Starting phenix.real_space_refine on Sun May 18 12:15:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pfb_17645/05_2025/8pfb_17645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pfb_17645/05_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_17645/05_2025/8pfb_17645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pfb_17645/05_2025/8pfb_17645.map" model { file = "/net/cci-nas-00/data/ceres_data/8pfb_17645/05_2025/8pfb_17645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pfb_17645/05_2025/8pfb_17645.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.89, per 1000 atoms: 0.52 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: 4.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.42 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: 5.55 Time building geometry restraints manager: 5.04 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: 1.330 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: 0.300 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.130 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.980 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.025 0.003 TRP I 131 HIS 0.005 0.001 HIS F 40 PHE 0.021 0.002 PHE H 27 TYR 0.018 0.003 TYR H 71 ARG 0.008 0.001 ARG E 35 Details of bonding type rmsd hydrogen bonds : bond 0.17685 ( 347) hydrogen bonds : angle 6.75878 ( 942) covalent geometry : bond 0.00417 ( 8659) covalent geometry : angle 0.89931 (11767) *********************** 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 : 1.292 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: 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: 0.4463 time to fit residues: 131.4247 Evaluate side-chains 134 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 94 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** I 104 GLN H 37 GLN H 110 HIS ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.067455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.054532 restraints weight = 115162.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.056970 restraints weight = 51366.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.058719 restraints weight = 30600.909| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8659 Z= 0.158 Angle : 0.660 6.461 11767 Z= 0.367 Chirality : 0.043 0.151 1432 Planarity : 0.005 0.068 1511 Dihedral : 6.347 25.533 1174 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.27 % Allowed : 16.45 % Favored : 82.27 % 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: -0.57 (0.24), residues: 1098 helix: -0.58 (0.26), residues: 381 sheet: 0.58 (0.37), residues: 174 loop : -0.42 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 131 HIS 0.005 0.001 HIS E 103 PHE 0.010 0.001 PHE G 27 TYR 0.007 0.001 TYR C 71 ARG 0.004 0.000 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.06737 ( 347) hydrogen bonds : angle 5.48286 ( 942) covalent geometry : bond 0.00346 ( 8659) covalent geometry : angle 0.66010 (11767) *********************** 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 161 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.452 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: G 28 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8454 (tm-30) REVERT: G 37 GLN cc_start: 0.9358 (tt0) cc_final: 0.8969 (tm-30) REVERT: C 106 ASP cc_start: 0.9328 (OUTLIER) cc_final: 0.9021 (t70) REVERT: I 54 GLN cc_start: 0.9212 (tp40) cc_final: 0.8244 (tt0) REVERT: I 55 ASP cc_start: 0.9256 (m-30) cc_final: 0.8900 (t0) REVERT: I 56 ASP cc_start: 0.9015 (m-30) cc_final: 0.7686 (p0) REVERT: I 106 ASP cc_start: 0.8332 (t0) cc_final: 0.8086 (t0) REVERT: H 5 GLU cc_start: 0.9114 (pt0) cc_final: 0.8663 (tm-30) REVERT: H 42 GLU cc_start: 0.9097 (tp30) cc_final: 0.8794 (tp30) REVERT: H 61 SER cc_start: 0.9339 (OUTLIER) cc_final: 0.9016 (t) REVERT: D 39 GLU cc_start: 0.8908 (tt0) cc_final: 0.8684 (tt0) REVERT: E 120 ASN cc_start: 0.9312 (t0) cc_final: 0.9074 (p0) outliers start: 12 outliers final: 5 residues processed: 159 average time/residue: 0.3591 time to fit residues: 83.4637 Evaluate side-chains 129 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 137 ASN 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 99 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 37 optimal weight: 0.0970 chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 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 = 0.3330 r_free = 0.3330 target = 0.067198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.054222 restraints weight = 115838.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.056691 restraints weight = 52085.