Starting phenix.real_space_refine on Wed Jul 23 18:54:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az3_15731/07_2025/8az3_15731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az3_15731/07_2025/8az3_15731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8az3_15731/07_2025/8az3_15731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az3_15731/07_2025/8az3_15731.map" model { file = "/net/cci-nas-00/data/ceres_data/8az3_15731/07_2025/8az3_15731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az3_15731/07_2025/8az3_15731.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 3 Type Number sf(0) Gaussians C 2500 2.51 5 N 760 2.21 5 O 780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4040 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, E, F, I, J, M, N, Q, R, D, G, H, K, L, O, P, S, T Time building chain proxies: 2.15, per 1000 atoms: 0.53 Number of scatterers: 4040 At special positions: 0 Unit cell: (91.56, 101.64, 42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 780 8.00 N 760 7.00 C 2500 6.00 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 418.5 milliseconds 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 23 removed outlier: 6.351A pdb=" N ASN A 22 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN E 22 " --> pdb=" O PHE I 23 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN I 22 " --> pdb=" O PHE M 23 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN M 22 " --> pdb=" O PHE Q 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32 removed outlier: 8.593A pdb=" N THR A 30 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR E 30 " --> pdb=" O ASN I 31 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR I 30 " --> pdb=" O ASN M 31 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N THR M 30 " --> pdb=" O ASN Q 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 19 removed outlier: 6.625A pdb=" N ALA F 13 " --> pdb=" O ASN J 14 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU J 16 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE F 15 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N HIS J 18 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL F 17 " --> pdb=" O HIS J 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 22 through 23 removed outlier: 6.569A pdb=" N ASN B 22 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN F 22 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN J 22 " --> pdb=" O PHE N 23 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN N 22 " --> pdb=" O PHE R 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 32 removed outlier: 8.603A pdb=" N THR B 30 " --> pdb=" O ASN F 31 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR F 30 " --> pdb=" O ASN J 31 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR J 30 " --> pdb=" O ASN N 31 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR N 30 " --> pdb=" O ASN R 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AB2, first strand: chain 'C' and resid 12 through 18 removed outlier: 6.424A pdb=" N LEU C 12 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE G 15 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN C 14 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL G 17 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 16 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU G 12 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE K 15 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN G 14 " --> pdb=" O PHE K 15 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL K 17 " --> pdb=" O ASN G 14 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU G 16 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU K 12 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE O 15 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN K 14 " --> pdb=" O PHE O 15 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL O 17 " --> pdb=" O ASN K 14 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU K 16 " --> pdb=" O VAL O 17 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU O 12 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE S 15 " --> pdb=" O LEU O 12 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN O 14 " --> pdb=" O PHE S 15 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL S 17 " --> pdb=" O ASN O 14 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU O 16 " --> pdb=" O VAL S 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 26 through 32 removed outlier: 6.403A pdb=" N ILE C 26 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N SER G 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER C 28 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN G 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR C 30 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE G 26 " --> pdb=" O LEU K 27 