Starting phenix.real_space_refine on Sat Jul 20 22:17:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e83_31009/07_2024/7e83_31009.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e83_31009/07_2024/7e83_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e83_31009/07_2024/7e83_31009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e83_31009/07_2024/7e83_31009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e83_31009/07_2024/7e83_31009.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e83_31009/07_2024/7e83_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 Residue "C GLU 127": "OE1" <-> "OE2" Residue "C ASP 131": "OD1" <-> "OD2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ASP 131": "OD1" <-> "OD2" Residue "F PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 176": "OD1" <-> "OD2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G ASP 131": "OD1" <-> "OD2" Residue "H PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 176": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.91, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 4.76 Conformation dependent library (CDL) restraints added in 2.1 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: 1.23 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: 3.18 Time building geometry restraints manager: 5.24 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: 99.03 - 106.02: 284 106.02 - 113.02: 6618 113.02 - 120.02: 4774 120.02 - 127.01: 5712 127.01 - 134.01: 148 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 2.440 nonbonded pdb=" OG1 THR C 65 " pdb=" OH TYR C 99 " model vdw 2.154 2.440 nonbonded pdb=" OG1 THR D 65 " pdb=" OH TYR D 99 " model vdw 2.154 2.440 nonbonded pdb=" OG1 THR G 65 " pdb=" OH TYR G 99 " model vdw 2.154 2.440 nonbonded pdb=" OE2 GLU G 71 " pdb=" OH TYR H 57 " model vdw 2.240 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' 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: 0.620 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.900 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.370 ------------------------------------------------------------------------------- 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= 0.205 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.366 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: 0.3310 time to fit residues: 121.9362 Evaluate side-chains 230 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.7980 chunk 116 optimal weight: 0.0170 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.0570 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN ** D 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1313 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= 0.182 Angle : 0.534 7.397 17536 Z= 0.280 Chirality : 0.039 0.143 1820 Planarity : 0.004 0.030 2308 Dihedral : 4.191 16.588 1700 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.02 % Favored : 91.71 % Rotamer: Outliers : 0.59 % Allowed : 7.77 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1496 helix: 1.73 (0.18), residues: 852 sheet: -1.48 (0.59), residues: 40 loop : -2.27 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 19 HIS 0.005 0.001 HIS D 94 PHE 0.014 0.002 PHE H 74 TYR 0.008 0.001 TYR G 137 ARG 0.003 0.000 ARG G 108 *********************** 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 239 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 231 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 492 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6510 (mp0) REVERT: A 492 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6512 (mp0) REVERT: D 492 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6502 (mp0) REVERT: G 492 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6505 (mp0) outliers start: 8 outliers final: 4 residues processed: 239 average time/residue: 0.3280 time to fit residues: 103.8008 Evaluate side-chains 214 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain G residue 112 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13004 Z= 0.272 Angle : 0.568 7.672 17536 Z= 0.295 Chirality : 0.043 0.269 1820 Planarity : 0.004 0.031 2308 Dihedral : 4.285 16.291 1700 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.29 % Favored : 91.44 % Rotamer: Outliers : 1.26 % Allowed : 9.54 % Favored : 89.20 % 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: 0.17 (0.22), residues: 1496 helix: 1.71 (0.18), residues: 852 sheet: -1.48 (0.64), residues: 40 loop : -2.25 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 55 HIS 0.004 0.001 HIS D 94 PHE 0.018 0.002 PHE B 178 TYR 0.010 0.001 TYR C 137 ARG 0.009 0.000 ARG A 51 *********************** 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 222 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 487 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7564 (ttmm) REVERT: A 487 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7569 (ttmm) REVERT: D 487 LYS cc_start: 0.7764 (ttmm) cc_final: 0.7532 (ttmm) REVERT: G 487 LYS cc_start: 0.7801 (ttmm) cc_final: 0.7565 (ttmm) outliers start: 17 outliers final: 8 residues processed: 218 average time/residue: 0.3026 time to fit residues: 89.0188 Evaluate side-chains 201 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 193 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain G residue 112 ILE 