Starting phenix.real_space_refine on Mon Jul 22 04:46:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfb_17645/07_2024/8pfb_17645.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfb_17645/07_2024/8pfb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfb_17645/07_2024/8pfb_17645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfb_17645/07_2024/8pfb_17645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfb_17645/07_2024/8pfb_17645.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pfb_17645/07_2024/8pfb_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 Residue "G TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "B ASP 55": "OD1" <-> "OD2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "H TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "E GLU 62": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 9.65, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.64 Conformation dependent library (CDL) restraints added in 1.9 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: 1.40 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: 4.95 Time building geometry restraints manager: 13.35 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: 99.98 - 106.80: 339 106.80 - 113.61: 21185 113.61 - 120.43: 5068 120.43 - 127.25: 4568 127.25 - 134.06: 84 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 1.850 nonbonded pdb=" OD1 ASP D 29 " pdb=" H ASN D 30 " model vdw 1.599 1.850 nonbonded pdb=" OD2 ASP D 106 " pdb="HD21 ASN D 109 " model vdw 1.615 1.850 nonbonded pdb=" OD1 ASN E 120 " pdb=" H GLY E 122 " model vdw 1.628 1.850 nonbonded pdb=" OD2 ASP E 29 " pdb=" HG SER E 119 " model vdw 1.637 1.850 ... (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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.740 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: 0.250 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 54.310 Find NCS groups from input model: 0.660 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.660 ------------------------------------------------------------------------------- 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= 0.276 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 215 time to evaluate : 1.440 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: 0.4527 time to fit residues: 133.1637 Evaluate side-chains 134 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8659 Z= 0.229 Angle : 0.644 6.721 11767 Z= 0.358 Chirality : 0.042 0.152 1432 Planarity : 0.004 0.063 1511 Dihedral : 6.235 25.857 1174 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.17 % Allowed : 16.45 % Favored : 82.38 % 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: -0.53 (0.24), residues: 1098 helix: -0.48 (0.26), residues: 386 sheet: 0.55 (0.36), residues: 174 loop : -0.42 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 131 HIS 0.004 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 *********************** 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 158 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 1.335 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: G 28 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8556 (tm-30) REVERT: F 6 LEU cc_start: 0.9478 (mp) cc_final: 0.9216 (tp) REVERT: I 54 GLN cc_start: 0.8966 (tp40) cc_final: 0.8399 (tt0) REVERT: I 56 ASP cc_start: 0.8633 (m-30) cc_final: 0.7896 (p0) REVERT: H 5 GLU cc_start: 0.8805 (pt0) cc_final: 0.8527 (tm-30) outliers start: 11 outliers final: 6 residues processed: 156 average time/residue: 0.3546 time to fit residues: 80.7220 Evaluate side-chains 130 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 137 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 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.3980 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8659 Z= 0.183 Angle : 0.578 5.934 11767 Z= 0.314 Chirality : 0.040 0.142 1432 Planarity : 0.004 0.054 1511 Dihedral : 5.551 21.806 1171 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.96 % Allowed : 17.83 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1098 helix: 0.18 (0.26), residues: 403 sheet: 0.55 (0.36), residues: 174 loop : -0.51 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 131 HIS 0.002 0.001 HIS D 103 PHE 0.007 0.001 PHE H 27 TYR 0.007 0.001 TYR B 50 ARG 0.001 0.000 ARG D 35 *********************** 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 fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.316 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: G 28 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8638 (tm-30) REVERT: G 111 LYS cc_start: 0.9010 (tttt) cc_final: 0.8807 (ttmt) REVERT: F 6 LEU cc_start: 0.9420 (mp) cc_final: 0.9182 (tp) REVERT: I 44 VAL cc_start: 0.9227 (t) cc_final: 0.9018 (t) REVERT: I 54 GLN cc_start: 0.9036 (tp40) cc_final: 0.8330 (tt0) REVERT: I 56 ASP cc_start: 0.8536 (m-30) cc_final: 0.7616 (p0) REVERT: H 5 GLU cc_start: 0.8801 (pt0) cc_final: 0.8500 (tm-30) outliers start: 9 outliers final: 4 residues processed: 134 average time/residue: 0.3534 time to fit residues: 69.0906 Evaluate side-chains 124 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain I residue 90 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 0.0050 