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER K 29 " --> pdb=" O ILE G 26 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER G 28 " --> pdb=" O SER K 29 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ASN K 31 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR G 30 " --> pdb=" O ASN K 31 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE O 26 " --> pdb=" O LEU S 27 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N SER S 29 " --> pdb=" O ILE O 26 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER O 28 " --> pdb=" O SER S 29 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN S 31 " --> pdb=" O SER O 28 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR O 30 " --> pdb=" O ASN S 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 36 removed outlier: 6.145A pdb=" N ASN C 35 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASN G 35 " --> pdb=" O THR K 36 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN K 35 " --> pdb=" O THR O 36 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN O 35 " --> pdb=" O THR S 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 12 through 18 removed outlier: 6.438A pdb=" N LEU D 12 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE H 15 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN D 14 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL H 17 " --> pdb=" O ASN D 14 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 16 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU H 12 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE L 15 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN H 14 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL L 17 " --> pdb=" O ASN H 14 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU H 16 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU L 12 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE P 15 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN L 14 " --> pdb=" O PHE P 15 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL P 17 " --> pdb=" O ASN L 14 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU L 16 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU P 12 " --> pdb=" O ALA T 13 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE T 15 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN P 14 " --> pdb=" O PHE T 15 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL T 17 " --> pdb=" O ASN P 14 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU P 16 " --> pdb=" O VAL T 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 26 through 32 removed outlier: 6.392A pdb=" N ILE D 26 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N SER H 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER D 28 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASN H 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR D 30 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE H 26 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N SER L 29 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER H 28 " --> pdb=" O SER L 29 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASN L 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR H 30 " --> pdb=" O ASN L 31 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE L 26 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N SER P 29 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER L 28 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN P 31 " --> pdb=" O SER L 28 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR L 30 " --> pdb=" O ASN P 31 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE P 26 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N SER T 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER P 28 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN T 31 " --> pdb=" O SER P 28 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR P 30 " --> pdb=" O ASN T 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.159A pdb=" N ASN D 35 " --> pdb=" O THR H 36 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASN H 35 " --> pdb=" O THR L 36 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN L 35 " --> pdb=" O THR P 36 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASN P 35 " --> pdb=" O THR T 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 71 hydrogen bonds defined for protein. 