Starting phenix.real_space_refine on Sun Aug 24 04:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pfb_17645/08_2025/8pfb_17645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pfb_17645/08_2025/8pfb_17645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pfb_17645/08_2025/8pfb_17645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pfb_17645/08_2025/8pfb_17645.map" model { file = "/net/cci-nas-00/data/ceres_data/8pfb_17645/08_2025/8pfb_17645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pfb_17645/08_2025/8pfb_17645.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 5343 2.51 5 N 1477 2.21 5 O 1710 1.98 5 H 8598 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17137 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1841 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain breaks: 2 Chain: "F" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1915 Classifications: {'peptide': 125} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1977 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain breaks: 1 Chain: "A" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1966 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "B" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1966 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "I" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1966 Classifications: {'peptide': 130} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "H" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1955 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "D" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1835 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain breaks: 1 Chain: "E" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1716 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Time building chain proxies: 4.08, per 1000 atoms: 0.24 Number of scatterers: 17137 At special positions: 0 Unit cell: (77.19, 80.91, 170.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 1710 8.00 N 1477 7.00 C 5343 6.00 H 8598 1.00 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: 1.57 Conformation dependent library (CDL) restraints added in 587.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 44.5% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'G' and resid 2 through 17 removed outlier: 4.815A pdb=" N VAL G 8 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL G 9 " --> pdb=" O GLU G 5 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE G 10 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 51 removed outlier: 4.019A pdb=" N PHE G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER G 34 " --> pdb=" O ASN G 30 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 70 through 72 No H-bonds generated for 'chain 'G' and resid 70 through 72' Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'F' and resid 2 through 17 removed outlier: 3.717A pdb=" N LEU F 6 " --> pdb=" O THR F 2 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE F 10 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA F 14 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE F 15 " --> pdb=" O ILE F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 51 removed outlier: 3.612A pdb=" N LYS F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE F 51 " --> pdb=" O ILE F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 69 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'C' and resid 2 through 17 removed outlier: 3.547A pdb=" N LEU C 6 " --> pdb=" O THR C 2 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 52 removed outlier: 4.218A pdb=" N ALA C 31 " --> pdb=" O PHE C 27 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'A' and resid 2 through 10 removed outlier: 4.070A pdb=" N VAL A 8 " --> pdb=" O VAL A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.686A pdb=" N ALA A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 28 through 51 removed outlier: 3.569A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.707A pdb=" N SER A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 4.440A pdb=" N VAL B 8 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 54 removed outlier: 3.928A pdb=" N PHE B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 31 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 34 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.819A pdb=" N SER B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 17 removed outlier: 3.595A pdb=" N