Starting phenix.real_space_refine on Fri Sep 11 06:21:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9px8_71961/09_2026/9px8_71961.cif Found real_map, /net/cci-nas-00/data/ceres_data/9px8_71961/09_2026/9px8_71961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9px8_71961/09_2026/9px8_71961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9px8_71961/09_2026/9px8_71961.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9px8_71961/09_2026/9px8_71961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9px8_71961/09_2026/9px8_71961.map" } resolution = 3.3 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= 0.003 sd= 0.371 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: 4 Type Number sf(0) Gaussians C 2520 2.51 5 N 915 2.21 5 O 720 1.98 5 H 3838 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7993 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 532 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "B" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 534 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 533 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "D" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 532 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 534 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 533 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "G" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 534 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "H" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 532 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 533 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 533 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "K" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 534 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 532 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "M" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 532 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "N" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 532 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 533 Classifications: {'peptide': 31} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 30} Time building chain proxies: 1.47, per 1000 atoms: 0.18 Number of scatterers: 7993 At special positions: 0 Unit cell: (106.704, 100.152, 39.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 720 8.00 N 915 7.00 C 2520 6.00 H 3838 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: 0.59 Conformation dependent library (CDL) restraints added in 354.5 milliseconds 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 930 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 15 removed outlier: 6.446A pdb=" N HIS A 11 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N HIS D 14 " --> pdb=" O HIS A 11 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLN A 13 " --> pdb=" O HIS D 14 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N HIS D 11 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N HIS G 14 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLN D 13 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N HIS G 11 " --> pdb=" O LEU J 12 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS J 14 " --> pdb=" O HIS G 11 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLN G 13 " --> pdb=" O HIS J 14 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS J 11 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N HIS M 14 " --> pdb=" O HIS J 11 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLN J 13 " --> pdb=" O HIS M 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 21 removed outlier: 8.732A pdb=" N LEU A 18 " --> pdb=" O GLN D 19 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N VAL D 21 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN A 20 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE D 23 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N LEU D 18 " --> pdb=" O GLN G 19 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N VAL G 21 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN D 20 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE G 23 " --> pdb=" O GLN D 20 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLN D 22 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N LEU G 18 " --> pdb=" O GLN J 19 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N VAL J 21 " --> pdb=" O LEU G 18 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN G 20 " --> pdb=" O VAL J 21 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE J 23 " --> pdb=" O GLN G 20 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLN G 22 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N LEU J 18 " --> pdb=" O GLN M 19 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N VAL M 21 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN J 20 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE M 23 " --> pdb=" O GLN J 20 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLN J 22 " --> pdb=" O PHE M 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.720A pdb=" N GLN A 28 " --> pdb=" O GLN D 29 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN D 28 " --> pdb=" O GLN G 29 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN G 28 " --> pdb=" O GLN J 29 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN J 28 " --> pdb=" O GLN M 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.437A pdb=" N HIS B 11 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N