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.058470 restraints weight = 31170.879| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3619 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= 0.154 Angle : 0.605 5.938 11767 Z= 0.333 Chirality : 0.041 0.146 1432 Planarity : 0.004 0.055 1511 Dihedral : 5.711 23.171 1171 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.74 % Allowed : 17.52 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1098 helix: 0.05 (0.26), residues: 404 sheet: 0.43 (0.36), residues: 174 loop : -0.61 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 131 HIS 0.004 0.001 HIS E 103 PHE 0.008 0.001 PHE H 27 TYR 0.008 0.001 TYR G 129 ARG 0.001 0.000 ARG D 35 Details of bonding type rmsd hydrogen bonds : bond 0.05791 ( 347) hydrogen bonds : angle 5.07730 ( 942) covalent geometry : bond 0.00338 ( 8659) covalent geometry : angle 0.60464 (11767) *********************** 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 133 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 1.324 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: G 28 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8552 (tm-30) REVERT: G 37 GLN cc_start: 0.9347 (tt0) cc_final: 0.9068 (tm-30) REVERT: I 44 VAL cc_start: 0.9038 (t) cc_final: 0.8811 (t) REVERT: I 54 GLN cc_start: 0.9245 (tp40) cc_final: 0.8044 (tt0) REVERT: I 55 ASP cc_start: 0.9162 (m-30) cc_final: 0.8848 (t0) REVERT: I 56 ASP cc_start: 0.8929 (m-30) cc_final: 0.7490 (p0) REVERT: I 106 ASP cc_start: 0.8191 (t0) cc_final: 0.7943 (t0) REVERT: H 5 GLU cc_start: 0.9151 (pt0) cc_final: 0.8665 (tm-30) REVERT: H 61 SER cc_start: 0.9357 (OUTLIER) cc_final: 0.9031 (t) outliers start: 7 outliers final: 3 residues processed: 129 average time/residue: 0.3872 time to fit residues: 72.7956 Evaluate side-chains 123 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain I residue 90 LYS Chi-restraints excluded: chain H residue 61 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 109 ASN A 54 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 = 0.3356 r_free = 0.3356 target = 0.068199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.055189 restraints weight = 114486.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057705 restraints weight = 51700.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059480 restraints weight = 30754.075| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8659 Z= 0.108 Angle : 0.559 5.704 11767 Z= 0.299 Chirality : 0.040 0.145 1432 Planarity : 0.004 0.047 1511 Dihedral : 5.116 20.450 1171 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.06 % Allowed : 18.37 % Favored : 80.57 % 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: 0.11 (0.24), residues: 1098 helix: 0.62 (0.26), residues: 405 sheet: 0.70 (0.36), residues: 174 loop : -0.51 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 131 HIS 0.003 0.001 HIS B 110 PHE 0.007 0.001 PHE B 1 TYR 0.007 0.001 TYR E 50 ARG 0.001 0.000 ARG I 32 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 347) hydrogen bonds : angle 4.50067 ( 942) covalent geometry : bond 0.00242 ( 8659) covalent geometry : angle 0.55922 (11767) *********************** 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 141 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.618 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: 0.8749 (tm-30) cc_final: 0.8255 (tm-30) REVERT: G 29 ASP cc_start: 0.8624 (p0) cc_final: 0.8393 (p0) REVERT: G 37 GLN cc_start: 0.9326 (tt0) cc_final: 0.9028 (tm-30) REVERT: G 111 LYS cc_start: 0.8858 (tttt) cc_final: 0.8477 (ttmt) REVERT: F 80 ASP cc_start: 0.7543 (p0) cc_final: 0.7333 (p0) REVERT: I 42 GLU cc_start: 0.8532 (tt0) cc_final: 0.8030 (tm-30) REVERT: I 44 VAL cc_start: 0.8982 (t) cc_final: 0.8746 (t) REVERT: I 56 ASP cc_start: 0.8868 (m-30) cc_final: 0.7721 (p0) REVERT: I 72 MET cc_start: 0.9084 (mmm) cc_final: 0.8747 (mmm) REVERT: I 106 ASP cc_start: 0.8195 (t0) cc_final: 0.7936 (t0) REVERT: H 5 GLU cc_start: 0.9129 (pt0) cc_final: 0.8707 (tt0) REVERT: H 42 GLU cc_start: 0.9091 (tp30) cc_final: 0.8821 (tt0) REVERT: E 120 ASN cc_start: 0.9357 (t0) cc_final: 0.9020 (p0) outliers start: 10 outliers final: 4 residues processed: 137 average time/residue: 0.3795 time to fit residues: 75.2483 Evaluate side-chains 128 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain H residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 48 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.066633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.054089 restraints weight = 114266.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.056433 restraints weight = 54821.