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 133 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 0.3980 chunk 70 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13004 Z= 0.276 Angle : 0.577 8.810 17536 Z= 0.298 Chirality : 0.042 0.147 1820 Planarity : 0.004 0.030 2308 Dihedral : 4.420 16.026 1700 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.29 % Favored : 91.44 % Rotamer: Outliers : 0.89 % Allowed : 12.57 % Favored : 86.54 % 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: 0.09 (0.22), residues: 1496 helix: 1.48 (0.18), residues: 880 sheet: -1.15 (0.69), residues: 40 loop : -2.21 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 19 HIS 0.004 0.001 HIS D 94 PHE 0.019 0.002 PHE B 178 TYR 0.010 0.001 TYR D 137 ARG 0.003 0.000 ARG A 51 *********************** 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 209 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 487 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7652 (ttmm) REVERT: C 492 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6554 (mp0) REVERT: A 487 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7615 (ttmm) REVERT: A 492 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6556 (mp0) REVERT: D 487 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7602 (ttmm) REVERT: D 492 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6532 (mp0) REVERT: G 487 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7632 (ttmm) REVERT: G 492 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6537 (mp0) outliers start: 12 outliers final: 8 residues processed: 205 average time/residue: 0.3080 time to fit residues: 85.2873 Evaluate side-chains 188 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain G residue 112 ILE 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 119 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2112 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= 0.190 Angle : 0.527 7.337 17536 Z= 0.274 Chirality : 0.039 0.143 1820 Planarity : 0.003 0.030 2308 Dihedral : 4.283 15.917 1700 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.09 % Favored : 91.64 % Rotamer: Outliers : 1.18 % Allowed : 14.94 % Favored : 83.88 % 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: 0.19 (0.22), residues: 1496 helix: 1.71 (0.18), residues: 852 sheet: -1.08 (0.68), residues: 40 loop : -2.26 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 19 HIS 0.004 0.001 HIS D 94 PHE 0.029 0.002 PHE E 178 TYR 0.007 0.001 TYR D 99 ARG 0.005 0.000 ARG A 51 *********************** 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 202 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.7516 (m-30) cc_final: 0.7246 (m-30) REVERT: C 492 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6505 (mp0) REVERT: A 475 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: A 492 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6503 (mp0) REVERT: D 492 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6486 (mp0) REVERT: G 492 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6495 (mp0) outliers start: 16 outliers final: 11 residues processed: 198 average time/residue: 0.2967 time to fit residues: 79.9191 Evaluate side-chains 188 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain E residue 64 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 112 ILE 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 F residue 64 CYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 112 ILE 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 48 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2219 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= 0.211 Angle : 0.557 10.423 17536 Z= 0.283 Chirality : 0.040 0.144 1820 Planarity : 0.004 0.030 2308 Dihedral : 4.229 16.077 1700 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.62 % Favored : 92.11 % Rotamer: Outliers : 2.29 % Allowed : 15.75 % 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: 0.29 (0.22), residues: 1496 helix: 1.79 (0.18), residues: 852 sheet: -0.93 (0.70), residues: 40 loop : -2.23 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 19 HIS 0.004 0.001 HIS A 94 PHE 0.027 0.002 PHE F 178 TYR 0.007 0.001 TYR A 99 ARG 0.004 0.000 ARG A 141 *********************** 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 214 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: C 475 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: C 492 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6558 (mp0) REVERT: A 475 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: A 492 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6559 (mp0) REVERT: D 475 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: D 492 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6544 (mp0) REVERT: G 475 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: G 492 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6547 (mp0) outliers start: 31 outliers final: 15 residues processed: 206 average time/residue: 0.2992 time to fit residues: 83.8203 Evaluate side-chains 196 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU 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 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 70 SER Chi-restraints excluded: chain D residue 112 ILE 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 70 SER