HIS E 11 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS H 14 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS H 11 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N HIS K 14 " --> pdb=" O HIS H 11 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N GLN H 13 " --> pdb=" O HIS K 14 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS K 11 " --> pdb=" O LEU N 12 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N HIS N 14 " --> pdb=" O HIS K 11 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLN K 13 " --> pdb=" O HIS N 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 21 removed outlier: 8.763A pdb=" N LEU B 18 " --> pdb=" O GLN E 19 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N VAL E 21 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN B 20 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LEU E 18 " --> pdb=" O GLN H 19 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N VAL H 21 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN E 20 " --> pdb=" O VAL H 21 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N LEU H 18 " --> pdb=" O GLN K 19 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N VAL K 21 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN H 20 " --> pdb=" O VAL K 21 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE K 23 " --> pdb=" O GLN H 20 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N VAL N 21 " --> pdb=" O LEU K 18 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN K 20 " --> pdb=" O VAL N 21 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE N 23 " --> pdb=" O GLN K 20 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLN K 22 " --> pdb=" O PHE N 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.729A pdb=" N GLN B 28 " --> pdb=" O GLN E 29 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN E 28 " --> pdb=" O GLN H 29 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN H 28 " --> pdb=" O GLN K 29 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN K 28 " --> pdb=" O GLN N 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AB1, first strand: chain 'C' and resid 7 through 8 removed outlier: 6.578A pdb=" N HIS C 7 " --> pdb=" O GLN F 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.342A pdb=" N HIS C 11 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N HIS F 14 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS F 11 " --> pdb=" O LEU I 12 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N HIS I 14 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLN F 13 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N HIS I 11 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N HIS L 14 " --> pdb=" O HIS I 11 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLN I 13 " --> pdb=" O HIS L 14 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS L 11 " --> pdb=" O LEU O 12 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N HIS O 14 " --> pdb=" O HIS L 11 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLN L 13 " --> pdb=" O HIS O 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 18 through 23 removed outlier: 8.735A pdb=" N LEU C 18 " --> pdb=" O GLN F 19 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N VAL F 21 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN C 20 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE F 23 " --> pdb=" O GLN C 20 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLN C 22 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN I 19 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLN F 20 " --> pdb=" O GLN I 19 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN L 19 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN I 20 " --> pdb=" O GLN L 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 28 through 29 removed outlier: 6.738A pdb=" N GLN C 28 " --> pdb=" O GLN F 29 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN F 28 " --> pdb=" O GLN I 29 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS L 26 " --> pdb=" O GLN O 27 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN O 29 " --> pdb=" O HIS L 26 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN L 28 " --> pdb=" O GLN O 29 " (cutoff:3.500A) 36 hydrogen bonds defined for protein. 105 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: 1.38 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 3838 0.98 - 1.12: 0 1.12 - 1.26: 705 1.26 - 1.40: 1305 1.40 - 1.54: 2250 Bond restraints: 8098 Sorted by residual: bond pdb=" CB GLN M 8 " pdb=" CG GLN M 8 " ideal model delta sigma weight residual 1.520 1.497 0.023 3.00e-02 1.11e+03 5.91e-01 bond pdb=" CB GLN H 8 " pdb=" CG GLN H 8 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.97e-01 bond pdb=" CG GLN K 27 " pdb=" CD GLN K 27 " ideal model delta sigma weight residual 1.516 1.499 0.017 2.50e-02 1.60e+03 4.69e-01 bond pdb=" CA GLN G 8 " pdb=" CB GLN G 8 " ideal model delta sigma weight residual 1.535 1.522 0.013 2.09e-02 2.29e+03 4.15e-01 bond pdb=" CA GLN L 8 " pdb=" CB GLN L 8 " ideal model delta sigma weight residual 1.535 1.523 0.013 2.09e-02 2.29e+03 3.64e-01 ... (remaining 8093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.06: 14336 7.06 - 14.12: 0 14.12 - 21.18: 0 21.18 - 28.24: 0 28.24 - 35.31: 45 Bond angle restraints: 14381 Sorted by residual: angle pdb=" C LEU N 2 " pdb=" CA LEU N 2 " pdb=" HA LEU N 2 " ideal model delta sigma weight residual 109.00 73.69 35.31 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C