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.058054 restraints weight = 33547.110| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8659 Z= 0.190 Angle : 0.579 5.658 11767 Z= 0.318 Chirality : 0.040 0.146 1432 Planarity : 0.004 0.041 1511 Dihedral : 5.148 20.930 1171 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.70 % Allowed : 18.05 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.04 (0.24), residues: 1098 helix: 0.69 (0.26), residues: 405 sheet: 0.58 (0.36), residues: 174 loop : -0.64 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 131 HIS 0.005 0.001 HIS E 103 PHE 0.007 0.001 PHE C 27 TYR 0.011 0.001 TYR G 129 ARG 0.002 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 347) hydrogen bonds : angle 4.76305 ( 942) covalent geometry : bond 0.00414 ( 8659) covalent geometry : angle 0.57891 (11767) *********************** 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 132 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.483 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: 0.9317 (tt0) cc_final: 0.9091 (tm-30) REVERT: G 111 LYS cc_start: 0.8980 (tttt) cc_final: 0.8629 (ttmt) REVERT: I 56 ASP cc_start: 0.8736 (m-30) cc_final: 0.7643 (p0) REVERT: I 106 ASP cc_start: 0.8125 (t0) cc_final: 0.7921 (t0) REVERT: H 5 GLU cc_start: 0.9119 (pt0) cc_final: 0.8690 (tt0) REVERT: H 39 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: H 42 GLU cc_start: 0.8991 (tp30) cc_final: 0.8759 (tt0) REVERT: E 120 ASN cc_start: 0.9344 (t0) cc_final: 0.9064 (p0) outliers start: 16 outliers final: 8 residues processed: 125 average time/residue: 0.3594 time to fit residues: 66.0903 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 : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 90 LYS 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 H residue 132 SER 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 94 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN A 30 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 = 0.3332 r_free = 0.3332 target = 0.066906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.054374 restraints weight = 114579.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.056745 restraints weight = 54650.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058417 restraints weight = 33504.544| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4535 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= 0.134 Angle : 0.552 5.430 11767 Z= 0.297 Chirality : 0.040 0.144 1432 Planarity : 0.003 0.040 1511 Dihedral : 4.901 19.873 1171 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.06 % Allowed : 19.11 % Favored : 79.83 % 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: 0.27 (0.24), residues: 1098 helix: 0.89 (0.26), residues: 411 sheet: 0.76 (0.36), residues: 174 loop : -0.56 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 131 HIS 0.004 0.001 HIS E 103 PHE 0.006 0.001 PHE C 27 TYR 0.007 0.001 TYR B 50 ARG 0.001 0.000 ARG E 35 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 347) hydrogen bonds : angle 4.49881 ( 942) covalent geometry : bond 0.00302 ( 8659) covalent geometry : angle 0.55229 (11767) *********************** 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 130 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.332 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: 0.9330 (tt0) cc_final: 0.9083 (tm-30) REVERT: G 111 LYS cc_start: 0.8959 (tttt) cc_final: 0.8616 (ttmt) REVERT: I 42 GLU cc_start: 0.8554 (tt0) cc_final: 0.8032 (tm-30) REVERT: I 56 ASP cc_start: 0.8757 (m-30) cc_final: 0.7646 (p0) REVERT: I 106 ASP cc_start: 0.8098 (t0) cc_final: 0.7877 (t0) REVERT: H 5 GLU cc_start: 0.9115 (pt0) cc_final: 0.8702 (tt0) REVERT: H 28 GLN cc_start: 0.9128 (pt0) cc_final: 0.8620 (pm20) REVERT: H 39 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: H 42 GLU cc_start: 0.8996 (tp30) cc_final: 0.8775 (tt0) REVERT: E 120 ASN cc_start: 0.9358 (t0) cc_final: 0.9076 (p0) outliers start: 10 outliers final: 7 residues processed: 125 average time/residue: 0.3538 time to fit residues: 64.8526 Evaluate side-chains 122 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain B residue 5 GLU 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 H residue 132 SER Chi-restraints excluded: chain E residue 123 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 105 optimal weight: 0.0060 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN E 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.067347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.054858 restraints weight = 113258.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.057263 restraints weight = 53565.