213 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: 1.12 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 640 1.29 - 1.36: 740 1.36 - 1.42: 500 1.42 - 1.48: 540 1.48 - 1.55: 1660 Bond restraints: 4080 Sorted by residual: bond pdb=" N VAL O 32 " pdb=" CA VAL O 32 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.29e-02 6.01e+03 7.08e+00 bond pdb=" N VAL L 32 " pdb=" CA VAL L 32 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.29e-02 6.01e+03 7.07e+00 bond pdb=" N VAL D 32 " pdb=" CA VAL D 32 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 7.05e+00 bond pdb=" N VAL C 32 " pdb=" CA VAL C 32 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 6.96e+00 bond pdb=" N VAL K 32 " pdb=" CA VAL K 32 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 6.92e+00 ... (remaining 4075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.63: 4307 0.63 - 1.25: 793 1.25 - 1.88: 243 1.88 - 2.51: 114 2.51 - 3.14: 63 Bond angle restraints: 5520 Sorted by residual: angle pdb=" CA ASN K 31 " pdb=" C ASN K 31 " pdb=" O ASN K 31 " ideal model delta sigma weight residual 120.33 117.66 2.67 1.08e+00 8.57e-01 6.12e+00 angle pdb=" CA ASN G 31 " pdb=" C ASN G 31 " pdb=" O ASN G 31 " ideal model delta sigma weight residual 120.33 117.73 2.60 1.08e+00 8.57e-01 5.81e+00 angle pdb=" CA ASN C 31 " pdb=" C ASN C 31 " pdb=" O ASN C 31 " ideal model delta sigma weight residual 120.33 117.73 2.60 1.08e+00 8.57e-01 5.81e+00 angle pdb=" CA ASN O 31 " pdb=" C ASN O 31 " pdb=" O ASN O 31 " ideal model delta sigma weight residual 120.33 117.73 2.60 1.08e+00 8.57e-01 5.80e+00 angle pdb=" CA ILE O 26 " pdb=" C ILE O 26 " pdb=" O ILE O 26 " ideal model delta sigma weight residual 120.48 117.84 2.64 1.10e+00 8.26e-01 5.78e+00 ... (remaining 5515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.53: 1970 8.53 - 17.07: 183 17.07 - 25.60: 77 25.60 - 34.14: 40 34.14 - 42.67: 10 Dihedral angle restraints: 2280 sinusoidal: 780 harmonic: 1500 Sorted by residual: dihedral pdb=" N HIS F 18 " pdb=" CA HIS F 18 " pdb=" CB HIS F 18 " pdb=" CG HIS F 18 " ideal model delta sinusoidal sigma weight residual -60.00 -89.44 29.44 3 1.50e+01 4.44e-03 4.60e+00 dihedral pdb=" N HIS N 18 " pdb=" CA HIS N 18 " pdb=" CB HIS N 18 " pdb=" CG HIS N 18 " ideal model delta sinusoidal sigma weight residual -60.00 -89.43 29.43 3 1.50e+01 4.44e-03 4.60e+00 dihedral pdb=" N HIS I 18 " pdb=" CA HIS I 18 " pdb=" CB HIS I 18 " pdb=" CG HIS I 18 " ideal model delta sinusoidal sigma weight residual -60.00 -89.43 29.43 3 1.50e+01 4.44e-03 4.60e+00 ... (remaining 2277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 467 0.049 - 0.098: 96 0.098 - 0.147: 57 0.147 - 0.196: 10 0.196 - 0.245: 10 Chirality restraints: 640 Sorted by residual: chirality pdb=" CA ILE P 26 " pdb=" N ILE P 26 " pdb=" C ILE P 26 " pdb=" CB ILE P 26 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ILE K 26 " pdb=" N ILE K 26 " pdb=" C ILE K 26 " pdb=" CB ILE K 26 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE D 26 " pdb=" N ILE D 26 " pdb=" C ILE D 26 " pdb=" CB ILE D 26 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 637 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR L 30 " 0.004 2.00e-02 2.50e+03 8.87e-03 7.88e-01 pdb=" C THR L 30 " -0.015 2.00e-02 2.50e+03 pdb=" O THR L 30 " 0.006 2.00e-02 2.50e+03 pdb=" N ASN L 31 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR O 30 " -0.004 2.00e-02 2.50e+03 8.82e-03 7.78e-01 pdb=" C THR O 30 " 0.015 2.00e-02 2.50e+03 pdb=" O THR O 30 " -0.006 2.00e-02 2.50e+03 pdb=" N ASN O 31 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 30 " 0.004 2.00e-02 2.50e+03 8.71e-03 7.59e-01 pdb=" C THR P 30 " -0.015 2.00e-02 2.50e+03 pdb=" O THR P 30 " 0.006 2.00e-02 2.50e+03 pdb=" N ASN P 31 " 0.005 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2107 2.99 - 3.47: 3556 3.47 - 3.94: 7022 3.94 - 4.42: 7831 4.42 - 4.90: 13831 Nonbonded interactions: 34347 Sorted by model distance: nonbonded pdb=" O LEU K 12 " pdb=" N ALA O 13 " model vdw 2.509 3.120 nonbonded pdb=" N LEU K 12 " pdb=" O ARG O 11 " model vdw 2.530 3.120 nonbonded pdb=" N ASN K 14 " pdb=" O ALA O 13 " model vdw 2.576 3.120 nonbonded pdb=" O ASN K 14 " pdb=" N PHE O 15 " model vdw 2.610 3.120 nonbonded pdb=" O VAL K 32 " pdb=" N GLY O 33 " model vdw 2.612 3.120 ... (remaining 34342 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' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 2.170 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.270 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.009 0.102 4100 Z= 0.796 Angle : 0.658 3.136 5520 Z= 0.461 Chirality : 0.060 0.245 640 Planarity : 0.002 0.009 720 Dihedral : 9.595 42.670 1320 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.88 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 18 PHE 0.003 0.001 PHE F 23 TYR 0.008 0.001 TYR O 37 ARG 0.001 0.000 ARG R 11 Details of bonding type rmsd hydrogen bonds : bond 0.13212 ( 71) hydrogen bonds : angle 9.17776 ( 213) covalent geometry : bond 0.00518 ( 4080) covalent geometry : angle 0.65817 ( 5520) Misc. bond : bond 0.10133 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.403 Fit side-chains REVERT: J 31 ASN cc_start: 0.8531 (t0) cc_final: 0.8278 (t0) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0834 time to fit residues: 6.5144 Evaluate