Starting phenix.real_space_refine on Wed Jul 23 18:58:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fh2_50437/07_2025/9fh2_50437.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fh2_50437/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fh2_50437/07_2025/9fh2_50437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fh2_50437/07_2025/9fh2_50437.map" model { file = "/net/cci-nas-00/data/ceres_data/9fh2_50437/07_2025/9fh2_50437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fh2_50437/07_2025/9fh2_50437.cif" } resolution = 3.7 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= 0.086 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 2.69, per 1000 atoms: 0.66 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: 0.97 Conformation dependent library (CDL) restraints added in 266.2 milliseconds 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: 0.39 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: 1.19 Time building geometry restraints manager: 1.21 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: 1.770 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: 0.090 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 13.950 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.49), 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 HIS 0.006 0.002 HIS G 6 TYR 0.088 0.032 TYR B 2 Details of bonding type rmsd hydrogen bonds : bond 0.11994 ( 32) hydrogen bonds : angle 7.94886 ( 96) covalent geometry : bond 0.01096 ( 2010) covalent geometry : angle 1.96515 ( 2690) *********************** 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 : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 ILE cc_start: 0.9221 (mt) cc_final: 0.9014 (mp) REVERT: E 3 GLU cc_start: 0.8876 (tt0) cc_final: 0.8393 (tp30) REVERT: F 3 GLU cc_start: 0.8927 (tt0) cc_final: 0.8515 (tp30) REVERT: F 17 ILE cc_start: 0.9285 (mt) cc_final: 0.9084 (mt) REVERT: G 2 TYR cc_start: 0.9010 (t80) cc_final: 0.8700 (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: 0.8988 (mt) REVERT: J 18 ILE cc_start: 0.9279 (mm) cc_final: 0.8941 (mt) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1486 time to fit residues: 16.8471 Evaluate side-chains 76 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.113038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.095995 restraints weight = 12910.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.099808 restraints weight = 4109.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.102489 restraints weight = 2140.841| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2010 Z= 0.170 Angle : 0.673 4.324 2690 Z= 0.357 Chirality : 0.059 0.150 320 Planarity : 0.002 0.010 330 Dihedral : 5.542 14.037 280 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.50 % Allowed : 14.50 % 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 (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: -1.04 (0.46), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.78 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 6 TYR 0.005 0.001 TYR D 2 Details of bonding type rmsd hydrogen bonds : bond 0.02731 ( 32) hydrogen bonds : angle 5.52862 ( 96) covalent geometry : bond 0.00393 ( 2010) covalent geometry : angle 0.67260 ( 2690) *********************** 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 69 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 3 GLU cc_start: 0.8730 (tt0) cc_final: 0.8493 (tp30) REVERT: H 4 VAL cc_start: 0.9395 (t) cc_final: 0.9117 (t) REVERT: H 9 LEU cc_start: 0.9346 (mp) cc_final: 0.9081 (mp) REVERT: I 13 ASN cc_start: 0.8430 (t0) cc_final: 0.8182 (t0) outliers start: 5 outliers final: 0 residues processed: 66 average time/residue: 0.1465 time to fit residues: 12.6184 Evaluate side-chains 58 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 5 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.115971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.097808 restraints weight = 13393.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.101625 restraints weight = 4392.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.104393 restraints weight = 2362.386| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2010 Z= 0.173 Angle : 0.567 3.857 2690 Z= 0.302 Chirality : 0.060 0.147 320 Planarity : 0.001 0.007 330 Dihedral : 4.484 10.390 280 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.50 % Allowed : 11.00 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.80 (0.44), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 6 TYR 0.006 0.001 TYR G 2 Details of bonding type rmsd hydrogen bonds : bond 0.02731 ( 32) hydrogen bonds : angle 5.20487 ( 96) covalent geometry : bond 0.00351 ( 2010) covalent geometry : angle 0.56746 ( 2690) *********************** 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 61 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.294 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: H 3 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7910 (tm-30) REVERT: H 9 LEU cc_start: 0.9345 (mp) cc_final: 0.9053 (mp) REVERT: I 3 GLU cc_start: 0.8305 (tp30) cc_final: 0.8044 (tm-30) REVERT: I 13 ASN cc_start: 0.8576 (t0) cc_final: 0.8368 (t0) REVERT: J 3 GLU cc_start: 0.8403 (tp30) cc_final: 0.8179 (tm-30) outliers start: 1 outliers final: 0 residues processed: 60 average time/residue: 0.1509 time to fit residues: 11.7023 Evaluate side-chains 60 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.114872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.098041 restraints weight = 12974.