ALA I 14 " --> pdb=" O ILE I 10 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA I 17 " --> pdb=" O ILE I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 54 removed outlier: 3.964A pdb=" N LYS I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG I 41 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU I 42 " --> pdb=" O SER I 38 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY I 52 " --> pdb=" O GLN I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 77 removed outlier: 4.098A pdb=" N ASN I 75 " --> pdb=" O MET I 72 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA I 76 " --> pdb=" O SER I 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS I 77 " --> pdb=" O LYS I 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 72 through 77' Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'H' and resid 3 through 17 removed outlier: 3.776A pdb=" N ILE H 10 " --> pdb=" O LEU H 6 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE H 11 " --> pdb=" O ILE H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 28 Processing helix chain 'H' and resid 29 through 51 removed outlier: 4.226A pdb=" N LYS H 33 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER H 34 " --> pdb=" O ASN H 30 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG H 35 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 38 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 69 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 81 through 85 Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing helix chain 'D' and resid 11 through 17 removed outlier: 3.804A pdb=" N ILE D 15 " --> pdb=" O ILE D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 28 through 51 removed outlier: 3.666A pdb=" N SER D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU D 39 " --> pdb=" O ARG D 35 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'E' and resid 23 through 54 removed outlier: 4.521A pdb=" N PHE E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN E 30 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG E 41 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 69 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'E' and resid 107 through 109 No H-bonds generated for 'chain 'E' and resid 107 through 109' Processing sheet with id=AA1, first strand: chain 'G' and resid 103 through 106 removed outlier: 3.641A pdb=" N SER G 114 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'C' and resid 103 through 106 removed outlier: 3.747A pdb=" N LYS C 111 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'I' and resid 103 through 106 Processing sheet with id=AA7, first strand: chain 'H' and resid 103 through 106 removed outlier: 4.040A pdb=" N LYS H 111 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 106 Processing sheet with id=AA9, first strand: chain 'E' and resid 103 through 105 347 hydrogen bonds defined for protein. 942 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: 3.83 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8598 1.03 - 1.23: 1 1.23 - 1.42: 3476 1.42 - 1.61: 5164 1.61 - 1.81: 18 Bond restraints: 17257 Sorted by residual: bond pdb=" CB GLU E 62 " pdb=" CG GLU E 62 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" N PHE H 27 " pdb=" CA PHE H 27 " ideal model delta sigma weight residual 1.458 1.477 -0.019 1.42e-02 4.96e+03 1.86e+00 bond pdb=" CA PHE C 27 " pdb=" C PHE C 27 " ideal model delta sigma weight residual 1.524 1.545 -0.021 1.57e-02 4.06e+03 1.83e+00 bond pdb=" CB LYS D 77 " pdb=" CG LYS D 77 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" C GLN B 28 " pdb=" O GLN B 28 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.15e-02 7.56e+03 1.61e+00 ... (remaining 17252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 30159 1.82 - 3.65: 999 3.65 - 5.47: 70 5.47 - 7.29: 12 7.29 - 9.11: 4 Bond angle restraints: 31244 Sorted by residual: angle pdb=" N ILE H 24 " pdb=" CA ILE H 24 " pdb=" C ILE H 24 " ideal model delta sigma weight residual 112.50 117.89 -5.39 1.39e+00 5.18e-01 1.51e+01 angle pdb=" N ASP I 29 " pdb=" CA ASP I 29 " pdb=" C ASP I 29 " ideal model delta sigma weight residual 111.28 115.45 -4.17 1.09e+00 8.42e-01 1.47e+01 angle pdb=" CA LYS D 77 " pdb=" CB LYS D 77 " pdb=" CG LYS D 77 " ideal model delta sigma weight residual 114.10 121.62 -7.52 2.00e+00 2.50e-01 1.41e+01 angle pdb=" N PHE C 27 " pdb=" CA PHE C 27 " pdb=" CB PHE C 27 " ideal model delta sigma weight residual 