Starting phenix.real_space_refine on Fri Aug 22 14:24:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh2_50437/08_2025/9fh2_50437.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh2_50437/08_2025/9fh2_50437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fh2_50437/08_2025/9fh2_50437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh2_50437/08_2025/9fh2_50437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fh2_50437/08_2025/9fh2_50437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh2_50437/08_2025/9fh2_50437.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.086 sd= 0.987 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 10 5.16 5 C 1280 2.51 5 N 360 2.21 5 O 340 1.98 5 H 2110 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4100 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "B" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "E" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "F" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "H" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "I" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "J" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 410 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Time building chain proxies: 0.85, per 1000 atoms: 0.21 Number of scatterers: 4100 At special positions: 0 Unit cell: (77.52, 53.04, 44.064, 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 10 16.00 O 340 8.00 N 360 7.00 C 1280 6.00 H 2110 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: 0.28 Conformation dependent library (CDL) restraints added in 64.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 440 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 67.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 13 removed outlier: 7.007A pdb=" N GLU A 3 " --> pdb=" O TYR C 2 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 4 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N HIS A 5 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N GLU C 3 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N HIS E 6 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N HIS C 5 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS E 8 " --> pdb=" O HIS C 5 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN C 7 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL E 10 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 9 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N SER E 12 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY C 11 " --> pdb=" O SER E 12 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N GLU E 3 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N HIS G 6 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N HIS E 5 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N LYS G 8 " --> pdb=" O HIS E 5 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN E 7 " --> pdb=" O LYS G 8 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N VAL G 10 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU E 9 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N SER G 12 " --> pdb=" O LEU E 9 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY E 11 " --> pdb=" O SER G 12 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR G 2 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N HIS I 5 " --> pdb=" O TYR G 2 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N VAL G 4 " --> pdb=" O HIS I 5 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN I 7 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N HIS G 6 " --> pdb=" O GLN I 7 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N LEU I 9 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N LYS G 8 " --> pdb=" O LEU I 9 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N GLY I 11 " --> pdb=" O LYS G 8 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N VAL G 10 " --> pdb=" O GLY I 11 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N ASN I 13 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N SER G 12 " --> pdb=" O ASN I 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 22 removed outlier: 8.937A pdb=" N ALA A 16 " --> pdb=" O ILE C 17 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N GLY C 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 18 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N MET C 21 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 20 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N ALA C 16 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N GLY E 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 18 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N MET E 21 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU C 20 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N ALA E 16 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N GLY G 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE E 18 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N MET G 21 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU E 20 " --> pdb=" O MET G 21 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N ALA G 16 " --> pdb=" O ILE I 17 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N GLY I 19 " --> pdb=" O ALA G 16 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE G 18 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N MET I 21 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU G 20 " --> pdb=" O MET I 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 13 removed outlier: 6.986A pdb=" N GLU B 3 " --> pdb=" O TYR D 2 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL D 4 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS B 5 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N GLU D 3 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N HIS F 6 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N HIS D 5 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N LYS F 8 " --> pdb=" O HIS D 5 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN D 7 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL F 10 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU D 9 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N SER F 12 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY D 11 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR F 2 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N HIS H 5 " --> pdb=" O TYR F 2 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N VAL F 4 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLN H 7 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N HIS F 6 " --> pdb=" O GLN H 7 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N LEU H 9 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N LYS F 8 " --> pdb=" O LEU H 9 " (cutoff:3.500A) removed outlier: 10.352A pdb=" N GLY H 11 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N VAL F 10 " --> pdb=" O GLY H 11 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N ASN H 13 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N SER F 12 " --> pdb=" O ASN H 13 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR H 2 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N HIS J 5 " --> pdb=" O TYR H 2 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N VAL H 4 " --> pdb=" O HIS J 5 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLN J 7 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N HIS H 6 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 10.610A pdb=" N LEU J 9 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N LYS H 8 " --> pdb=" O LEU J 9 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N GLY J 11 " --> pdb=" O LYS H 8 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N VAL H 10 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N ASN J 13 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N SER H 12 " --> pdb=" O ASN J 13 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 22 removed outlier: 8.939A pdb=" N ALA B 16 " --> pdb=" O ILE D 17 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N GLY D 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE B 18 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N MET D 21 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 20 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N ALA D 16 " --> pdb=" O ILE F 17 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N GLY F 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE D 18 " --> pdb=" O GLY F 19 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N MET F 21 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU D 20 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ALA F 16 " --> pdb=" O ILE H 17 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N GLY H 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE F 18 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N MET H 21 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU F 20 " --> pdb=" O MET H 21 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ALA H 16 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 10.183A pdb=" N GLY J 19 " --> pdb=" O ALA H 16 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE H 18 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N MET J 21 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU H 20 " --> pdb=" O MET J 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 27 32 hydrogen bonds defined for protein. 96 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: 0.79 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 2110 1.13 - 1.30: 320 1.30 - 1.47: 646 1.47 - 1.64: 1024 1.64 - 1.81: 20 Bond restraints: 4120 Sorted by residual: bond pdb=" CD2 HIS F 5 " pdb=" HD2 HIS F 5 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLY F 15 " pdb=" H GLY F 15 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N MET J 21 " pdb=" H MET J 21 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLU G 3 " pdb=" H GLU G 3 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY A 24 " pdb=" H GLY A 24 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 4115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 5045 1.58 - 3.16: 1586 3.16 - 4.74: 490 4.74 - 6.32: 271 6.32 - 7.90: 88 Bond angle restraints: 7480 Sorted by residual: angle pdb=" N GLN E 7 " pdb=" CA GLN E 7 " pdb=" C GLN E 7 " ideal model delta sigma weight residual 108.79 116.69 -7.90 1.53e+00 4.27e-01 2.66e+01 angle pdb=" N GLN D 7 " pdb=" CA GLN D 7 " pdb=" C GLN D 7 " ideal model delta sigma weight residual 108.79 116.61 -7.82 1.53e+00 4.27e-01 2.61e+01 angle pdb=" N GLN F 7 " pdb=" CA GLN F 7 " pdb=" C GLN F 7 " ideal model delta sigma weight residual 108.79 116.58 -7.79 1.53e+00 4.27e-01 2.59e+01 angle pdb=" N GLN G 7 " pdb=" CA GLN G 7 " pdb=" C GLN G 7 " ideal model delta sigma weight residual 108.79 116.52 -7.73 1.53e+00 4.27e-01 2.55e+01 angle pdb=" N GLN C 7 " pdb=" CA GLN C 7 " pdb=" C GLN C 7 " ideal model delta sigma weight residual 108.79 116.50 -7.71 1.53e+00 4.27e-01 2.54e+01 ... (remaining 7475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.83: 1653 13.83 - 27.65: 73 27.65 - 41.47: 45 41.47 - 55.29: 44 55.29 - 69.11: 45 Dihedral angle restraints: 1860 sinusoidal: 1040 harmonic: 820 Sorted by residual: dihedral pdb=" CA VAL A 22 " pdb=" C VAL A 22 " pdb=" N GLY A 23 " pdb=" CA GLY A 23 " ideal model delta harmonic sigma weight residual 180.00 165.52 14.48 0 5.00e+00 4.00e-02 8.39e+00 dihedral pdb=" CA VAL B 22 " pdb=" C VAL B 22 " pdb=" N GLY B 23 " pdb=" CA GLY B 23 " ideal model delta harmonic sigma weight residual 180.00 166.53 13.47 0 5.00e+00 4.00e-02 7.26e+00 dihedral pdb=" CA SER G 12 " pdb=" C SER G 12 " pdb=" N ASN G 13 " pdb=" CA ASN G 13 " ideal model delta harmonic sigma weight residual 180.00 166.61 13.39 0 5.00e+00 4.00e-02 7.17e+00 ... (remaining 1857 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.038: 56 0.038 - 0.075: 125 0.075 - 0.112: 64 0.112 - 0.149: 49 0.149 - 0.186: 26 Chirality restraints: 320 Sorted by residual: chirality pdb=" CB ILE C 18 " pdb=" CA ILE C 18 " pdb=" CG1 ILE C 18 " pdb=" CG2 ILE C 18 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CB ILE D 18 " pdb=" CA ILE D 18 " pdb=" CG1 ILE D 18 " pdb=" CG2 ILE D 18 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CB ILE E 18 " pdb=" CA ILE E 18 " pdb=" CG1 ILE E 18 " pdb=" CG2 ILE E 18 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 317 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 2 " -0.094 2.00e-02 2.50e+03 4.05e-02 4.91e+01 pdb=" CG TYR B 2 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 2 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR B 2 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR B 2 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 2 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 2 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 2 " -0.078 2.00e-02 2.50e+03 pdb=" HD1 TYR B 2 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR B 2 " 0.022 2.00e-02 2.50e+03 pdb=" HE1 TYR B 2 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR B 2 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 2 " 0.093 2.00e-02 2.50e+03 3.94e-02 4.65e+01 pdb=" CG TYR G 2 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR G 2 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR G 2 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR G 2 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR G 2 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR G 2 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 2 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 TYR G 2 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 TYR G 2 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TYR G 2 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 TYR G 2 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 2 " 0.091 2.00e-02 2.50e+03 3.80e-02 4.32e+01 pdb=" CG TYR I 2 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR I 2 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR I 2 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR I 2 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR I 2 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR I 2 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 2 " 0.065 2.00e-02 2.50e+03 pdb=" HD1 TYR I 2 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR I 2 " -0.024 2.00e-02 2.50e+03 pdb=" HE1 TYR I 2 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 TYR I 2 " 0.008 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 609 2.32 - 2.89: 8830 2.89 - 3.46: 10600 3.46 - 4.03: 15351 4.03 - 4.60: 21232 Nonbonded interactions: 56622 Sorted by model distance: nonbonded pdb=" O LEU C 20 " pdb=" H MET E 21 " model vdw 1.753 2.450 nonbonded pdb=" O LEU E 20 " pdb=" H MET G 21 " model vdw 1.755 2.450 nonbonded pdb=" O LEU F 20 " pdb=" H MET H 21 " model vdw 1.756 2.450 nonbonded pdb=" O LEU D 20 " pdb=" H MET F 21 " model vdw 1.756 2.450 nonbonded pdb=" O LEU B 20 " pdb=" H MET D 21 " model vdw 1.778 2.450 ... (remaining 56617 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.011 0.032 2010 Z= 0.716 Angle : 1.965 7.896 2690 Z= 1.286 Chirality : 0.089 0.186 320 Planarity : 0.010 0.048 330 Dihedral : 9.540 33.258 690 Min Nonbonded Distance : 2.734 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.49), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.21 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.088 0.032 TYR B 2 HIS 0.006 0.002 HIS G 6 Details of bonding type rmsd covalent geometry : bond 0.01096 ( 2010) covalent geometry : angle 1.96515 ( 2690) hydrogen bonds : bond 0.11994 ( 32) hydrogen bonds : angle 7.94886 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 17 ILE cc_start: 0.9221 (mt) cc_final: 0.9012 (mp) REVERT: E 3 GLU cc_start: 0.8876 (tt0) cc_final: 0.8391 (tp30) REVERT: E 18 ILE cc_start: 0.9444 (mm) cc_final: 0.9200 (mt) REVERT: F 3 GLU cc_start: 0.8927 (tt0) cc_final: 0.8515 (tp30) REVERT: G 2 TYR cc_start: 0.9010 (t80) cc_final: 0.8709 (t80) REVERT: H 3 GLU cc_start: 0.8967 (tt0) cc_final: 0.8574 (tm-30) REVERT: I 18 ILE cc_start: 0.9257 (mm) cc_final: 0.9032 (mt) REVERT: J 18 ILE cc_start: 0.9279 (mm) cc_final: 0.8977 (mt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0543 time to fit residues: 6.3448 Evaluate side-chains 74 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 HIS I 5 HIS J 5 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.115399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.097302 restraints weight = 13551.