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN C 109 ASN A 75 ASN I 104 GLN H 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4042 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= 0.164 Angle : 0.543 5.573 11767 Z= 0.291 Chirality : 0.040 0.139 1432 Planarity : 0.003 0.045 1511 Dihedral : 5.053 20.260 1171 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1098 helix: 0.70 (0.27), residues: 405 sheet: 0.70 (0.36), residues: 174 loop : -0.56 (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 F 40 PHE 0.006 0.001 PHE H 27 TYR 0.007 0.001 TYR B 50 ARG 0.001 0.000 ARG D 35 *********************** 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 138 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 1.446 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: 0.8851 (tm-30) cc_final: 0.8345 (tm-30) REVERT: G 29 ASP cc_start: 0.8114 (p0) cc_final: 0.7849 (p0) REVERT: G 111 LYS cc_start: 0.9008 (tttt) cc_final: 0.8690 (ttmt) REVERT: I 42 GLU cc_start: 0.7900 (tt0) cc_final: 0.7691 (tm-30) REVERT: I 44 VAL cc_start: 0.9181 (t) cc_final: 0.8977 (t) REVERT: I 56 ASP cc_start: 0.8611 (m-30) cc_final: 0.7660 (p0) REVERT: H 5 GLU cc_start: 0.8837 (pt0) cc_final: 0.8522 (tm-30) outliers start: 10 outliers final: 5 residues processed: 131 average time/residue: 0.3485 time to fit residues: 67.3234 Evaluate side-chains 124 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** H 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4260 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= 0.222 Angle : 0.548 6.830 11767 Z= 0.297 Chirality : 0.039 0.142 1432 Planarity : 0.003 0.038 1511 Dihedral : 4.959 19.598 1171 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.27 % Allowed : 19.11 % 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: 0.17 (0.24), residues: 1098 helix: 0.81 (0.27), residues: 405 sheet: 0.71 (0.36), residues: 174 loop : -0.59 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 131 HIS 0.004 0.001 HIS E 103 PHE 0.008 0.001 PHE H 27 TYR 0.009 0.001 TYR G 129 ARG 0.001 0.000 ARG G 35 *********************** 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 131 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.302 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 111 LYS cc_start: 0.9019 (tttt) cc_final: 0.8726 (ttmt) REVERT: I 56 ASP cc_start: 0.8435 (m-30) cc_final: 0.7531 (p0) outliers start: 12 outliers final: 7 residues processed: 126 average time/residue: 0.3550 time to fit residues: 65.7448 Evaluate side-chains 117 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain E residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 H 37 GLN E 48 GLN ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8659 Z= 0.165 Angle : 0.525 6.428 11767 Z= 0.279 Chirality : 0.039 0.140 1432 Planarity : 0.003 0.036 1511 Dihedral : 4.680 18.080 1171 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.38 % Allowed : 19.11 % 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 (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: 0.44 (0.25), residues: 1098 helix: 1.09 (0.27), residues: 404 sheet: 0.85 (0.36), residues: 174 loop : -0.50 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 131 HIS 0.003 0.001 HIS D 40 PHE 0.006 0.001 PHE C 27 TYR 0.007 0.001 TYR E 129 ARG 0.001 0.000 ARG H 35 *********************** 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 131 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.210 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 111 LYS cc_start: 0.8994 (tttt) cc_final: 0.8730 (ttmt) REVERT: I 42 GLU cc_start: 0.7983 (tt0) cc_final: 0.7749 (tm-30) REVERT: I 56 ASP cc_start: 0.8451 (m-30) cc_final: 0.7523 (p0) REVERT: H 5 GLU cc_start: 0.8594 (mp0) cc_final: 0.8307 (tt0) REVERT: H 39 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7982 (tt0) outliers start: 13 outliers final: 7 residues processed: 127 average time/residue: 0.3591 time to fit residues: 66.8382 Evaluate side-chains 119 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 59 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** I 134 ASN H 37 GLN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8659 Z= 0.217 Angle : 0.533 6.061 11767 Z= 0.288 Chirality : 0.039 0.150 1432 Planarity : 0.003 0.032 1511 Dihedral : 4.695 18.309 1171 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.49 % Allowed : 19.96 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1098 helix: 1.13 (0.27), residues: 405 sheet: 0.74 (0.37), residues: 170 loop : -0.58 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 131 HIS 0.003 0.001 HIS E 103 PHE 0.006 0.001 PHE C 27 TYR 0.009 0.001 TYR G 129 ARG 0.002 0.000 ARG D 41 *********************** 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 124 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.318 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 111 LYS cc_start: 0.9012 (tttt) cc_final: 0.8738 (ttmt) REVERT: I 42 GLU cc_start: 0.7998 (tt0) cc_final: 0.7765 (tm-30) REVERT: I 56 ASP cc_start: 0.8405 (m-30) cc_final: 0.7524 (p0) REVERT: H 39 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8113 (tt0) outliers start: 14 outliers final: 10 residues processed: 119 average time/residue: 0.3305 time to fit