112.41 106.81 5.60 1.55e+00 4.16e-01 1.30e+01 angle pdb=" CB GLU E 62 " pdb=" CG GLU E 62 " pdb=" CD GLU E 62 " ideal model delta sigma weight residual 112.60 118.72 -6.12 1.70e+00 3.46e-01 1.30e+01 ... (remaining 31239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 7391 17.84 - 35.68: 497 35.68 - 53.52: 151 53.52 - 71.36: 69 71.36 - 89.20: 20 Dihedral angle restraints: 8128 sinusoidal: 4469 harmonic: 3659 Sorted by residual: dihedral pdb=" CA ILE H 24 " pdb=" C ILE H 24 " pdb=" N THR H 25 " pdb=" CA THR H 25 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASP I 130 " pdb=" C ASP I 130 " pdb=" N TRP I 131 " pdb=" CA TRP I 131 " ideal model delta harmonic sigma weight residual -180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLU E 79 " pdb=" C GLU E 79 " pdb=" N ASP E 80 " pdb=" CA ASP E 80 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 8125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 773 0.033 - 0.065: 414 0.065 - 0.098: 173 0.098 - 0.131: 61 0.131 - 0.163: 11 Chirality restraints: 1432 Sorted by residual: chirality pdb=" CA TYR D 71 " pdb=" N TYR D 71 " pdb=" C TYR D 71 " pdb=" CB TYR D 71 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CB ILE A 47 " pdb=" CA ILE A 47 " pdb=" CG1 ILE A 47 " pdb=" CG2 ILE A 47 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA TYR B 71 " pdb=" N TYR B 71 " pdb=" C TYR B 71 " pdb=" CB TYR B 71 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 1429 not shown) Planarity restraints: 2585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F 69 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO F 70 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO F 70 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO F 70 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 34 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C SER B 34 " -0.063 2.00e-02 2.50e+03 pdb=" O SER B 34 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 35 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 41 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.78e+00 pdb=" C ARG B 41 " -0.054 2.00e-02 2.50e+03 pdb=" O ARG B 41 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 42 " 0.018 2.00e-02 2.50e+03 ... (remaining 2582 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 870 2.19 - 2.79: 32944 2.79 - 3.39: 43679 3.39 - 4.00: 52443 4.00 - 4.60: 81675 Nonbonded interactions: 211611 Sorted by model distance: nonbonded pdb=" OD1 ASN C 75 " pdb=" H LYS C 77 " model vdw 1.582 2.450 nonbonded pdb=" OD1 ASP D 29 " pdb=" H ASN D 30 " model vdw 1.599 2.450 nonbonded pdb=" OD2 ASP D 106 " pdb="HD21 ASN D 109 " model vdw 1.615 2.450 nonbonded pdb=" OD1 ASN E 120 " pdb=" H GLY E 122 " model vdw 1.628 2.450 nonbonded pdb=" OD2 ASP E 29 " pdb=" HG SER E 119 " model vdw 1.637 2.450 ... (remaining 211606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 54 or resid 64 through 91 or resid 101 through \ 134)) selection = (chain 'B' and (resid 16 through 54 or resid 64 through 91 or resid 101 through \ 134)) selection = (chain 'C' and (resid 16 through 54 or resid 64 through 91 or resid 101 through \ 134)) selection = (chain 'D' and (resid 16 through 54 or resid 64 through 91 or resid 101 through \ 134)) selection = (chain 'E' and (resid 16 through 54 or resid 64 through 91 or resid 101 through \ 134)) selection = (chain 'F' and (resid 16 through 54 or resid 64 through 134)) selection = (chain 'G' and (resid 16 through 91 or resid 101 through 134)) selection = (chain 'H' and (resid 16 through 54 or resid 64 through 91 or resid 101 through \ 134)) selection = (chain 'I' and (resid 16 through 54 or resid 64 through 91 or resid 101 through \ 134)) } 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 group one per residue 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: 3.370 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: 0.140 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.550 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.004 0.042 8659 Z= 0.223 Angle : 0.899 9.114 11767 Z= 0.528 Chirality : 0.048 0.163 1432 Planarity : 0.007 0.114 1511 Dihedral : 14.616 89.204 3111 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.32 % Allowed : 13.80 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.23), residues: 1098 helix: -1.89 (0.24), residues: 362 sheet: 0.89 (0.38), residues: 169 loop : -0.26 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 35 TYR 0.018 0.003 TYR H 