LEU M 2 " pdb=" CA LEU M 2 " pdb=" HA LEU M 2 " ideal model delta sigma weight residual 109.00 73.70 35.30 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C LEU O 2 " pdb=" CA LEU O 2 " pdb=" HA LEU O 2 " ideal model delta sigma weight residual 109.00 73.76 35.24 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C LEU J 2 " pdb=" CA LEU J 2 " pdb=" HA LEU J 2 " ideal model delta sigma weight residual 109.00 73.77 35.23 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C LEU F 2 " pdb=" CA LEU F 2 " pdb=" HA LEU F 2 " ideal model delta sigma weight residual 109.00 73.78 35.22 3.00e+00 1.11e-01 1.38e+02 ... (remaining 14376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 3197 16.91 - 33.81: 415 33.81 - 50.72: 114 50.72 - 67.62: 27 67.62 - 84.53: 40 Dihedral angle restraints: 3793 sinusoidal: 2010 harmonic: 1783 Sorted by residual: dihedral pdb=" CA PHE I 23 " pdb=" C PHE I 23 " pdb=" N HIS I 24 " pdb=" CA HIS I 24 " ideal model delta harmonic sigma weight residual 180.00 -160.55 -19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE G 23 " pdb=" C PHE G 23 " pdb=" N HIS G 24 " pdb=" CA HIS G 24 " ideal model delta harmonic sigma weight residual -180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PHE C 23 " pdb=" C PHE C 23 " pdb=" N HIS C 24 " pdb=" CA HIS C 24 " ideal model delta harmonic sigma weight residual -180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 3790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 508 0.072 - 0.144: 32 0.144 - 0.216: 0 0.216 - 0.288: 0 0.288 - 0.360: 15 Chirality restraints: 555 Sorted by residual: chirality pdb=" CA LEU B 2 " pdb=" N LEU B 2 " pdb=" C LEU B 2 " pdb=" CB LEU B 2 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA LEU D 2 " pdb=" N LEU D 2 " pdb=" C LEU D 2 " pdb=" CB LEU D 2 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA LEU J 2 " pdb=" N LEU J 2 " pdb=" C LEU J 2 " pdb=" CB LEU J 2 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 552 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN M 27 " -0.005 2.00e-02 2.50e+03 9.22e-03 1.27e+00 pdb=" CD GLN M 27 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN M 27 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN M 27 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN M 27 " -0.004 2.00e-02 2.50e+03 pdb="HE22 GLN M 27 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS I 26 " -0.011 2.00e-02 2.50e+03 6.19e-03 8.62e-01 pdb=" CG HIS I 26 " 0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS I 26 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS I 26 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS I 26 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS I 26 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS I 26 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS I 26 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS I 26 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 26 " -0.000 2.00e-02 2.50e+03 4.97e-03 5.57e-01 pdb=" CG HIS H 26 " 0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS H 26 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS H 26 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS H 26 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS H 26 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 HIS H 26 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS H 26 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS H 26 " 0.000 2.00e-02 2.50e+03 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.16: 338 2.16 - 2.74: 14053 2.74 - 3.33: 21028 3.33 - 3.91: 27254 3.91 - 4.50: 40963 Nonbonded interactions: 103636 Sorted by model distance: nonbonded pdb=" H LEU I 2 " pdb=" HA LEU I 2 " model vdw 1.573 1.816 nonbonded pdb=" H LEU A 2 " pdb=" HA LEU A 2 " model vdw 1.573 1.816 nonbonded pdb=" H LEU C 2 " pdb=" HA LEU C 2 " model vdw 1.574 1.816 nonbonded pdb=" H LEU D 2 " pdb=" HA LEU D 2 " model vdw 1.574 1.816 nonbonded pdb=" H LEU F 2 " pdb=" HA LEU F 2 " model vdw 1.574 1.816 ... (remaining 103631 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' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 12 through 25 or (resid 26 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 27 through 31)) selection = (chain 'C' and (resid 1 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 27 through 31)) selection = chain 'D' selection = (chain 'E' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 12 through 25 or (resid 26 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid 27 through 31)) selection = (chain 'F' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 12 through 31)) selection = (chain 'G' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 12 through 23 or (resid 24 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or r \ esid 25 through 31)) selection = chain 'H' selection = (chain 'I' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 12 through 31)) selection = (chain 'J' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 12 through 31)) selection = (chain 'K' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 12 through 23 or (resid 24 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or r \ esid 25 through 31)) selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = (chain 'O' and (resid 1 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 27 through 31)) } 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 individual isotropic 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: 