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.101576 restraints weight = 3953.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.104552 restraints weight = 2104.156| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2010 Z= 0.087 Angle : 0.518 3.352 2690 Z= 0.263 Chirality : 0.061 0.140 320 Planarity : 0.001 0.007 330 Dihedral : 3.976 9.751 280 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.50 % Allowed : 12.00 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.40 (0.48), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 6 TYR 0.004 0.001 TYR G 2 Details of bonding type rmsd hydrogen bonds : bond 0.02488 ( 32) hydrogen bonds : angle 4.96874 ( 96) covalent geometry : bond 0.00193 ( 2010) covalent geometry : angle 0.51820 ( 2690) *********************** 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 76 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.287 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: H 3 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7899 (tm-30) REVERT: H 7 GLN cc_start: 0.9108 (pt0) cc_final: 0.8834 (pt0) REVERT: H 9 LEU cc_start: 0.9324 (mp) cc_final: 0.9022 (mp) REVERT: I 13 ASN cc_start: 0.8682 (t0) cc_final: 0.8388 (t0) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1366 time to fit residues: 13.3361 Evaluate side-chains 69 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.121379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.102447 restraints weight = 13400.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.106484 restraints weight = 4315.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.109292 restraints weight = 2250.755| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2010 Z= 0.099 Angle : 0.522 4.387 2690 Z= 0.264 Chirality : 0.061 0.142 320 Planarity : 0.001 0.004 330 Dihedral : 3.826 8.837 280 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.50 % Allowed : 14.50 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.49), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 6 TYR 0.004 0.001 TYR F 2 Details of bonding type rmsd hydrogen bonds : bond 0.02292 ( 32) hydrogen bonds : angle 4.74975 ( 96) covalent geometry : bond 0.00217 ( 2010) covalent geometry : angle 0.52242 ( 2690) *********************** 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 76 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.496 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: A 7 GLN cc_start: 0.8742 (pt0) cc_final: 0.7546 (tp40) REVERT: B 7 GLN cc_start: 0.8694 (pt0) cc_final: 0.7602 (tp40) REVERT: I 13 ASN cc_start: 0.8715 (t0) cc_final: 0.8503 (t0) outliers start: 1 outliers final: 1 residues processed: 75 average time/residue: 0.1598 time to fit residues: 15.6606 Evaluate side-chains 73 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.116963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098090 restraints weight = 13450.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.102045 restraints weight = 4636.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.105047 restraints weight = 2470.488| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2010 Z= 0.171 Angle : 0.534 3.441 2690 Z= 0.280 Chirality : 0.060 0.139 320 Planarity : 0.001 0.008 330 Dihedral : 3.891 10.581 280 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 21.00 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.53 (0.49), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 5 TYR 0.004 0.001 TYR F 2 Details of bonding type rmsd hydrogen bonds : bond 0.02190 ( 32) hydrogen bonds : angle 4.64168 ( 96) covalent geometry : bond 0.00352 ( 2010) covalent geometry : angle 0.53367 ( 2690) *********************** 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 70 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8804 (pt0) cc_final: 0.7656 (tp40) REVERT: B 7 GLN cc_start: 0.8754 (pt0) cc_final: 0.7652 (tp40) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1456 time to fit residues: 13.2604 Evaluate side-chains 68 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 0 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 7 GLN ** 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 = 0.4067 r_free = 0.4067 target = 0.117062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.099841 restraints weight = 13004.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.103577 restraints weight = 4158.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.106726 restraints weight = 2245.604| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2010 Z= 0.093 Angle : 0.563 4.702 2690 Z= 0.281 Chirality : 0.062 0.151 320 Planarity : 0.001 0.009 330 Dihedral : 3.766 12.016 280 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.50 % Allowed : 22.00 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.27 (0.51), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 6 TYR 0.004 0.001 TYR G 2 Details of bonding type rmsd hydrogen bonds : bond 0.02055 ( 32) hydrogen bonds : angle 4.55873 ( 96) covalent geometry : bond 0.00216 ( 2010) covalent geometry : angle 0.56343 ( 2690) *********************** 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 82 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8765 (pt0) cc_final: 0.7620 (tp40) REVERT: B 7 GLN cc_start: 0.8695 (pt0) cc_final: 0.7593 (tp40) REVERT: H 7 GLN cc_start: 0.9018 (pt0) cc_final: 0.8817 (tt0) outliers start: 1 outliers final: 1 residues processed: 81 average time/residue: 0.1561 time to fit residues: 16.4712 Evaluate side-chains 79 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 13 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.116401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.099351 restraints weight = 12869.