71 PHE 0.021 0.002 PHE H 27 TRP 0.025 0.003 TRP I 131 HIS 0.005 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8659) covalent geometry : angle 0.89931 (11767) hydrogen bonds : bond 0.17685 ( 347) hydrogen bonds : angle 6.75878 ( 942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 PHE cc_start: 0.7718 (m-80) cc_final: 0.7518 (m-80) REVERT: I 56 ASP cc_start: 0.8637 (m-30) cc_final: 0.8245 (p0) REVERT: H 5 GLU cc_start: 0.8751 (pt0) cc_final: 0.8510 (tm-30) REVERT: E 30 ASN cc_start: 0.9263 (m-40) cc_final: 0.9040 (m110) outliers start: 3 outliers final: 2 residues processed: 218 average time/residue: 0.2130 time to fit residues: 63.1012 Evaluate side-chains 133 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 109 ASN F 59 ASN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN I 104 GLN H 37 GLN H 110 HIS E 134 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.065829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.052956 restraints weight = 117509.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.055339 restraints weight = 53220.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057061 restraints weight = 32048.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.058232 restraints weight = 22377.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.059119 restraints weight = 17204.452| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8659 Z= 0.243 Angle : 0.691 6.380 11767 Z= 0.389 Chirality : 0.043 0.152 1432 Planarity : 0.005 0.066 1511 Dihedral : 6.541 27.008 1174 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.49 % Allowed : 16.67 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.24), residues: 1098 helix: -0.69 (0.25), residues: 387 sheet: 0.24 (0.36), residues: 174 loop : -0.59 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 35 TYR 0.011 0.001 TYR G 129 PHE 0.010 0.001 PHE G 27 TRP 0.009 0.002 TRP F 131 HIS 0.007 0.002 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 8659) covalent geometry : angle 0.69123 (11767) hydrogen bonds : bond 0.06837 ( 347) hydrogen bonds : angle 5.75768 ( 942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 GLN cc_start: 0.9363 (tt0) cc_final: 0.9024 (tm-30) REVERT: F 6 LEU cc_start: 0.9309 (mp) cc_final: 0.9094 (tp) REVERT: A 75 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7162 (p0) REVERT: B 2 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8846 (p) REVERT: I 42 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7569 (tm-30) REVERT: I 54 GLN cc_start: 0.9227 (tp40) cc_final: 0.8088 (tt0) REVERT: I 55 ASP cc_start: 0.9159 (m-30) cc_final: 0.8867 (t0) REVERT: I 56 ASP cc_start: 0.9003 (m-30) cc_final: 0.7721 (p0) REVERT: I 106 ASP cc_start: 0.8257 (t0) cc_final: 0.8036 (t0) REVERT: H 5 GLU cc_start: 0.9138 (pt0) cc_final: 0.8678 (tm-30) REVERT: H 42 GLU cc_start: 0.9133 (tp30) cc_final: 0.8815 (tp30) REVERT: H 61 SER cc_start: 0.9334 (OUTLIER) cc_final: 0.9007 (t) REVERT: D 39 GLU cc_start: 0.8981 (tt0) cc_final: 0.8760 (tt0) outliers start: 14 outliers final: 7 residues processed: 148 average time/residue: 0.1709 time to fit residues: 37.1050 Evaluate side-chains 127 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain I residue 104 GLN Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 0.0020 chunk 61 optimal weight: 7.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 75 ASN B 37 GLN I 28 GLN I 104 GLN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN D 137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.053844 restraints weight = 115718.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.056294 restraints weight = 51224.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.058053 restraints weight = 30481.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059254 restraints weight = 21096.