2.220 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: 0.060 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.480 Find NCS groups from input model: 0.100 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 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 : 0.003 0.023 4260 Z= 0.153 Angle : 0.563 4.722 5730 Z= 0.328 Chirality : 0.071 0.360 555 Planarity : 0.002 0.011 810 Dihedral : 23.196 84.531 1575 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 23.01 % Favored : 76.99 % 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 are not related in a simple way. whole: -4.08 (0.21), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.16), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE B 23 HIS 0.009 0.001 HIS H 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 4260) covalent geometry : angle 0.56327 / 0.33 ( 5730) hydrogen bonds : bond 0.14266 / 10.99 ( 36) hydrogen bonds : angle 8.17881 / 5.94 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.228 Fit side-chains REVERT: E 27 GLN cc_start: 0.7954 (mt0) cc_final: 0.7717 (mt0) REVERT: G 27 GLN cc_start: 0.8058 (mt0) cc_final: 0.7794 (mt0) REVERT: J 27 GLN cc_start: 0.8033 (mt0) cc_final: 0.7676 (mt0) REVERT: K 27 GLN cc_start: 0.8015 (mt0) cc_final: 0.7616 (mt0) REVERT: L 18 LEU cc_start: 0.7885 (tp) cc_final: 0.7663 (tp) REVERT: L 29 GLN cc_start: 0.7875 (tt0) cc_final: 0.7491 (tt0) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0984 time to fit residues: 2.3671 Evaluate side-chains 15 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 GLN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 GLN L 13 GLN M 13 GLN M 25 GLN N 25 GLN O 25 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5940 r_free = 0.5940 target = 0.495269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 138)---------------| | r_work = 0.6035 r_free = 0.6035 target = 0.422119 restraints weight = 14365.437| |-----------------------------------------------------------------------------| r_work (start): 0.5694 rms_B_bonded: 0.94 r_work: 0.5505 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.5401 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.5401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4260 Z= 0.219 Angle : 0.584 4.572 5730 Z= 0.337 Chirality : 0.070 0.361 555 Planarity : 0.002 0.013 810 Dihedral : 5.988 19.363 450 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.43 % Allowed : 23.87 % Favored : 75.70 % 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 are not related in a simple way. whole: -3.85 (0.23), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.17), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.000 PHE L 23 HIS 0.006 0.001 HIS H 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 ( 4260) covalent geometry : angle 0.58357 / 0.34 ( 5730) hydrogen bonds : bond 0.02750 / 2.11 ( 36) hydrogen bonds : angle 5.47931 / 3.97 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.229 Fit side-chains REVERT: J 27 GLN cc_start: 0.7990 (mt0) cc_final: 0.7778 (mt0) REVERT: L 29 GLN cc_start: 0.7993 (tt0) cc_final: 0.7595 (tt0) outliers start: 2 outliers final: 0 residues processed: 16 average time/residue: 0.0998 time to fit residues: 2.5450 Evaluate side-chains 14 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 2 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 HIS ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5938 r_free = 0.5938 target = 0.485695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 144)---------------| | r_work = 0.6008 r_free = 0.6008 target = 0.438602 restraints weight = 14203.006| |-----------------------------------------------------------------------------| r_work (start): 0.5742 rms_B_bonded: 0.70 r_work: 0.5556 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.5465 rms_B_bonded: 1.74 restraints_weight: 0.2500 r_work (final): 0.5465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4260 Z= 0.143 Angle : 0.512 4.379 5730 Z= 0.297 Chirality : 0.068 0.347 555 Planarity : 0.001 0.009 810 Dihedral : 5.404 17.123 450 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.29 % Allowed : 22.80 % Favored : 75.91 % 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 are not related in a simple way. whole: -3.65 (0.24), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.18), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE M 23 HIS 0.005 0.001 HIS N 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 4260) covalent geometry : angle 0.51233 / 0.30 ( 5730) hydrogen bonds : bond 0.02486 / 1.92 ( 36) hydrogen bonds : angle 4.90443 / 3.49 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 12 time to evaluate : 0.237 Fit side-chains REVERT: L 29 GLN cc_start: 0.7933 (tt0) cc_final: 0.7523 (tt0) REVERT: N 27 GLN cc_start: 0.7601 (mt0) cc_final: 0.6648 (mt0) REVERT: O 29 GLN cc_start: 0.7724 (tt0) cc_final: 0.7021 (mt0) REVERT: O 30 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6670 (mp) outliers start: 6 outliers final: 3 residues processed: 17 average time/residue: 0.0952 time to fit residues: 2.6112 Evaluate side-chains 15 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 30 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 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 = 0.5956 r_free = 0.5956 target = 0.496553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 191)---------------| | r_work = 0.6059 r_free = 0.6059 target = 0.423550 restraints weight = 