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.103019 restraints weight = 4058.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.106028 restraints weight = 2177.308| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2010 Z= 0.119 Angle : 0.557 4.427 2690 Z= 0.282 Chirality : 0.061 0.166 320 Planarity : 0.001 0.013 330 Dihedral : 3.720 14.940 280 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.34 (0.51), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 6 TYR 0.004 0.001 TYR G 2 Details of bonding type rmsd hydrogen bonds : bond 0.01980 ( 32) hydrogen bonds : angle 4.45530 ( 96) covalent geometry : bond 0.00257 ( 2010) covalent geometry : angle 0.55684 ( 2690) *********************** 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 75 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8681 (pt0) cc_final: 0.7697 (tp40) REVERT: B 7 GLN cc_start: 0.8727 (pt0) cc_final: 0.7618 (tp40) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1518 time to fit residues: 14.7171 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 : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.124117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.104750 restraints weight = 12771.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.108349 restraints weight = 4253.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.111669 restraints weight = 2350.117| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2010 Z= 0.097 Angle : 0.557 4.039 2690 Z= 0.279 Chirality : 0.062 0.162 320 Planarity : 0.001 0.013 330 Dihedral : 3.618 14.303 280 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 25.50 % 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 (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: -1.21 (0.52), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 6 TYR 0.004 0.001 TYR G 2 Details of bonding type rmsd hydrogen bonds : bond 0.01913 ( 32) hydrogen bonds : angle 4.38987 ( 96) covalent geometry : bond 0.00219 ( 2010) covalent geometry : angle 0.55707 ( 2690) *********************** 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 79 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8656 (pt0) cc_final: 0.7675 (tp40) REVERT: B 7 GLN cc_start: 0.8637 (pt0) cc_final: 0.7596 (tp40) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1531 time to fit residues: 15.7519 Evaluate side-chains 75 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.126596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.107069 restraints weight = 12495.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.111082 restraints weight = 4188.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.114287 restraints weight = 2181.852| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2010 Z= 0.093 Angle : 0.564 4.750 2690 Z= 0.276 Chirality : 0.062 0.158 320 Planarity : 0.002 0.016 330 Dihedral : 3.513 15.773 280 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 25.50 % 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 (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: -1.09 (0.53), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 6 TYR 0.006 0.001 TYR G 2 Details of bonding type rmsd hydrogen bonds : bond 0.01852 ( 32) hydrogen bonds : angle 4.28673 ( 96) covalent geometry : bond 0.00221 ( 2010) covalent geometry : angle 0.56431 ( 2690) ********************** 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 80 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8634 (pt0) cc_final: 0.7672 (tp40) REVERT: B 7 GLN cc_start: 0.8663 (pt0) cc_final: 0.7660 (tp-100) REVERT: G 12 SER cc_start: 0.9175 (t) cc_final: 0.8834 (p) REVERT: H 12 SER cc_start: 0.9054 (t) cc_final: 0.8690 (p) REVERT: J 12 SER cc_start: 0.9063 (t) cc_final: 0.8626 (p) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1691 time to fit residues: 17.5575 Evaluate side-chains 78 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.125571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.107085 restraints weight = 12550.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.111133 restraints weight = 4156.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.113971 restraints weight = 2120.468| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2010 Z= 0.093 Angle : 0.541 3.989 2690 Z= 0.266 Chirality : 0.062 0.155 320 Planarity : 0.001 0.013 330 Dihedral : 3.360 14.710 280 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 26.50 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.07 (0.53), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 6 TYR 0.006 0.001 TYR F 2 Details of bonding type rmsd hydrogen bonds : bond 0.01840 ( 32) hydrogen bonds : angle 4.22932 ( 96) covalent geometry : bond 0.00217 ( 2010) covalent geometry : angle 0.54113 ( 2690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.45 seconds wall clock time: 44 minutes 39.21 seconds (2679.21 seconds total)