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.101205 restraints weight = 4559.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.104020 restraints weight = 2415.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.105952 restraints weight = 1563.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.107380 restraints weight = 1145.417| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 2010 Z= 0.218 Angle : 0.686 4.319 2690 Z= 0.369 Chirality : 0.059 0.151 320 Planarity : 0.002 0.010 330 Dihedral : 5.624 13.083 280 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.00 % Allowed : 13.50 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.45), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR D 2 HIS 0.004 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 2010) covalent geometry : angle 0.68568 ( 2690) hydrogen bonds : bond 0.02693 ( 32) hydrogen bonds : angle 5.35149 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8684 (pt0) cc_final: 0.7620 (tp40) REVERT: H 4 VAL cc_start: 0.9394 (t) cc_final: 0.8950 (t) REVERT: H 9 LEU cc_start: 0.9295 (mp) cc_final: 0.8968 (mp) REVERT: I 13 ASN cc_start: 0.8434 (t0) cc_final: 0.8163 (t0) outliers start: 6 outliers final: 1 residues processed: 65 average time/residue: 0.0429 time to fit residues: 3.7951 Evaluate side-chains 57 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.115705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.097517 restraints weight = 13269.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.101041 restraints weight = 4474.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.104060 restraints weight = 2476.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.105971 restraints weight = 1602.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.107099 restraints weight = 1162.923| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2010 Z= 0.167 Angle : 0.589 4.752 2690 Z= 0.306 Chirality : 0.060 0.142 320 Planarity : 0.001 0.007 330 Dihedral : 4.757 10.728 280 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.50 % Allowed : 12.00 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.43), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR G 2 HIS 0.002 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 2010) covalent geometry : angle 0.58903 ( 2690) hydrogen bonds : bond 0.02618 ( 32) hydrogen bonds : angle 5.05784 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8746 (pt0) cc_final: 0.7698 (tp40) REVERT: I 13 ASN cc_start: 0.8694 (t0) cc_final: 0.8442 (t0) outliers start: 5 outliers final: 3 residues processed: 64 average time/residue: 0.0517 time to fit residues: 4.4666 Evaluate side-chains 63 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain J residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.119829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.100728 restraints weight = 13007.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.104981 restraints weight = 4355.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.107732 restraints weight = 2249.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.109976 restraints weight = 1475.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.111049 restraints weight = 1055.783| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2010 Z= 0.099 Angle : 0.543 3.957 2690 Z= 0.277 Chirality : 0.061 0.141 320 Planarity : 0.001 0.005 330 Dihedral : 4.040 9.718 280 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.00 % Allowed : 15.00 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.46), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR J 2 HIS 0.002 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 2010) covalent geometry : angle 0.54308 ( 2690) hydrogen bonds : bond 0.02377 ( 32) hydrogen bonds : angle 4.77523 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8707 (pt0) cc_final: 0.7700 (tp40) REVERT: B 7 GLN cc_start: 0.8694 (pt0) cc_final: 0.7577 (tp40) REVERT: H 9 LEU cc_start: 0.9199 (mp) cc_final: 0.8967 (mp) REVERT: I 13 ASN cc_start: 0.8718 (t0) cc_final: 0.8437 (t0) outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.0593 time to fit residues: 5.9068 Evaluate side-chains 75 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain J residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.115122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.098377 restraints weight = 12994.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.102368 restraints weight = 4194.