14462.666| |-----------------------------------------------------------------------------| r_work (start): 0.5690 rms_B_bonded: 0.92 r_work: 0.5512 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.5410 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.5410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4260 Z= 0.151 Angle : 0.513 4.438 5730 Z= 0.299 Chirality : 0.068 0.348 555 Planarity : 0.001 0.008 810 Dihedral : 5.301 16.245 450 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.66 % Allowed : 20.43 % Favored : 75.91 % 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 are not related in a simple way. whole: -3.62 (0.25), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.19), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE B 23 HIS 0.005 0.001 HIS N 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 4260) covalent geometry : angle 0.51340 / 0.30 ( 5730) hydrogen bonds : bond 0.02014 / 1.52 ( 36) hydrogen bonds : angle 4.58691 / 3.25 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 13 time to evaluate : 0.229 Fit side-chains REVERT: J 27 GLN cc_start: 0.8117 (mt0) cc_final: 0.7890 (mt0) REVERT: L 29 GLN cc_start: 0.7943 (tt0) cc_final: 0.7553 (tt0) REVERT: M 30 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6871 (mp) REVERT: N 27 GLN cc_start: 0.7803 (mt0) cc_final: 0.6751 (mt0) REVERT: O 29 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.6955 (mt0) REVERT: O 30 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6597 (mp) outliers start: 17 outliers final: 5 residues processed: 28 average time/residue: 0.0895 time to fit residues: 3.8702 Evaluate side-chains 21 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 13 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain O residue 30 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 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 = 0.5949 r_free = 0.5949 target = 0.495339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.6051 r_free = 0.6051 target = 0.422167 restraints weight = 14213.705| |-----------------------------------------------------------------------------| r_work (start): 0.5667 rms_B_bonded: 0.93 r_work: 0.5484 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.5391 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.5391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4260 Z= 0.159 Angle : 0.518 4.455 5730 Z= 0.301 Chirality : 0.068 0.348 555 Planarity : 0.001 0.006 810 Dihedral : 5.318 15.853 450 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.66 % Allowed : 20.00 % Favored : 76.34 % 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 are not related in a simple way. whole: -3.64 (0.26), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.20), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE M 23 HIS 0.006 0.001 HIS O 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 4260) covalent geometry : angle 0.51779 / 0.30 ( 5730) hydrogen bonds : bond 0.02086 / 1.55 ( 36) hydrogen bonds : angle 4.44783 / 3.12 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 12 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: J 27 GLN cc_start: 0.8204 (mt0) cc_final: 0.7875 (mt0) REVERT: L 29 GLN cc_start: 0.7975 (tt0) cc_final: 0.7559 (tt0) REVERT: M 30 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6777 (mp) REVERT: O 29 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6933 (mt0) REVERT: O 30 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6707 (mp) outliers start: 17 outliers final: 13 residues processed: 27 average time/residue: 0.0760 time to fit residues: 3.3200 Evaluate side-chains 28 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 12 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 24 HIS Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain O residue 30 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 HIS ** 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 = 0.5951 r_free = 0.5951 target = 0.495525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 166)---------------| | r_work = 0.6057 r_free = 0.6057 target = 0.422504 restraints weight = 14136.389| |-----------------------------------------------------------------------------| r_work (start): 0.5665 rms_B_bonded: 0.90 r_work: 0.5494 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.5398 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.5398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4260 Z= 0.147 Angle : 0.506 4.506 5730 Z= 0.295 Chirality : 0.067 0.346 555 Planarity : 0.001 0.006 810 Dihedral : 5.198 15.461 450 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.73 % Allowed : 19.14 % Favored : 76.13 % 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 are not related in a simple way. whole: -3.65 (0.26), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.20), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE M 23 HIS 0.004 0.001 HIS O 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 4260) covalent geometry : angle 0.50597 / 0.29 ( 5730) hydrogen bonds : bond 0.01917 / 1.40 ( 36) hydrogen bonds : angle 4.38669 / 3.09 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 13 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: J 27 GLN cc_start: 0.8232 (mt0) cc_final: 0.7881 (mt0) REVERT: J 30 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6741 (mp) REVERT: L 29 GLN cc_start: 0.7754 (tt0) cc_final: 0.7415 (tt0) REVERT: M 30 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6860 (mp) REVERT: O 