side-chains 50 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN H 35 ASN I 14 ASN I 22 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN L 35 ASN M 14 ASN M 22 ASN ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN N 22 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN P 35 ASN Q 14 ASN Q 22 ASN R 22 ASN S 35 ASN T 35 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.132110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.085017 restraints weight = 4185.033| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.42 r_work: 0.3262 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4100 Z= 0.216 Angle : 0.490 5.417 5520 Z= 0.272 Chirality : 0.045 0.145 640 Planarity : 0.002 0.010 720 Dihedral : 5.264 17.499 560 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: -3.36 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS N 18 PHE 0.011 0.002 PHE M 15 TYR 0.012 0.002 TYR F 37 ARG 0.001 0.000 ARG A 11 Details of bonding type rmsd hydrogen bonds : bond 0.02267 ( 71) hydrogen bonds : angle 5.32380 ( 213) covalent geometry : bond 0.00465 ( 4080) covalent geometry : angle 0.48998 ( 5520) Misc. bond : bond 0.00096 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.412 Fit side-chains REVERT: T 23 PHE cc_start: 0.7896 (m-80) cc_final: 0.7582 (m-80) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0925 time to fit residues: 5.1822 Evaluate side-chains 35 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.0980 chunk 4 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.129262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.081067 restraints weight = 4249.730| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.52 r_work: 0.3226 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 4100 Z= 0.303 Angle : 0.520 2.973 5520 Z= 0.298 Chirality : 0.046 0.126 640 Planarity : 0.003 0.011 720 Dihedral : 5.879 21.882 560 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.68 % Allowed : 5.68 % Favored : 93.64 % 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: -3.69 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS N 18 PHE 0.011 0.002 PHE N 23 TYR 0.013 0.003 TYR J 37 ARG 0.001 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 71) hydrogen bonds : angle 4.58731 ( 213) covalent geometry : bond 0.00660 ( 4080) covalent geometry : angle 0.52046 ( 5520) Misc. bond : bond 0.00130 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.408 Fit side-chains REVERT: G 37 TYR cc_start: 0.8149 (p90) cc_final: 0.7642 (p90) REVERT: O 37 TYR cc_start: 0.8013 (p90) cc_final: 0.7652 (p90) REVERT: S 18 HIS cc_start: 0.7781 (t-170) cc_final: 0.7546 (t-90) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.0934 time to fit residues: 6.8188 Evaluate side-chains 50 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain R residue 29 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 18 HIS ** 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 = 0.3956 r_free = 0.3956 target = 0.132453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083648 restraints weight = 4259.316| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.55 r_work: 0.3257 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4100 Z= 0.182 Angle : 0.455 3.236 5520 Z= 0.256 Chirality : 0.044 0.128 640 Planarity : 0.002 0.007 720 Dihedral : 5.160 19.452 560 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.45 % Allowed : 7.50 % Favored : 92.05 % 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: -3.89 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS Q 18 PHE 0.009 0.001 PHE H 15 TYR 0.016 0.002 TYR R 37 ARG 0.001 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.02137 ( 71) hydrogen bonds : angle 4.37628 ( 213) covalent geometry : bond 0.00394 ( 4080) covalent geometry : angle 0.45523 ( 5520) Misc. bond : bond 0.00081 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.451 Fit side-chains REVERT: G 37 TYR cc_start: 0.8002 (p90) cc_final: 0.7438 (p90) REVERT: H 37 TYR cc_start: 0.7787 (p90) cc_final: 0.7415 (p90) REVERT: K 37 TYR cc_start: 0.7593 (p90) cc_final: 0.7302 (p90) REVERT: L 37 TYR cc_start: 0.7752 (p90) cc_final: 0.7422 (p90) REVERT: O 37 TYR cc_start: 0.7963 (p90) cc_final: 0.7611 (p90) REVERT: P 37 TYR cc_start: 0.7893 (p90) cc_final: 0.7464 (p90) REVERT: T 23 PHE cc_start: 0.7877 (m-80) cc_final: 0.7483 (m-80) outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 0.0951 time to fit residues: 7.2553 Evaluate side-chains 53 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain R residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 30 optimal weight: 40.0000 chunk 32 optimal weight: 0.1980 chunk 24 optimal weight: 7.