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058925 restraints weight = 32755.216| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4716 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= 0.108 Angle : 0.543 5.425 11767 Z= 0.289 Chirality : 0.040 0.141 1432 Planarity : 0.003 0.039 1511 Dihedral : 4.638 18.865 1171 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.06 % Allowed : 19.32 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1098 helix: 1.14 (0.27), residues: 411 sheet: 0.87 (0.36), residues: 175 loop : -0.52 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 131 HIS 0.003 0.001 HIS B 110 PHE 0.008 0.001 PHE F 1 TYR 0.007 0.001 TYR B 50 ARG 0.002 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 347) hydrogen bonds : angle 4.22389 ( 942) covalent geometry : bond 0.00252 ( 8659) covalent geometry : angle 0.54261 (11767) *********************** 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 132 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.371 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: 0.9330 (tt0) cc_final: 0.9081 (tm-30) REVERT: G 111 LYS cc_start: 0.8908 (tttt) cc_final: 0.8571 (ttmt) REVERT: I 42 GLU cc_start: 0.8543 (tt0) cc_final: 0.8000 (tm-30) REVERT: I 56 ASP cc_start: 0.8723 (m-30) cc_final: 0.7576 (p0) REVERT: I 106 ASP cc_start: 0.8061 (t0) cc_final: 0.7844 (t0) REVERT: H 5 GLU cc_start: 0.9100 (pt0) cc_final: 0.8706 (tt0) REVERT: H 28 GLN cc_start: 0.9094 (pt0) cc_final: 0.8566 (pm20) REVERT: H 39 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: H 42 GLU cc_start: 0.8981 (tp30) cc_final: 0.8766 (tt0) outliers start: 10 outliers final: 7 residues processed: 128 average time/residue: 0.3497 time to fit residues: 65.4457 Evaluate side-chains 123 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain A residue 38 SER 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 H residue 132 SER Chi-restraints excluded: chain D residue 39 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.066839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.054321 restraints weight = 114148.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.056694 restraints weight = 54607.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.058350 restraints weight = 33541.118| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8659 Z= 0.119 Angle : 0.547 6.877 11767 Z= 0.290 Chirality : 0.040 0.142 1432 Planarity : 0.003 0.037 1511 Dihedral : 4.530 18.532 1171 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.17 % Allowed : 19.00 % Favored : 79.83 % 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: 0.57 (0.25), residues: 1098 helix: 1.29 (0.27), residues: 410 sheet: 0.95 (0.36), residues: 170 loop : -0.53 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 131 HIS 0.003 0.001 HIS B 110 PHE 0.005 0.001 PHE C 27 TYR 0.007 0.001 TYR B 50 ARG 0.001 0.000 ARG I 32 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 347) hydrogen bonds : angle 4.19728 ( 942) covalent geometry : bond 0.00275 ( 8659) covalent geometry : angle 0.54653 (11767) *********************** 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 129 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.509 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: 0.9345 (tt0) cc_final: 0.9086 (tm-30) REVERT: G 111 LYS cc_start: 0.8887 (tttt) cc_final: 0.8564 (ttmt) REVERT: I 42 GLU cc_start: 0.8599 (tt0) cc_final: 0.8056 (tm-30) REVERT: I 56 ASP cc_start: 0.8719 (m-30) cc_final: 0.7545 (p0) REVERT: I 72 MET cc_start: 0.8896 (mmm) cc_final: 0.8661 (mmm) REVERT: I 106 ASP cc_start: 0.8031 (t0) cc_final: 0.7801 (t0) REVERT: H 5 GLU cc_start: 0.9102 (pt0) cc_final: 0.8711 (tt0) REVERT: H 28 GLN cc_start: 0.9107 (pt0) cc_final: 0.8556 (pm20) REVERT: H 39 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8469 (tt0) outliers start: 11 outliers final: 6 residues processed: 125 average time/residue: 0.3550 time to fit residues: 65.4434 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 : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER 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 H residue 132 SER Chi-restraints excluded: chain D residue 39 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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** ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.065877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.053495 restraints weight = 115828.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055825 restraints weight = 55806.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057485 restraints weight = 34461.621| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5072 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= 0.152 Angle : 0.563 6.241 11767 Z= 0.303 Chirality : 0.040 0.145 1432 Planarity : 0.003 0.037 1511 Dihedral : 4.580 18.997 1171 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.96 % Allowed : 19.64 % Favored : 79.41 % 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: 0.49 (0.25), residues: 1098 helix: 1.26 (0.27), residues: 406 sheet: 0.86 (0.37), residues: 170 loop : -0.58 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 131 HIS 0.004 0.001 HIS E 103 PHE 0.009 0.001 PHE F 1 TYR 0.009 0.001 TYR D 129 ARG 0.002 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 347) hydrogen bonds : angle 4.36481 ( 942) covalent geometry : bond 0.00340 ( 8659) covalent