 (0.18), residues: 852 sheet: -1.44 (0.64), residues: 40 loop : -2.21 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 55 HIS 0.004 0.001 HIS A 94 PHE 0.022 0.002 PHE E 131 TYR 0.010 0.001 TYR D 137 ARG 0.004 0.000 ARG G 141 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 640) hydrogen bonds : angle 4.41384 ( 1860) covalent geometry : bond 0.00246 (13004) covalent geometry : angle 0.52320 (17536) *********************** 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 226 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ARG cc_start: 0.8587 (mtt180) cc_final: 0.8376 (mtt180) REVERT: C 445 MET cc_start: 0.7812 (mmm) cc_final: 0.7599 (mmt) REVERT: C 492 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6505 (mp0) REVERT: A 13 ARG cc_start: 0.8583 (mtt180) cc_final: 0.8372 (mtt180) REVERT: A 445 MET cc_start: 0.7827 (mmm) cc_final: 0.7612 (mmt) REVERT: A 492 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6480 (mp0) REVERT: D 13 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8373 (mtt180) REVERT: D 445 MET cc_start: 0.7823 (mmm) cc_final: 0.7606 (mmt) REVERT: D 492 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6519 (mp0) REVERT: G 13 ARG cc_start: 0.8587 (mtt180) cc_final: 0.8375 (mtt180) REVERT: G 445 MET cc_start: 0.7805 (mmm) cc_final: 0.7588 (mmt) REVERT: G 492 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6466 (mp0) outliers start: 16 outliers final: 4 residues processed: 218 average time/residue: 0.3169 time to fit residues: 92.9298 Evaluate side-chains 209 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 80 optimal weight: 3.9990 chunk 110 optimal weight: 0.0270 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 120 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 G 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.192383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131177 restraints weight = 13034.718| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.84 r_work: 0.3126 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13004 Z= 0.107 Angle : 0.522 8.575 17536 Z= 0.269 Chirality : 0.039 0.143 1820 Planarity : 0.003 0.031 2308 Dihedral : 4.083 16.321 1700 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.55 % Favored : 93.18 % Rotamer: Outliers : 0.89 % Allowed : 11.17 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1496 helix: 1.83 (0.18), residues: 852 sheet: -1.14 (0.66), residues: 40 loop : -2.16 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 19 HIS 0.003 0.001 HIS A 94 PHE 0.021 0.002 PHE E 178 TYR 0.007 0.001 TYR D 137 ARG 0.004 0.000 ARG G 141 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 640) hydrogen bonds : angle 4.32552 ( 1860) covalent geometry : bond 0.00245 (13004) covalent geometry : angle 0.52210 (17536) *********************** 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 218 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 MET cc_start: 0.3392 (tmm) cc_final: 0.2937 (tmm) REVERT: C 141 ARG cc_start: 0.8102 (ttt-90) cc_final: 0.7869 (ttt180) REVERT: C 492 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6572 (mp0) REVERT: A 13 ARG cc_start: 0.8589 (mtt180) cc_final: 0.8379 (mtt180) REVERT: A 27 MET cc_start: 0.3388 (tmm) cc_final: 0.2935 (tmm) REVERT: A 141 ARG cc_start: 0.8163 (ttt-90) cc_final: 0.7931 (ttt180) REVERT: A 492 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6523 (mp0) REVERT: D 27 MET cc_start: 0.3403 (tmm) cc_final: 0.2942 (tmm) REVERT: D 141 ARG cc_start: 0.8177 (ttt-90) cc_final: 0.7950 (ttt180) REVERT: D 492 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6577 (mp0) REVERT: G 13 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8387 (mtt180) REVERT: G 27 MET cc_start: 0.3380 (tmm) cc_final: 0.2924 (tmm) REVERT: G 141 ARG cc_start: 0.8159 (ttt-90) cc_final: 0.7931 (ttt180) REVERT: G 492 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6575 (mp0) outliers start: 12 outliers final: 8 residues processed: 210 average time/residue: 0.3206 time to fit residues: 90.5766 Evaluate side-chains 208 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 200 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain G residue 42 LEU 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 67 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 113 optimal weight: 0.0070 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.191595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129305 restraints weight = 13009.282| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.87 r_work: 0.3130 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13004 Z= 0.110 Angle : 0.513 7.323 17536 Z= 0.264 Chirality : 0.039 0.144 1820 Planarity : 0.003 0.031 2308 Dihedral : 4.045 16.881 1700 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.02 % Favored : 91.71 % Rotamer: Outliers : 1.48 % Allowed : 12.20 % Favored : 86.32 % 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: 0.39 (0.22), residues: 1496 helix: 1.87 (0.18), residues: 852 sheet: -0.94 (0.70), residues: 40 loop : -2.16 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 8 HIS 0.003 0.001 HIS D 94 PHE 0.029 0.002 PHE F 178 TYR 0.006 0.001 TYR G 137 ARG 0.003 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 640) hydrogen bonds : angle 4.27987 ( 1860) covalent geometry : bond 0.00257 (13004) covalent geometry : angle 0.51264 (17536) *********************** 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 218 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 445 MET cc_start: 0.7669 (mmm) cc_final: 0.7399 (mmt) REVERT: C 492 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6564 (mp0) REVERT: A 141 ARG cc_start: 0.8125 (ttt-90) cc_final: 0.7908 (ttt180) REVERT: A 445 MET cc_start: 0.7670 (mmm) cc_final: 0.7404 (mmt) REVERT: A 492 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6505 (mp0) REVERT: D 141 ARG cc_start: 0.8135 (ttt-90) cc_final: 0.7919 (ttt180) REVERT: D 445 MET cc_start: 0.7670 (mmm) cc_final: 0.7400 (mmt) REVERT: D 492 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6548 (mp0) REVERT: G 90 ASP cc_start: 0.8180 (m-30) cc_final: 0.7902 (m-30) REVERT: G 141 ARG cc_start: 0.8096 (ttt-90) cc_final: 0.7879 (ttt180) REVERT: G 445 MET cc_start: 0.7663 (mmm) cc_final: 0.7395 (mmt) REVERT: G 492 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6550 (mp0) outliers start: 20 outliers final: 8 residues processed: 206 average time/residue: 0.3147 time to fit residues: 89.4017 Evaluate side-chains 202 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 66 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 113 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 G 77 HIS H 210 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.190412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133207 restraints weight = 13140.862| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.06 r_work: 0.3071 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13004 Z= 0.137 Angle : 0.553 9.929 17536 Z= 0.281 Chirality : 0.040 0.145 1820 Planarity : 0.003 0.032 2308 Dihedral : 4.096 16.584 1700 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.09 % Favored : 92.65 % Rotamer: Outliers : 1.78 % Allowed : 13.61 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1496 helix: 1.83 (0.18), residues: 856 sheet: -0.83 (0.70), residues: 40 loop : -2.15 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.003 0.001 HIS C 94 PHE 0.032 0.002 PHE E 178 TYR 0.007 0.001 TYR D 137 ARG 0.002 0.000 ARG G 141 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 640) hydrogen bonds : angle 4.30519 ( 1860) covalent geometry : bond 0.00328 (13004) covalent geometry : angle 0.55264 (17536) *********************** 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 225 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8304 (m) REVERT: C 492 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6577 (mp0) REVERT: E 158 MET cc_start: 0.7178 (mtp) cc_final: 0.6741 (mtm) REVERT: A 69 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8309 (m) REVERT: A 492 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6525 (mp0) REVERT: B 158 MET cc_start: 0.7169 (mtp) cc_final: 0.6733 (mtm) REVERT: D 69 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8322 (m) REVERT: D 492 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6552 (mp0) REVERT: F 158 MET cc_start: 0.7192 (mtp) cc_final: 0.6749 (mtm) REVERT: G 492 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6549 (mp0) REVERT: H 158 MET cc_start: 0.7185 (mtp) cc_final: 0.6744 (mtm) outliers start: 24 outliers final: 12 residues processed: 213 average time/residue: 0.3040 time to fit residues: 88.2757 Evaluate side-chains 214 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 69 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 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 69 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 H residue 64 CYS Chi-restraints excluded: chain H residue 66 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 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 = 0.4025 r_free = 0.4025 target = 0.188627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127268 restraints weight = 12914.594| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.01 r_work: 0.3045 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13004 Z= 0.149 Angle : 0.570 9.188 17536 Z= 0.290 Chirality : 0.041 0.145 1820 Planarity : 0.004 0.032 2308 Dihedral : 4.166 16.531 1700 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.49 % Favored : 92.25 % Rotamer: Outliers : 1.41 % Allowed : 14.87 % Favored : 83.73 % 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: 0.36 (0.22), residues: 1496 helix: 1.82 (0.18), residues: 856 sheet: -0.63 (0.74), residues: 40 loop : -2.18 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 19 HIS 0.004 0.001 HIS C 94 PHE 0.033 0.002 PHE B 178 TYR 0.009 0.001 TYR C 137 ARG 0.002 0.000 ARG G 51 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 640) hydrogen bonds : angle 4.32902 ( 1860) covalent geometry : bond 0.00363 (13004) covalent geometry : angle 0.57050 (17536) *********************** 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 208 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8278 (m) REVERT: C 492 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6637 (mp0) REVERT: A 69 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8283 (m) REVERT: A 492 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6597 (mp0) REVERT: D 69 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8285 (m) REVERT: D 492 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6621 (mp0) REVERT: G 69 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8293 (m) REVERT: G 492 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6594 (mp0) outliers start: 19 outliers final: 7 residues processed: 201 average time/residue: 0.2885 time to fit residues: 80.4077 Evaluate side-chains 195 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain D residue 69 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 H residue 64 CYS Chi-restraints excluded: chain H residue 66 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 G 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.189615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130942 restraints weight = 12993.861| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.95 r_work: 0.3123 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13004 Z= 0.133 Angle : 0.577 9.796 17536 Z= 0.290 Chirality : 0.040 0.145 1820 Planarity : 0.004 0.033 2308 Dihedral : 4.164 16.593 1700 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.09 % Favored : 92.65 % Rotamer: Outliers : 1.48 % Allowed : 15.01 % Favored : 83.51 % 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: 0.38 (0.22), residues: 1496 helix: 1.84 (0.18), residues: 856 sheet: -0.47 (0.76), residues: 40 loop : -2.19 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 19 HIS 0.003 0.001 HIS D 94 PHE 0.039 0.002 PHE B 178 TYR 0.008 0.001 TYR C 137 ARG 0.002 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 640) hydrogen bonds : angle 4.30263 ( 1860) covalent geometry : bond 0.00323 (13004) covalent geometry : angle 0.57709 (17536) *********************** 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 207 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 475 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: C 492 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6653 (mp0) REVERT: A 475 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: A 492 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6649 (mp0) REVERT: D 475 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: D 492 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6654 (mp0) REVERT: G 492 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6654 (mp0) outliers start: 20 outliers final: 10 residues processed: 197 average time/residue: 0.2746 time to fit residues: 75.0877 Evaluate side-chains 199 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU 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 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 F residue 66 SER Chi-restraints excluded: chain G residue 42 LEU 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 80 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 33 optimal weight: 0.0670 chunk 79 optimal weight: 0.4980 chunk 143 optimal weight: 0.5980 chunk 76 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 76 GLN A 77 HIS B 76 GLN B 210 GLN D 77 HIS G 77 HIS H 76 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.192731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.132413 restraints weight = 12929.849| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.11 r_work: 0.3060 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13004 Z= 0.112 Angle : 0.580 10.397 17536 Z= 0.289 Chirality : 0.039 0.142 1820 Planarity : 0.003 0.033 2308 Dihedral : 4.064 16.777 1700 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.35 % Favored : 92.38 % Rotamer: Outliers : 1.55 % Allowed : 15.68 % Favored : 82.77 % 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: 0.46 (0.22), residues: 1496 helix: 1.94 (0.18), residues: 852 sheet: -0.41 (0.78), residues: 40 loop : -2.20 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP G 55 HIS 0.003 