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** 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 = 0.3921 r_free = 0.3921 target = 0.129586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.081817 restraints weight = 4614.458| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.56 r_work: 0.3233 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 4100 Z= 0.315 Angle : 0.530 3.249 5520 Z= 0.301 Chirality : 0.046 0.124 640 Planarity : 0.003 0.010 720 Dihedral : 5.742 21.927 560 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.68 % Allowed : 9.09 % Favored : 90.23 % 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: -4.26 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS Q 18 PHE 0.012 0.002 PHE L 15 TYR 0.018 0.003 TYR R 37 ARG 0.002 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 71) hydrogen bonds : angle 4.43498 ( 213) covalent geometry : bond 0.00681 ( 4080) covalent geometry : angle 0.52956 ( 5520) Misc. bond : bond 0.00143 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.441 Fit side-chains REVERT: G 23 PHE cc_start: 0.8050 (m-80) cc_final: 0.7737 (m-80) REVERT: H 37 TYR cc_start: 0.7755 (p90) cc_final: 0.7438 (p90) REVERT: P 37 TYR cc_start: 0.7980 (p90) cc_final: 0.7693 (p90) REVERT: T 23 PHE cc_start: 0.7975 (m-80) cc_final: 0.7580 (m-80) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.0921 time to fit residues: 8.1537 Evaluate side-chains 59 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain R residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.132620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082834 restraints weight = 4638.345| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.66 r_work: 0.3233 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4100 Z= 0.295 Angle : 0.523 3.277 5520 Z= 0.295 Chirality : 0.046 0.123 640 Planarity : 0.003 0.010 720 Dihedral : 5.579 21.598 560 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.36 % Allowed : 9.77 % Favored : 88.86 % 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: -4.38 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS Q 18 PHE 0.009 0.002 PHE N 23 TYR 0.023 0.003 TYR O 37 ARG 0.001 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 71) hydrogen bonds : angle 4.37567 ( 213) covalent geometry : bond 0.00638 ( 4080) covalent geometry : angle 0.52306 ( 5520) Misc. bond : bond 0.00146 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.433 Fit side-chains REVERT: G 23 PHE cc_start: 0.8038 (m-80) cc_final: 0.7757 (m-80) REVERT: G 37 TYR cc_start: 0.8062 (p90) cc_final: 0.7825 (p90) REVERT: H 37 TYR cc_start: 0.7796 (p90) cc_final: 0.7485 (p90) REVERT: T 23 PHE cc_start: 0.7989 (m-80) cc_final: 0.7585 (m-80) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.0922 time to fit residues: 8.0763 Evaluate side-chains 57 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain N residue 29 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.132557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.082669 restraints weight = 4457.499| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.62 r_work: 0.3247 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 4100 Z= 0.306 Angle : 0.538 3.339 5520 Z= 0.302 Chirality : 0.046 0.123 640 Planarity : 0.003 0.015 720 Dihedral : 5.580 21.622 560 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.59 % Allowed : 10.45 % Favored : 87.95 % 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: -4.41 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS Q 18 PHE 0.009 0.002 PHE B 23 TYR 0.035 0.004 TYR O 37 ARG 0.002 0.000 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 71) hydrogen bonds : angle 4.40933 ( 213) covalent geometry : bond 0.00665 ( 4080) covalent geometry : angle 0.53845 ( 5520) Misc. bond : bond 0.00156 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.488 Fit side-chains REVERT: D 37 TYR cc_start: 0.7795 (p90) cc_final: 0.7340 (p90) REVERT: F 28 SER cc_start: 0.8774 (m) cc_final: 0.8542 (m) REVERT: G 23 PHE cc_start: 0.8067 (m-80) cc_final: 0.7804 (m-80) REVERT: K 37 TYR cc_start: 0.7700 (p90) cc_final: 0.7416 (p90) REVERT: T 23 PHE cc_start: 0.8008 (m-80) cc_final: 0.7619 (m-80) outliers start: 7 outliers final: 7 residues processed: 54 average time/residue: 0.1129 time to fit residues: 9.2078 Evaluate side-chains 59 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain R residue 28 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.136105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.086617 restraints weight = 4236.633| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.59 r_work: 0.3320 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4100 Z= 0.135 Angle : 0.449 3.609 5520 Z= 0.249 Chirality : 0.044 0.127 640 Planarity : 0.002 0.012 720 Dihedral : 4.836 18.894 560 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.91 % Allowed : 11.14 % Favored : 87.95 % 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: -4.38 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS Q 18 PHE 0.009 0.001 PHE P 23 TYR 0.029 0.003 TYR L 37 ARG 0.001 0.000 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.01842 ( 71) hydrogen bonds : angle 4.31259 ( 213) covalent geometry : bond 0.00292 ( 4080) covalent geometry : angle 0.44938 ( 5520) Misc. bond : bond 0.00070 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.444 Fit side-chains REVERT: D 37 TYR cc_start: 0.7652 (p90) cc_final: 0.7207 (p90) REVERT: K 37 TYR cc_start: 0.7689 (p90) cc_final: 0.7426 (p90) REVERT: T 23 PHE cc_start: 0.7988 (m-80) cc_final: 0.7610 (m-80) outliers start: 4 outliers final: 4 residues processed: 55 average time/residue: 0.0924 time to fit residues: 7.5241 Evaluate side-chains 59 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain R residue 28 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.130984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080913 restraints weight = 4478.589| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.62 r_work: 0.3229 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.053 4100 Z= 0.462 Angle : 0.646 3.608 5520 Z= 0.366 Chirality : 0.049 0.117 640 Planarity : 0.004 0.023 720 Dihedral : 6.029 22.749 560 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.36 % Allowed : 11.59 % Favored : 87.05 % 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: -4.56 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS B 18 PHE 0.015 0.002 PHE P 15 TYR 0.053 0.005 TYR O 37 ARG 0.003 0.001 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 71) hydrogen bonds : angle 4.57492 ( 213) covalent geometry : bond 0.01000 ( 4080) covalent geometry : angle 0.64618 ( 5520) Misc. bond : bond 0.00257 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.543 Fit side-chains REVERT: C 37 TYR cc_start: 0.7662 (p90) cc_final: 0.7289 (p90) REVERT: D 37 TYR cc_start: 0.7887 (p90) cc_final: 0.7528 (p90) REVERT: G 23 PHE cc_start: 0.8126 (m-80) cc_final: 0.7871 (m-80) REVERT: K 37 TYR cc_start: 0.7779 (p90) cc_final: 0.7533 (p90) REVERT: T 23 PHE cc_start: 0.8076 (m-80) cc_final: 0.7696 (m-80) outliers start: 6 outliers final: 6 residues processed: 55 average time/residue: 0.1082 time to fit residues: 8.9118 Evaluate side-chains 60 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain R residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.135208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085196 restraints weight = 4373.030| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.63 r_work: 0.3298 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4100 Z= 0.185 Angle : 0.485 3.400 5520 Z= 0.269 Chirality : 0.044 0.126 640 Planarity : 0.002 0.016 720 Dihedral : 5.106 19.411 560 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.36 % Allowed : 11.14 % 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: -4.57 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS Q 18 PHE 0.013 0.001 PHE P 15 TYR 0.038 0.003 TYR L 37 ARG 0.001 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.02327 ( 71) hydrogen bonds : angle 4.33554 ( 213) covalent geometry : bond 0.00402 ( 4080) covalent geometry : angle 0.48479 ( 5520) Misc. bond : bond 0.00101 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.404 Fit side-chains REVERT: D 37 TYR cc_start: 0.7827 (p90) cc_final: 0.7445 (p90) REVERT: G 23 PHE cc_start: 0.8002 (m-80) cc_final: 0.7723 (m-80) REVERT: K 37 TYR cc_start: 0.7701 (p90) cc_final: 0.7458 (p90) REVERT: T 23 PHE cc_start: 0.7974 (m-80) cc_final: 0.7550 (m-80) outliers start: 6 outliers final: 6 residues processed: 55 average time/residue: 0.0956 time to fit residues: 7.8820 Evaluate side-chains 58 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain R residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 30.0000 chunk 35 optimal weight: 0.0020 chunk 13 optimal weight: 10.0000 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.134806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.084881 restraints weight = 4338.712| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.64 r_work: 0.3298 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4100 Z= 0.188 Angle : 0.475 3.337 5520 Z= 0.265 Chirality : 0.044 0.124 640 Planarity : 0.002 0.016 720 Dihedral : 5.009 19.836 560 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.36 % Allowed : 10.91 % Favored : 87.73 % 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: -4.57 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 18 PHE 0.012 0.001 PHE P 15 TYR 0.038 0.003 TYR L 37 ARG 0.001 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.02329 ( 71) hydrogen bonds : angle 4.32252 ( 213) covalent geometry : bond 0.00410 ( 4080) covalent geometry : angle 0.47537 ( 5520) Misc. bond : bond 0.00107 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.00 seconds wall clock time: 40 minutes 48.74 seconds (2448.74 seconds total)