geometry : angle 0.56264 (11767) *********************** 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 117 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 1.509 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: 0.9345 (tt0) cc_final: 0.9114 (tm-30) REVERT: G 111 LYS cc_start: 0.8968 (tttt) cc_final: 0.8649 (ttmt) REVERT: I 42 GLU cc_start: 0.8533 (tt0) cc_final: 0.8038 (tm-30) REVERT: I 56 ASP cc_start: 0.8733 (m-30) cc_final: 0.7594 (p0) REVERT: I 72 MET cc_start: 0.8836 (mmm) cc_final: 0.8628 (mmm) REVERT: I 106 ASP cc_start: 0.8007 (t0) cc_final: 0.7805 (t0) REVERT: H 5 GLU cc_start: 0.9130 (pt0) cc_final: 0.8750 (tt0) REVERT: H 28 GLN cc_start: 0.9095 (pt0) cc_final: 0.8600 (pm20) REVERT: H 39 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8416 (tt0) outliers start: 9 outliers final: 8 residues processed: 114 average time/residue: 0.3683 time to fit residues: 61.3004 Evaluate side-chains 115 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER 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 H residue 132 SER Chi-restraints excluded: chain D residue 39 GLU 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 109 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 85 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 ASN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.066519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.054075 restraints weight = 115083.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.056440 restraints weight = 54862.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058121 restraints weight = 33686.113| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.5198 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= 0.111 Angle : 0.551 6.488 11767 Z= 0.293 Chirality : 0.040 0.139 1432 Planarity : 0.003 0.035 1511 Dihedral : 4.400 18.035 1171 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.85 % Allowed : 19.32 % Favored : 79.83 % 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: 0.66 (0.25), residues: 1098 helix: 1.40 (0.27), residues: 412 sheet: 0.99 (0.37), residues: 170 loop : -0.51 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 131 HIS 0.003 0.001 HIS B 110 PHE 0.006 0.001 PHE C 27 TYR 0.007 0.001 TYR B 50 ARG 0.001 0.000 ARG I 32 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 347) hydrogen bonds : angle 4.12971 ( 942) covalent geometry : bond 0.00260 ( 8659) covalent geometry : angle 0.55062 (11767) ********************** 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 127 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 1.321 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: 0.9343 (tt0) cc_final: 0.9085 (tm-30) REVERT: G 42 GLU cc_start: 0.9065 (tt0) cc_final: 0.8227 (tm-30) REVERT: G 111 LYS cc_start: 0.8939 (tttt) cc_final: 0.8619 (ttmt) REVERT: F 15 ILE cc_start: 0.9118 (pt) cc_final: 0.8903 (tp) REVERT: I 42 GLU cc_start: 0.8536 (tt0) cc_final: 0.8002 (tm-30) REVERT: I 56 ASP cc_start: 0.8724 (m-30) cc_final: 0.7549 (p0) REVERT: I 106 ASP cc_start: 0.7956 (t0) cc_final: 0.7736 (t0) REVERT: H 5 GLU cc_start: 0.9128 (pt0) cc_final: 0.8734 (tt0) REVERT: H 28 GLN cc_start: 0.9066 (pt0) cc_final: 0.8560 (pm20) REVERT: H 39 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8277 (tt0) outliers start: 8 outliers final: 6 residues processed: 125 average time/residue: 0.3498 time to fit residues: 64.2358 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 : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER 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 39 GLU 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 63 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.067097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.054647 restraints weight = 114018.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.057065 restraints weight = 53990.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058760 restraints weight = 32890.749| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8659 Z= 0.103 Angle : 0.549 6.458 11767 Z= 0.287 Chirality : 0.040 0.139 1432 Planarity : 0.003 0.034 1511 Dihedral : 4.210 17.260 1171 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.74 % Allowed : 19.64 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1098 helix: 1.60 (0.28), residues: 404 sheet: 1.10 (0.37), residues: 170 loop : -0.40 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 131 HIS 0.004 0.001 HIS B 110 PHE 0.006 0.000 PHE F 1 TYR 0.008 0.001 TYR E 50 ARG 0.002 0.000 ARG I 32 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 347) hydrogen bonds : angle 3.95378 ( 942) covalent geometry : bond 0.00244 ( 8659) covalent geometry : angle 0.54874 (11767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4537.29 seconds wall clock time: 79 minutes 19.69 seconds (4759.69 seconds total)