0.001 HIS D 94 PHE 0.042 0.002 PHE B 178 TYR 0.006 0.001 TYR C 137 ARG 0.002 0.000 ARG G 108 Details of bonding type rmsd hydrogen bonds : bond 0.02915 ( 640) hydrogen bonds : angle 4.21653 ( 1860) covalent geometry : bond 0.00262 (13004) covalent geometry : angle 0.57979 (17536) *********************** 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 214 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 492 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6600 (mp0) REVERT: A 492 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6557 (mp0) REVERT: D 492 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6602 (mp0) REVERT: G 475 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: G 492 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6603 (mp0) outliers start: 21 outliers final: 8 residues processed: 206 average time/residue: 0.2744 time to fit residues: 78.9122 Evaluate side-chains 195 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain H residue 64 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 117 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 76 GLN E 210 GLN A 77 HIS D 77 HIS F 210 GLN G 77 HIS H 76 GLN H 210 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.188740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125576 restraints weight = 12804.879| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.84 r_work: 0.3048 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2366 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= 0.165 Angle : 0.620 10.497 17536 Z= 0.314 Chirality : 0.042 0.146 1820 Planarity : 0.004 0.034 2308 Dihedral : 4.199 15.903 1700 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.49 % Favored : 92.25 % Rotamer: Outliers : 1.41 % Allowed : 16.27 % Favored : 82.32 % 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: 0.41 (0.22), residues: 1496 helix: 1.84 (0.18), residues: 856 sheet: -0.42 (0.77), residues: 40 loop : -2.15 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 55 HIS 0.004 0.001 HIS C 94 PHE 0.033 0.002 PHE B 178 TYR 0.007 0.001 TYR F 57 ARG 0.002 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 640) hydrogen bonds : angle 4.31028 ( 1860) covalent geometry : bond 0.00401 (13004) covalent geometry : angle 0.62021 (17536) ********************** 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 203 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 475 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: A 475 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: D 475 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: G 475 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7645 (mt-10) outliers start: 19 outliers final: 10 residues processed: 193 average time/residue: 0.3025 time to fit residues: 80.1032 Evaluate side-chains 194 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 475 GLU 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 475 GLU 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 475 GLU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain H residue 64 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 4.9990 chunk 143 optimal weight: 0.0980 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 114 optimal weight: 0.0770 chunk 65 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 113 optimal weight: 0.0030 overall best weight: 0.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 HIS E 76 GLN A 77 HIS B 76 GLN D 77 HIS G 77 HIS H 76 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.193552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 127)---------------| | r_work = 0.3445 r_free = 0.3445 target = 0.134286 restraints weight = 13027.448| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.83 r_work: 0.3150 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2421 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= 0.110 Angle : 0.572 10.153 17536 Z= 0.290 Chirality : 0.039 0.140 1820 Planarity : 0.003 0.034 2308 Dihedral : 4.036 16.958 1700 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.89 % Favored : 92.85 % Rotamer: Outliers : 1.11 % Allowed : 16.94 % Favored : 81.95 % 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: 0.58 (0.22), residues: 1496 helix: 2.01 (0.18), residues: 852 sheet: -0.17 (0.81), residues: 40 loop : -2.11 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 55 HIS 0.003 0.001 HIS D 94 PHE 0.032 0.002 PHE B 178 TYR 0.009 0.001 TYR F 78 ARG 0.002 0.000 ARG G 108 Details of bonding type rmsd hydrogen bonds : bond 0.02816 ( 640) hydrogen bonds : angle 4.19176 ( 1860) covalent geometry : bond 0.00258 (13004) covalent geometry : angle 0.57198 (17536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6909.97 seconds wall clock time: 121 minutes 5.07 seconds (7265.07 seconds total)