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.060066 restraints weight = 16119.711| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8659 Z= 0.125 Angle : 0.592 6.127 11767 Z= 0.323 Chirality : 0.041 0.145 1432 Planarity : 0.004 0.057 1511 Dihedral : 5.749 22.892 1171 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.96 % Allowed : 18.15 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.24), residues: 1098 helix: -0.00 (0.26), residues: 404 sheet: 0.34 (0.35), residues: 174 loop : -0.61 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 41 TYR 0.010 0.001 TYR B 50 PHE 0.007 0.001 PHE C 27 TRP 0.007 0.001 TRP G 131 HIS 0.003 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8659) covalent geometry : angle 0.59150 (11767) hydrogen bonds : bond 0.05713 ( 347) hydrogen bonds : angle 5.06549 ( 942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8544 (tm-30) REVERT: G 37 GLN cc_start: 0.9349 (tt0) cc_final: 0.9104 (tm-30) REVERT: I 44 VAL cc_start: 0.9025 (t) cc_final: 0.8808 (t) REVERT: I 54 GLN cc_start: 0.9205 (tp40) cc_final: 0.8027 (tt0) REVERT: I 55 ASP cc_start: 0.9112 (m-30) cc_final: 0.8880 (t0) REVERT: I 56 ASP cc_start: 0.8897 (m-30) cc_final: 0.7476 (p0) REVERT: I 106 ASP cc_start: 0.8155 (t0) cc_final: 0.7907 (t0) REVERT: H 5 GLU cc_start: 0.9136 (pt0) cc_final: 0.8669 (tm-30) REVERT: E 120 ASN cc_start: 0.9306 (t0) cc_final: 0.8994 (p0) outliers start: 9 outliers final: 4 residues processed: 136 average time/residue: 0.1648 time to fit residues: 32.5963 Evaluate side-chains 121 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 137 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN A 75 ASN B 37 GLN H 37 GLN D 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.067448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.054878 restraints weight = 113089.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.057272 restraints weight = 53526.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058906 restraints weight = 32702.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060116 restraints weight = 23081.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060963 restraints weight = 17717.410| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8659 Z= 0.116 Angle : 0.563 5.451 11767 Z= 0.304 Chirality : 0.040 0.144 1432 Planarity : 0.004 0.050 1511 Dihedral : 5.327 20.937 1171 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.27 % Allowed : 17.94 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.24), residues: 1098 helix: 0.53 (0.26), residues: 403 sheet: 0.58 (0.36), residues: 174 loop : -0.59 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 41 TYR 0.007 0.001 TYR B 50 PHE 0.011 0.001 PHE C 116 TRP 0.006 0.001 TRP G 131 HIS 0.002 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8659) covalent geometry : angle 0.56276 (11767) hydrogen bonds : bond 0.04876 ( 347) hydrogen bonds : angle 4.72602 ( 942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 28 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8290 (tm-30) REVERT: G 29 ASP cc_start: 0.8555 (p0) cc_final: 0.8287 (p0) REVERT: G 37 GLN cc_start: 0.9319 (tt0) cc_final: 0.9091 (tm-30) REVERT: G 111 LYS cc_start: 0.8936 (tttt) cc_final: 0.8537 (ttmt) REVERT: I 44 VAL cc_start: 0.9067 (t) cc_final: 0.8839 (t) REVERT: I 56 ASP cc_start: 0.8808 (m-30) cc_final: 0.7798 (p0) REVERT: I 59 ASN cc_start: 0.9186 (t0) cc_final: 0.8971 (t0) REVERT: I 106 ASP cc_start: 0.8128 (t0) cc_final: 0.7915 (t0) REVERT: H 5 GLU cc_start: 0.9130 (pt0) cc_final: 0.8654 (tm-30) REVERT: H 39 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: E 120 ASN cc_start: 0.9257 (t0) cc_final: 0.9049 (p0) outliers start: 12 outliers final: 5 residues processed: 131 average time/residue: 0.1654 time to fit residues: 32.0938 Evaluate side-chains 124 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain I residue 90 LYS Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 109 ASN H 37 GLN ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.066300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.053750 restraints weight = 114032.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.056130 restraints weight = 55176.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057759 restraints weight = 33983.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058920 restraints weight = 24120.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059764 restraints weight = 18661.709| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8659 Z= 0.155 Angle : 0.560 5.208 11767 Z= 0.305 Chirality : 0.040 0.145 1432 Planarity : 0.004 0.042 1511 Dihedral : 5.166 20.822 1171 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.38 % Allowed : 18.26 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.24), residues: 1098 helix: 0.75 (0.26), residues: 398 sheet: 0.57 (0.36), residues: 174 loop : -0.65 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 35 TYR 0.010 0.001 TYR G 129 PHE 0.011 0.001 PHE H 27 TRP 0.005 0.001 TRP F 131 HIS 0.004 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8659) covalent