18 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7804 (tt) REVERT: O 29 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7027 (mt0) outliers start: 22 outliers final: 12 residues processed: 32 average time/residue: 0.0773 time to fit residues: 3.8850 Evaluate side-chains 30 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 14 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 24 HIS Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 24 HIS Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 29 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 HIS ** 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 = 0.5777 r_free = 0.5777 target = 0.246400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5401 r_free = 0.5401 target = 0.208825 restraints weight = 11815.476| |-----------------------------------------------------------------------------| r_work (start): 0.5430 rms_B_bonded: 2.99 r_work: 0.5237 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.5237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4260 Z= 0.190 Angle : 0.544 4.577 5730 Z= 0.315 Chirality : 0.068 0.351 555 Planarity : 0.002 0.007 810 Dihedral : 5.490 16.445 450 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 5.16 % Allowed : 18.92 % Favored : 75.91 % 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 are not related in a simple way. whole: -3.59 (0.27), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.21), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE M 23 HIS 0.005 0.001 HIS O 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 4260) covalent geometry : angle 0.54384 / 0.31 ( 5730) hydrogen bonds : bond 0.02163 / 1.56 ( 36) hydrogen bonds : angle 4.41382 / 3.11 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 13 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: J 27 GLN cc_start: 0.8346 (mt0) cc_final: 0.8024 (mt0) REVERT: J 30 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6709 (mp) REVERT: M 30 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6229 (mp) REVERT: O 18 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7715 (tt) REVERT: O 29 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7054 (mt0) outliers start: 24 outliers final: 15 residues processed: 34 average time/residue: 0.0759 time to fit residues: 4.0318 Evaluate side-chains 32 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 13 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 24 HIS Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain M residue 24 HIS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 24 HIS Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain O residue 30 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.0030 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 HIS ** 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 = 0.5923 r_free = 0.5923 target = 0.485131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 187)---------------| | r_work = 0.5995 r_free = 0.5995 target = 0.437910 restraints weight = 14298.562| |-----------------------------------------------------------------------------| r_work (start): 0.5724 rms_B_bonded: 0.68 r_work: 0.5561 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.5466 rms_B_bonded: 1.68 restraints_weight: 0.2500 r_work (final): 0.5466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 4260 Z= 0.122 Angle : 0.499 4.522 5730 Z= 0.292 Chirality : 0.067 0.345 555 Planarity : 0.001 0.006 810 Dihedral : 5.141 15.211 450 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 5.59 % Allowed : 18.71 % Favored : 75.70 % 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 are not related in a simple way. whole: -3.58 (0.27), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.21), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE M 23 HIS 0.004 0.001 HIS O 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4260) covalent geometry : angle 0.49893 / 0.29 ( 5730) hydrogen bonds : bond 0.01858 / 1.34 ( 36) hydrogen bonds : angle 4.31391 / 3.04 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 14 time to evaluate : 0.181 Fit side-chains REVERT: J 27 GLN cc_start: 0.8223 (mt0) cc_final: 0.7853 (mt0) REVERT: M 30 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6909 (mp) REVERT: N 27 GLN cc_start: 0.7794 (mt0) cc_final: 0.6578 (mt0) REVERT: O 18 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7952 (tt) REVERT: O 29 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7103 (mt0) outliers start: 26 outliers final: 19 residues processed: 37 average time/residue: 0.0827 time to fit residues: 4.6186 Evaluate side-chains 34 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 12 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain F residue 24 HIS Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 24 HIS Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain M residue 24 HIS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 24 HIS Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain O residue 30 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 HIS ** 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 = 0.5728 r_free = 0.5728 target = 0.232547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5331 r_free = 0.5331 target = 0.194064 restraints weight = 11943.152| |-----------------------------------------------------------------------------| r_work (start): 0.5421 rms_B_bonded: 2.95 r_work: 0.5244 