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.105106 restraints weight = 2162.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.106860 restraints weight = 1390.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.107994 restraints weight = 997.262| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2010 Z= 0.118 Angle : 0.539 4.507 2690 Z= 0.269 Chirality : 0.060 0.142 320 Planarity : 0.001 0.006 330 Dihedral : 3.852 9.196 280 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.00 % Allowed : 20.00 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.48), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR F 2 HIS 0.002 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 2010) covalent geometry : angle 0.53854 ( 2690) hydrogen bonds : bond 0.02209 ( 32) hydrogen bonds : angle 4.64513 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8721 (pt0) cc_final: 0.7700 (tp40) REVERT: A 9 LEU cc_start: 0.8959 (mp) cc_final: 0.8728 (mp) REVERT: B 7 GLN cc_start: 0.8731 (pt0) cc_final: 0.7615 (tp40) REVERT: B 9 LEU cc_start: 0.8987 (mp) cc_final: 0.8786 (mp) REVERT: H 9 LEU cc_start: 0.9213 (mp) cc_final: 0.8939 (mp) REVERT: I 13 ASN cc_start: 0.8713 (t0) cc_final: 0.8432 (t0) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.0521 time to fit residues: 5.1127 Evaluate side-chains 73 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain J residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.115918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.098022 restraints weight = 13573.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.101732 restraints weight = 4381.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.104467 restraints weight = 2314.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.106378 restraints weight = 1522.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.107616 restraints weight = 1112.052| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2010 Z= 0.186 Angle : 0.541 4.278 2690 Z= 0.278 Chirality : 0.059 0.140 320 Planarity : 0.001 0.004 330 Dihedral : 3.963 10.570 280 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.00 % Allowed : 23.50 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.47), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR F 2 HIS 0.002 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2010) covalent geometry : angle 0.54114 ( 2690) hydrogen bonds : bond 0.02166 ( 32) hydrogen bonds : angle 4.58568 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8728 (pt0) cc_final: 0.7756 (tp40) REVERT: A 9 LEU cc_start: 0.9029 (mp) cc_final: 0.8801 (mp) REVERT: B 7 GLN cc_start: 0.8788 (pt0) cc_final: 0.7646 (tp40) REVERT: B 9 LEU cc_start: 0.9045 (mp) cc_final: 0.8844 (mp) REVERT: H 9 LEU cc_start: 0.9265 (mp) cc_final: 0.8987 (mp) outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.0467 time to fit residues: 4.2731 Evaluate side-chains 70 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain J residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.118095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.099747 restraints weight = 13624.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.103231 restraints weight = 4470.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.106030 restraints weight = 2460.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.108413 restraints weight = 1617.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.109433 restraints weight = 1131.513| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2010 Z= 0.125 Angle : 0.536 4.343 2690 Z= 0.270 Chirality : 0.061 0.142 320 Planarity : 0.001 0.008 330 Dihedral : 3.793 12.242 280 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.00 % Allowed : 24.00 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.48), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR G 2 HIS 0.002 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 2010) covalent geometry : angle 0.53615 ( 2690) hydrogen bonds : bond 0.02014 ( 32) hydrogen bonds : angle 4.52028 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8683 (pt0) cc_final: 0.7779 (tp40) REVERT: B 7 GLN cc_start: 0.8778 (pt0) cc_final: 0.7655 (tp40) REVERT: F 3 GLU cc_start: 0.7729 (mp0) cc_final: 0.7344 (mp0) REVERT: H 9 LEU cc_start: 0.9255 (mp) cc_final: 0.9028 (mp) REVERT: I 13 ASN cc_start: 0.8904 (t0) cc_final: 0.8698 (t0) outliers start: 4 outliers final: 4 residues processed: 73 average time/residue: 0.0540 time to fit residues: 5.3038 Evaluate side-chains 77 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain J residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 HIS E 5 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.116459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.097718 restraints weight = 13377.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.101382 restraints weight = 4577.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.104114 restraints weight = 2445.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.106021 restraints weight = 1632.