geometry : angle 0.56034 (11767) hydrogen bonds : bond 0.04823 ( 347) hydrogen bonds : angle 4.75879 ( 942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 GLN cc_start: 0.9334 (tt0) cc_final: 0.9108 (tm-30) REVERT: G 111 LYS cc_start: 0.8941 (tttt) cc_final: 0.8571 (ttmt) REVERT: I 42 GLU cc_start: 0.8546 (tt0) cc_final: 0.8181 (tm-30) REVERT: I 56 ASP cc_start: 0.8685 (m-30) cc_final: 0.7622 (p0) REVERT: I 106 ASP cc_start: 0.8066 (t0) cc_final: 0.7859 (t0) REVERT: H 5 GLU cc_start: 0.9115 (pt0) cc_final: 0.8733 (tt0) REVERT: H 39 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8266 (tt0) outliers start: 13 outliers final: 8 residues processed: 124 average time/residue: 0.1637 time to fit residues: 30.0568 Evaluate side-chains 118 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 134 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN I 104 GLN H 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.053941 restraints weight = 114774.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.056371 restraints weight = 54195.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058031 restraints weight = 33121.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059255 restraints weight = 23342.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060060 restraints weight = 17859.092| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8659 Z= 0.129 Angle : 0.546 5.110 11767 Z= 0.295 Chirality : 0.040 0.143 1432 Planarity : 0.003 0.041 1511 Dihedral : 4.936 19.933 1171 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.06 % Allowed : 18.58 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.24), residues: 1098 helix: 0.93 (0.27), residues: 411 sheet: 0.69 (0.36), residues: 175 loop : -0.59 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 35 TYR 0.008 0.001 TYR B 50 PHE 0.010 0.001 PHE H 27 TRP 0.006 0.001 TRP F 131 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8659) covalent geometry : angle 0.54596 (11767) hydrogen bonds : bond 0.04430 ( 347) hydrogen bonds : angle 4.51811 ( 942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 GLN cc_start: 0.9347 (tt0) cc_final: 0.9096 (tm-30) REVERT: G 111 LYS cc_start: 0.8928 (tttt) cc_final: 0.8573 (ttmt) REVERT: I 42 GLU cc_start: 0.8517 (tt0) cc_final: 0.8116 (tm-30) REVERT: I 56 ASP cc_start: 0.8715 (m-30) cc_final: 0.7601 (p0) REVERT: I 106 ASP cc_start: 0.8033 (t0) cc_final: 0.7816 (t0) REVERT: H 5 GLU cc_start: 0.9086 (pt0) cc_final: 0.8727 (tt0) REVERT: H 28 GLN cc_start: 0.9129 (pt0) cc_final: 0.8616 (pm20) REVERT: H 39 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8310 (tt0) outliers start: 10 outliers final: 6 residues processed: 122 average time/residue: 0.1577 time to fit residues: 28.7643 Evaluate side-chains 119 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 134 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 14 optimal weight: 0.0030 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 0.1980 chunk 111 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.066472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.054014 restraints weight = 114640.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.056415 restraints weight = 54382.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058091 restraints weight = 33241.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059236 restraints weight = 23353.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060075 restraints weight = 18005.148| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8659 Z= 0.123 Angle : 0.539 5.267 11767 Z= 0.290 Chirality : 0.040 0.142 1432 Planarity : 0.003 0.041 1511 Dihedral : 4.753 19.413 1171 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.17 % Allowed : 18.79 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.25), residues: 1098 helix: 1.11 (0.26), residues: 410 sheet: 0.81 (0.36), residues: 170 loop : -0.56 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 41 TYR 0.008 0.001 TYR B 50 PHE 0.011 0.001 PHE H 27 TRP 0.006 0.001 TRP F 131 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8659) covalent geometry : angle 0.53918 (11767) hydrogen bonds : bond 0.04197 ( 347) hydrogen bonds : angle 4.36551 ( 942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 GLN cc_start: 0.9349 (tt0) cc_final: 0.9115 (tm-30) REVERT: G 111 LYS cc_start: 0.8910 (tttt) cc_final: 0.8563 (ttmt) REVERT: I 42 GLU cc_start: 0.8521 (tt0) cc_final: 0.8137 (tm-30) REVERT: I 