Chi-restraints excluded: chain G residue 112 ILE 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 138 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 B 76 GLN D 77 HIS F 76 GLN F 210 GLN G 77 HIS H 76 GLN H 210 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2313 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= 0.230 Angle : 0.551 8.445 17536 Z= 0.283 Chirality : 0.040 0.145 1820 Planarity : 0.004 0.030 2308 Dihedral : 4.265 16.341 1700 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.29 % Favored : 91.44 % Rotamer: Outliers : 2.81 % Allowed : 14.79 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.22), residues: 1496 helix: 1.82 (0.18), residues: 852 sheet: -0.76 (0.72), residues: 40 loop : -2.22 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 19 HIS 0.004 0.001 HIS A 94 PHE 0.032 0.002 PHE F 178 TYR 0.008 0.001 TYR C 99 ARG 0.005 0.000 ARG C 141 *********************** 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 218 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: C 445 MET cc_start: 0.7961 (mmm) cc_final: 0.7648 (mmt) REVERT: C 475 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: C 492 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6578 (mp0) REVERT: A 445 MET cc_start: 0.7938 (mmm) cc_final: 0.7637 (mmt) REVERT: A 475 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: A 492 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6651 (mp0) REVERT: D 445 MET cc_start: 0.7929 (mmm) cc_final: 0.7625 (mmt) REVERT: D 475 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: D 492 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6537 (mp0) REVERT: G 445 MET cc_start: 0.7912 (mmm) cc_final: 0.7603 (mmt) REVERT: G 475 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: G 492 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6542 (mp0) outliers start: 38 outliers final: 21 residues processed: 202 average time/residue: 0.3048 time to fit residues: 83.5781 Evaluate side-chains 206 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU 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 E residue 66 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 112 ILE 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 70 SER Chi-restraints excluded: chain D residue 112 ILE 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 G residue 50 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 475 GLU 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 56 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 B 76 GLN D 77 HIS F 76 GLN F 210 GLN G 77 HIS H 76 GLN H 210 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13004 Z= 0.322 Angle : 0.609 7.703 17536 Z= 0.312 Chirality : 0.042 0.148 1820 Planarity : 0.004 0.031 2308 Dihedral : 4.443 16.108 1700 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.56 % Favored : 91.18 % Rotamer: Outliers : 2.37 % Allowed : 16.49 % Favored : 81.14 % 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: 0.20 (0.22), residues: 1496 helix: 1.56 (0.18), residues: 880 sheet: -0.58 (0.78), residues: 40 loop : -2.19 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.005 0.001 HIS G 94 PHE 0.039 0.003 PHE F 178 TYR 0.011 0.001 TYR C 99 ARG 0.003 0.000 ARG C 141 *********************** 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 217 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 MET cc_start: 0.3517 (tmm) cc_final: 0.3029 (tmm) REVERT: C 445 MET cc_start: 0.8045 (mmm) cc_final: 0.7802 (mmt) REVERT: C 475 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: A 27 MET cc_start: 0.3481 (tmm) cc_final: 0.2987 (tmm) REVERT: A 445 MET cc_start: 0.8028 (mmm) cc_final: 0.7799 (mmt) REVERT: A 475 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: D 27 MET cc_start: 0.3505 (tmm) cc_final: 0.3012 (tmm) REVERT: D 445 MET cc_start: 0.8016 (mmm) cc_final: 0.7784 (mmt) REVERT: D 475 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: G 27 MET cc_start: 0.3527 (tmm) cc_final: 0.3031 (tmm) REVERT: G 445 MET cc_start: 0.8000 (mmm) cc_final: 0.7763 (mmt) REVERT: G 475 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7489 (mt-10) outliers start: 32 outliers final: 18 residues processed: 205 average time/residue: 0.3007 time to fit residues: 84.2289 Evaluate side-chains 210 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU 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 E residue 66 SER Chi-restraints excluded: chain A residue 42 LEU 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 B residue 66 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 112 ILE 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 G residue 70 SER Chi-restraints excluded: chain G residue 475 GLU 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 136 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 125 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 210 GLN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** D 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN F 210 GLN ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2513 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= 0.220 Angle : 0.562 7.269 17536 Z= 0.291 Chirality : 0.040 0.147 1820 Planarity : 0.004 0.033 2308 Dihedral : 4.370 16.448 1700 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.29 % Favored : 91.44 % Rotamer: Outliers : 2.29 % Allowed : 16.12 % Favored : 81.58 % 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: 0.32 (0.22), residues: 1496 helix: 1.77 (0.18), residues: 856 sheet: -0.51 (0.77), residues: 40 loop : -2.20 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 55 HIS 0.005 0.001 HIS A 94 PHE 0.039 0.002 PHE B 178 TYR 0.008 0.001 TYR G 106 ARG 0.004 0.000 ARG G 141 *********************** 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 212 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8277 (mt) REVERT: C 445 MET cc_start: 0.8058 (mmm) cc_final: 0.7841 (mmt) REVERT: C 475 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: C 492 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6763 (mp0) REVERT: A 45 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8257 (mt) REVERT: A 475 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: A 492 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6724 (mp0) REVERT: D 45 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8252 (mt) REVERT: D 445 MET cc_start: 0.8030 (mmm) cc_final: 0.7829 (mmt) REVERT: D 475 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: D 492 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6707 (mp0) REVERT: G 45 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8293 (mt) REVERT: G 445 MET cc_start: 0.8012 (mmm) cc_final: 0.7806 (mmt) REVERT: G 475 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: G 492 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6713 (mp0) outliers start: 31 outliers final: 13 residues processed: 208 average time/residue: 0.2870 time to fit residues: 82.1832 Evaluate side-chains 203 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 45 LEU 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 45 LEU Chi-restraints excluded: chain A residue 50 THR 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 45 LEU Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 475 GLU 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 G residue 45 LEU Chi-restraints excluded: chain G residue 475 GLU 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 85 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 210 GLN A 77 HIS B 76 GLN D 77 HIS F 76 GLN F 210 GLN G 77 HIS H 76 GLN H 210 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2625 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= 0.281 Angle : 0.623 13.990 17536 Z= 0.314 Chirality : 0.042 0.146 1820 Planarity : 0.004 0.034 2308 Dihedral : 4.404 16.353 1700 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.62 % Favored : 91.11 % Rotamer: Outliers : 2.07 % Allowed : 16.35 % Favored : 81.58 % 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: 0.13 (0.22), residues: 1496 helix: 1.48 (0.17), residues: 892 sheet: -0.50 (0.78), residues: 40 loop : -2.27 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 19 HIS 0.005 0.001 HIS D 94 PHE 0.033 0.002 PHE E 178 TYR 0.011 0.001 TYR C 99 ARG 0.003 0.000 ARG G 141 ********************** 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 213 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 445 MET cc_start: 0.8071 (mmm) cc_final: 0.7860 (mmt) REVERT: C 475 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: A 45 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8276 (mt) REVERT: A 445 MET cc_start: 0.8003 (mmt) cc_final: 0.7645 (mmm) REVERT: A 475 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: D 45 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8270 (mt) REVERT: D 475 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: G 445 MET cc_start: 0.8030 (mmm) cc_final: 0.7820 (mmt) REVERT: G 475 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7578 (mt-10) outliers start: 28 outliers final: 10 residues processed: 206 average time/residue: 0.3121 time to fit residues: 87.5749 Evaluate side-chains 198 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 64 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 45 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 45 LEU Chi-restraints excluded: chain D residue 112 ILE 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 35 optimal weight: 0.0870 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 210 GLN ** D 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** G 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.188970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131462 restraints weight = 12984.544| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.04 r_work: 0.3059 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2628 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= 0.194 Angle : 0.582 12.514 17536 Z= 0.296 Chirality : 0.040 0.149 1820 Planarity : 0.004 0.033 2308 Dihedral : 4.234 16.456 1700 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.95 % Favored : 91.78 % Rotamer: Outliers : 0.74 % Allowed : 17.68 % Favored : 81.58 % 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: 0.25 (0.22), residues: 1496 helix: 1.70 (0.18), residues: 868 sheet: -0.52 (0.76), residues: 40 loop : -2.28 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 55 HIS 0.004 0.001 HIS D 94 PHE 0.032 0.002 PHE F 178 TYR 0.007 0.001 TYR A 106 ARG 0.004 0.000 ARG C 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2715.51 seconds wall clock time: 49 minutes 18.69 seconds (2958.69 seconds total)