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.107303 restraints weight = 1195.424| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2010 Z= 0.203 Angle : 0.574 4.267 2690 Z= 0.295 Chirality : 0.059 0.139 320 Planarity : 0.002 0.009 330 Dihedral : 4.060 13.810 280 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.50 % Allowed : 26.50 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.47), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR D 2 HIS 0.003 0.001 HIS J 6 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 2010) covalent geometry : angle 0.57399 ( 2690) hydrogen bonds : bond 0.02100 ( 32) hydrogen bonds : angle 4.47781 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8662 (pt0) cc_final: 0.7600 (tp40) REVERT: B 7 GLN cc_start: 0.8722 (pt0) cc_final: 0.7601 (tp40) REVERT: H 9 LEU cc_start: 0.9308 (mp) cc_final: 0.9045 (mp) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.0562 time to fit residues: 5.0355 Evaluate side-chains 69 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain J residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.118557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.099752 restraints weight = 13356.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.103467 restraints weight = 4522.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.106175 restraints weight = 2403.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.108430 restraints weight = 1601.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.109803 restraints weight = 1146.147| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2010 Z= 0.121 Angle : 0.556 3.898 2690 Z= 0.278 Chirality : 0.061 0.136 320 Planarity : 0.001 0.010 330 Dihedral : 3.910 15.265 280 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.00 % Allowed : 27.50 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.48), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR D 2 HIS 0.002 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 2010) covalent geometry : angle 0.55586 ( 2690) hydrogen bonds : bond 0.01961 ( 32) hydrogen bonds : angle 4.40924 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8567 (pt0) cc_final: 0.7697 (tp40) REVERT: B 7 GLN cc_start: 0.8708 (pt0) cc_final: 0.7606 (tp40) REVERT: F 7 GLN cc_start: 0.9013 (pt0) cc_final: 0.8799 (tt0) REVERT: G 17 ILE cc_start: 0.9191 (mt) cc_final: 0.8979 (mp) REVERT: H 3 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7917 (tm-30) REVERT: H 9 LEU cc_start: 0.9275 (mp) cc_final: 0.9014 (mp) REVERT: I 13 ASN cc_start: 0.8886 (t0) cc_final: 0.8654 (t0) outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 0.0616 time to fit residues: 5.8751 Evaluate side-chains 74 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain J residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.117667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.098378 restraints weight = 13127.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.101631 restraints weight = 4416.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.104548 restraints weight = 2455.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.106295 restraints weight = 1607.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.107546 restraints weight = 1202.172| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2010 Z= 0.183 Angle : 0.567 4.470 2690 Z= 0.288 Chirality : 0.059 0.131 320 Planarity : 0.001 0.010 330 Dihedral : 4.030 18.329 280 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.50 % Allowed : 27.50 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.47), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR D 2 HIS 0.002 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 2010) covalent geometry : angle 0.56747 ( 2690) hydrogen bonds : bond 0.02047 ( 32) hydrogen bonds : angle 4.39722 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8621 (pt0) cc_final: 0.7636 (tp40) REVERT: B 7 GLN cc_start: 0.8734 (pt0) cc_final: 0.7629 (tp40) REVERT: F 7 GLN cc_start: 0.9025 (pt0) cc_final: 0.8800 (tt0) REVERT: H 9 LEU cc_start: 0.9303 (mp) cc_final: 0.9057 (mp) outliers start: 3 outliers final: 3 residues processed: 65 average time/residue: 0.0631 time to fit residues: 5.4408 Evaluate side-chains 67 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain J residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.117932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099546 restraints weight = 13223.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.102985 restraints weight = 4444.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.105976 restraints weight = 2451.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.108410 restraints weight = 1588.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.109687 restraints weight = 1095.874| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2010 Z= 0.126 Angle : 0.566 4.358 2690 Z= 0.282 Chirality : 0.061 0.134 320 Planarity : 0.001 0.005 330 Dihedral : 3.816 17.026 280 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.00 % Allowed : 28.00 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.48), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR D 2 HIS 0.002 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 2010) covalent geometry : angle 0.56570 ( 2690) hydrogen bonds : bond 0.01953 ( 32) hydrogen bonds : angle 4.28810 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1189.84 seconds wall clock time: 20 minutes 53.85 seconds (1253.85 seconds total)