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.5244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4260 Z= 0.189 Angle : 0.542 4.600 5730 Z= 0.315 Chirality : 0.068 0.352 555 Planarity : 0.002 0.007 810 Dihedral : 5.455 16.566 450 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 5.38 % Allowed : 19.14 % Favored : 75.48 % 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 are not related in a simple way. whole: -3.66 (0.27), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.21), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE M 23 HIS 0.005 0.001 HIS O 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 4260) covalent geometry : angle 0.54186 / 0.32 ( 5730) hydrogen bonds : bond 0.02088 / 1.48 ( 36) hydrogen bonds : angle 4.35503 / 3.08 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 13 time to evaluate : 0.224 Fit side-chains REVERT: J 27 GLN cc_start: 0.8372 (mt0) cc_final: 0.8051 (mt0) REVERT: M 30 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6339 (mp) REVERT: N 27 GLN cc_start: 0.7928 (mt0) cc_final: 0.6732 (mt0) REVERT: O 18 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7626 (tt) REVERT: O 29 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7122 (mt0) outliers start: 25 outliers final: 19 residues processed: 35 average time/residue: 0.0859 time to fit residues: 4.6192 Evaluate side-chains 35 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 13 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain F residue 24 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 24 HIS Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain M residue 24 HIS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 24 HIS Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 24 HIS Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain O residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 HIS ** 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 = 0.5915 r_free = 0.5915 target = 0.484515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 166)---------------| | r_work = 0.5988 r_free = 0.5988 target = 0.436168 restraints weight = 14133.865| |-----------------------------------------------------------------------------| r_work (start): 0.5693 rms_B_bonded: 0.69 r_work: 0.5533 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.5441 rms_B_bonded: 1.67 restraints_weight: 0.2500 r_work (final): 0.5441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4260 Z= 0.147 Angle : 0.513 4.561 5730 Z= 0.300 Chirality : 0.067 0.347 555 Planarity : 0.001 0.006 810 Dihedral : 5.246 15.837 450 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.38 % Allowed : 19.35 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.27), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.21), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE M 23 HIS 0.005 0.001 HIS O 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 4260) covalent geometry : angle 0.51269 / 0.30 ( 5730) hydrogen bonds : bond 0.01930 / 1.37 ( 36) hydrogen bonds : angle 4.32410 / 3.06 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 12 time to evaluate : 0.225 Fit side-chains REVERT: J 27 GLN cc_start: 0.8255 (mt0) cc_final: 0.7924 (mt0) REVERT: M 30 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6409 (mp) REVERT: N 27 GLN cc_start: 0.7862 (mt0) cc_final: 0.6670 (mt0) REVERT: O 18 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7894 (tt) REVERT: O 29 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7128 (mt0) outliers start: 25 outliers final: 19 residues processed: 35 average time/residue: 0.0858 time to fit residues: 4.6485 Evaluate side-chains 34 residues out of total 465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 12 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain B residue 24 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain F residue 24 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 24 HIS Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain M residue 24 HIS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 24 HIS Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 24 HIS Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain O residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.0670 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 HIS ** 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 = 0.5872 r_free = 0.5872 target = 0.269318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5558 r_free = 0.5558 target = 0.225629 restraints weight = 12658.370| |-----------------------------------------------------------------------------| r_work (start): 0.5447 rms_B_bonded: 3.10 r_work: 0.5313 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.5313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 4260 Z= 0.123 Angle : 0.498 4.572 5730 Z= 0.293 Chirality : 0.067 0.347 555 Planarity : 0.001 0.006 810 Dihedral : 5.056 16.409 450 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.81 % Allowed : 18.92 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.28), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.21), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.000 PHE M 23 HIS 0.004 0.001 HIS O 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4260) covalent geometry : angle 0.49844 / 0.29 ( 5730) hydrogen bonds : bond 0.01812 / 1.30 ( 36) hydrogen bonds : angle 4.29806 / 3.04 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2669.06 seconds wall clock time: 45 minutes 59.16 seconds (2759.16 seconds total)