56 ASP cc_start: 0.8667 (m-30) cc_final: 0.7533 (p0) REVERT: I 59 ASN cc_start: 0.9233 (t0) cc_final: 0.9029 (t0) REVERT: I 72 MET cc_start: 0.8907 (mmm) cc_final: 0.8696 (mmm) REVERT: I 106 ASP cc_start: 0.8023 (t0) cc_final: 0.7820 (t0) REVERT: H 5 GLU cc_start: 0.9095 (pt0) cc_final: 0.8722 (tt0) REVERT: H 28 GLN cc_start: 0.9084 (pt0) cc_final: 0.8583 (pm20) REVERT: H 39 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8272 (tt0) outliers start: 11 outliers final: 7 residues processed: 124 average time/residue: 0.1600 time to fit residues: 29.7617 Evaluate side-chains 120 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain E residue 123 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 97 optimal weight: 0.0270 chunk 100 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN E 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.067340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054889 restraints weight = 114057.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.057318 restraints weight = 53787.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059025 restraints weight = 32767.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.059995 restraints weight = 22899.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060905 restraints weight = 18167.322| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8659 Z= 0.102 Angle : 0.538 6.901 11767 Z= 0.285 Chirality : 0.040 0.139 1432 Planarity : 0.003 0.040 1511 Dihedral : 4.463 18.114 1171 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.96 % Allowed : 19.32 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.25), residues: 1098 helix: 1.40 (0.27), residues: 410 sheet: 1.04 (0.36), residues: 170 loop : -0.46 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 32 TYR 0.008 0.001 TYR E 50 PHE 0.009 0.001 PHE H 27 TRP 0.007 0.001 TRP G 131 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8659) covalent geometry : angle 0.53817 (11767) hydrogen bonds : bond 0.03664 ( 347) hydrogen bonds : angle 4.06120 ( 942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 GLN cc_start: 0.9334 (tt0) cc_final: 0.9047 (tm-30) REVERT: G 42 GLU cc_start: 0.9013 (tt0) cc_final: 0.8190 (tm-30) REVERT: G 111 LYS cc_start: 0.8873 (tttt) cc_final: 0.8543 (ttmt) REVERT: F 1 PHE cc_start: 0.5568 (m-80) cc_final: 0.5295 (m-80) REVERT: F 5 GLU cc_start: 0.8698 (mp0) cc_final: 0.8412 (mp0) REVERT: F 15 ILE cc_start: 0.9092 (pt) cc_final: 0.8885 (tp) REVERT: I 42 GLU cc_start: 0.8480 (tt0) cc_final: 0.8090 (tm-30) REVERT: I 56 ASP cc_start: 0.8644 (m-30) cc_final: 0.7501 (p0) REVERT: I 106 ASP cc_start: 0.7961 (t0) cc_final: 0.7751 (t0) REVERT: H 5 GLU cc_start: 0.9076 (pt0) cc_final: 0.8704 (tt0) REVERT: H 28 GLN cc_start: 0.9038 (pt0) cc_final: 0.8535 (pm20) REVERT: H 39 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8216 (tt0) outliers start: 9 outliers final: 6 residues processed: 130 average time/residue: 0.1543 time to fit residues: 30.1129 Evaluate side-chains 122 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 0.0060 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.067397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.054998 restraints weight = 114158.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057445 restraints weight = 53783.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059130 restraints weight = 32684.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060333 restraints weight = 22887.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060996 restraints weight = 17439.034| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8659 Z= 0.100 Angle : 0.539 5.785 11767 Z= 0.282 Chirality : 0.040 0.140 1432 Planarity : 0.003 0.036 1511 Dihedral : 4.263 17.014 1171 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.06 % Allowed : 19.43 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.25), residues: 1098 helix: 1.59 (0.27), residues: 405 sheet: 1.08 (0.36), residues: 170 loop : -0.34 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 32 TYR 0.008 0.001 TYR E 50 PHE 0.011 0.001 PHE H 27 TRP 0.006 0.001 TRP G 131 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8659) covalent geometry : angle 0.53886 (11767) hydrogen bonds : bond 0.03419 ( 347) hydrogen bonds : angle 3.95493 ( 942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 GLN cc_start: 0.9323 (tt0) cc_final: 0.8995 (tm-30) REVERT: G 42 GLU cc_start: 0.8997 (tt0) cc_final: 0.8192 (tm-30) REVERT: G 111 LYS cc_start: 0.8851 (tttt) cc_final: 0.8522 (ttmt) REVERT: F 1 PHE cc_start: 0.5692 (m-80) cc_final: 0.5357 (m-80) REVERT: F 5 GLU cc_start: 0.8853 (mp0) cc_final: 0.8605 (mp0) REVERT: I 42 GLU cc_start: 0.8507 (tt0) cc_final: 0.8101 (tm-30) REVERT: I 56 ASP cc_start: 0.8617 (m-30) cc_final: 0.7462 (p0) REVERT: I 106 ASP cc_start: 0.7902 (t0) cc_final: 0.7687 (t0) REVERT: H 5 GLU cc_start: 0.9055 (pt0) cc_final: 0.8680 (tt0) REVERT: H 28 GLN cc_start: 0.9033 (pt0) cc_final: 0.8513 (pm20) REVERT: H 39 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8259 (tt0) outliers start: 10 outliers final: 7 residues processed: 131 average time/residue: 0.1365 time to fit residues: 26.9858 Evaluate side-chains 125 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 134 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 0.0060 chunk 110 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN H 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.067548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.055186 restraints weight = 113150.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.057633 restraints weight = 53398.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059332 restraints weight = 32481.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060454 restraints weight = 22688.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061325 restraints weight = 17451.723| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8659 Z= 0.100 Angle : 0.548 7.071 11767 Z= 0.284 Chirality : 0.040 0.175 1432 Planarity : 0.003 0.033 1511 Dihedral : 4.196 16.607 1171 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.64 % Allowed : 20.28 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.25), residues: 1098 helix: 1.68 (0.27), residues: 410 sheet: 1.19 (0.36), residues: 169 loop : -0.35 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 32 TYR 0.008 0.001 TYR E 50 PHE 0.009 0.001 PHE H 27 TRP 0.006 0.001 TRP G 131 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8659) covalent geometry : angle 0.54833 (11767) hydrogen bonds : bond 0.03380 ( 347) hydrogen bonds : angle 3.92047 ( 942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 37 GLN cc_start: 0.9324 (tt0) cc_final: 0.8993 (tm-30) REVERT: G 42 GLU cc_start: 0.9002 (tt0) cc_final: 0.8199 (tm-30) REVERT: G 111 LYS cc_start: 0.8840 (tttt) cc_final: 0.8513 (ttmt) REVERT: I 42 GLU cc_start: 0.8504 (tt0) cc_final: 0.8110 (tm-30) REVERT: I 56 ASP cc_start: 0.8618 (m-30) cc_final: 0.7473 (p0) REVERT: I 106 ASP cc_start: 0.7885 (t0) cc_final: 0.7668 (t0) REVERT: H 5 GLU cc_start: 0.9049 (pt0) cc_final: 0.8665 (tt0) REVERT: H 28 GLN cc_start: 0.9026 (pt0) cc_final: 0.8510 (pm20) REVERT: H 42 GLU cc_start: 0.8957 (tp30) cc_final: 0.8739 (tt0) outliers start: 6 outliers final: 5 residues processed: 124 average time/residue: 0.1467 time to fit residues: 27.1948 Evaluate side-chains 122 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 11 optimal weight: 0.1980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN H 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.067551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.055174 restraints weight = 114038.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.057632 restraints weight = 53631.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059297 restraints weight = 32520.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060526 restraints weight = 22811.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061332 restraints weight = 17342.215| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 8659 Z= 0.182 Angle : 0.863 59.158 11767 Z= 0.506 Chirality : 0.041 0.404 1432 Planarity : 0.003 0.032 1511 Dihedral : 4.194 16.621 1171 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.74 % Allowed : 20.28 % Favored : 78.98 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.25), residues: 1098 helix: 1.69 (0.27), residues: 410 sheet: 1.19 (0.36), residues: 169 loop : -0.35 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 32 TYR 0.007 0.001 TYR B 50 PHE 0.017 0.001 PHE F 1 TRP 0.006 0.001 TRP G 131 HIS 0.005 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8659) covalent geometry : angle 0.86288 (11767) hydrogen bonds : bond 0.03360 ( 347) hydrogen bonds : angle 3.92034 ( 942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2591.12 seconds wall clock time: 45 minutes 11.80 seconds (2711.80 seconds total)