residues: 59.2078 Evaluate side-chains 116 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 132 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 134 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8659 Z= 0.168 Angle : 0.526 5.986 11767 Z= 0.279 Chirality : 0.039 0.140 1432 Planarity : 0.003 0.032 1511 Dihedral : 4.491 16.664 1171 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.06 % Allowed : 20.38 % Favored : 78.56 % 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: 0.59 (0.25), residues: 1098 helix: 1.34 (0.27), residues: 404 sheet: 0.91 (0.37), residues: 170 loop : -0.51 (0.25), residues: 524 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 D 129 ARG 0.001 0.000 ARG A 41 *********************** 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 128 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.224 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 42 GLU cc_start: 0.8297 (tt0) cc_final: 0.7717 (tm-30) REVERT: G 111 LYS cc_start: 0.8983 (tttt) cc_final: 0.8706 (ttmt) REVERT: I 42 GLU cc_start: 0.7886 (tt0) cc_final: 0.7563 (tm-30) REVERT: I 56 ASP cc_start: 0.8453 (m-30) cc_final: 0.7497 (p0) REVERT: H 39 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7863 (tt0) outliers start: 10 outliers final: 8 residues processed: 127 average time/residue: 0.3310 time to fit residues: 63.5715 Evaluate side-chains 121 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 59 ASN 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 94 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8659 Z= 0.162 Angle : 0.533 6.212 11767 Z= 0.280 Chirality : 0.039 0.141 1432 Planarity : 0.003 0.031 1511 Dihedral : 4.340 16.110 1171 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.38 % Allowed : 19.75 % Favored : 78.87 % 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: 0.79 (0.25), residues: 1098 helix: 1.54 (0.27), residues: 400 sheet: 0.97 (0.37), residues: 170 loop : -0.39 (0.26), residues: 528 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 0.005 0.000 PHE C 27 TYR 0.007 0.001 TYR D 129 ARG 0.001 0.000 ARG G 35 *********************** 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 129 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.373 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 42 GLU cc_start: 0.8461 (tt0) cc_final: 0.7840 (tm-30) REVERT: G 111 LYS cc_start: 0.8986 (tttt) cc_final: 0.8712 (ttmt) REVERT: I 42 GLU cc_start: 0.7939 (tt0) cc_final: 0.7658 (tm-30) REVERT: I 56 ASP cc_start: 0.8446 (m-30) cc_final: 0.7479 (p0) REVERT: H 39 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7990 (tt0) outliers start: 13 outliers final: 11 residues processed: 127 average time/residue: 0.3173 time to fit residues: 61.4392 Evaluate side-chains 125 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 59 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8659 Z= 0.187 Angle : 0.533 6.845 11767 Z= 0.282 Chirality : 0.039 0.140 1432 Planarity : 0.003 0.031 1511 Dihedral : 4.353 17.360 1171 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.70 % Allowed : 19.53 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1098 helix: 1.52 (0.27), residues: 405 sheet: 0.92 (0.37), residues: 170 loop : -0.47 (0.25), residues: 523 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 0.006 0.001 PHE C 27 TYR 0.007 0.001 TYR G 129 ARG 0.002 0.000 ARG H 35 ********************** 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 126 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.360 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 111 LYS cc_start: 0.9014 (tttt) cc_final: 0.8735 (ttmt) REVERT: I 42 GLU cc_start: 0.7942 (tt0) cc_final: 0.7626 (tm-30) REVERT: I 56 ASP cc_start: 0.8457 (m-30) cc_final: 0.7493 (p0) REVERT: H 39 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7993 (tt0) outliers start: 16 outliers final: 12 residues processed: 123 average time/residue: 0.3370 time to fit residues: 62.9559 Evaluate side-chains 122 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 59 ASN 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 75 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.0570 chunk 5 optimal weight: 1.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.066899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.054647 restraints weight = 113162.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057028 restraints weight = 53891.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.058654 restraints weight = 33010.164| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8659 Z= 0.158 Angle : 0.536 7.071 11767 Z= 0.280 Chirality : 0.039 0.141 1432 Planarity : 0.003 0.034 1511 Dihedral : 4.189 17.150 1171 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.17 % Allowed : 19.96 % Favored : 78.87 % 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: 0.93 (0.25), residues: 1098 helix: 1.67 (0.27), residues: 406 sheet: 1.04 (0.37), residues: 170 loop : -0.34 (0.26), residues: 522 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 0.005 0.000 PHE C 27 TYR 0.007 0.001 TYR E 50 ARG 0.001 0.000 ARG H 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3305.05 seconds wall clock time: 58 minutes 45.10 seconds (3525.10 seconds total)