Starting phenix.real_space_refine on Fri Aug 22 14:23:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az3_15731/08_2025/8az3_15731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az3_15731/08_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_15731/08_2025/8az3_15731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az3_15731/08_2025/8az3_15731.map" model { file = "/net/cci-nas-00/data/ceres_data/8az3_15731/08_2025/8az3_15731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az3_15731/08_2025/8az3_15731.cif" } resolution = 3.4 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= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 0.72, per 1000 atoms: 0.18 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: 0.29 Conformation dependent library (CDL) restraints added in 126.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.18 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: 0.44 Time building geometry restraints manager: 0.39 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: 2.250 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.240 Find NCS groups from input model: 0.090 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.980 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (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 ARG 0.001 0.000 ARG R 11 TYR 0.008 0.001 TYR O 37 PHE 0.003 0.001 PHE F 23 HIS 0.002 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 4080) covalent geometry : angle 0.65817 ( 5520) hydrogen bonds : bond 0.13212 ( 71) hydrogen bonds : angle 9.17776 ( 213) 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 : 0.196 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: 0.0308 time to fit residues: 2.4960 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 : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.0370 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN 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 22 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN L 35 ASN M 22 ASN ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN P 35 ASN Q 22 ASN R 22 ASN S 35 ASN T 35 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.138797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090019 restraints weight = 4084.670| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.50 r_work: 0.3359 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4100 Z= 0.087 Angle : 0.437 5.673 5520 Z= 0.237 Chirality : 0.043 0.128 640 Planarity : 0.002 0.006 720 Dihedral : 4.538 14.298 560 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.010 0.002 TYR E 37 PHE 0.012 0.001 PHE T 23 HIS 0.005 0.002 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 4080) covalent geometry : angle 0.43730 ( 5520) hydrogen bonds : bond 0.01655 ( 71) hydrogen bonds : angle 5.51353 ( 213) Misc. bond : bond 0.00038 ( 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 45 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.128 Fit side-chains REVERT: C 37 TYR cc_start: 0.7947 (p90) cc_final: 0.7552 (p90) REVERT: J 31 ASN cc_start: 0.8539 (t0) cc_final: 0.8309 (t0) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0331 time to fit residues: 2.3730 Evaluate side-chains 42 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 14 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN E 14 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 14 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN ** 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 14 ASN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.127109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079346 restraints weight = 4385.729| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.55 r_work: 0.3203 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.042 4100 Z= 0.410 Angle : 0.596 3.497 5520 Z= 0.344 Chirality : 0.049 0.122 640 Planarity : 0.004 0.016 720 Dihedral : 6.303 24.308 560 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.82 % Allowed : 3.41 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 11 TYR 0.015 0.004 TYR R 37 PHE 0.018 0.003 PHE N 23 HIS 0.015 0.005 HIS N 18 Details of bonding type rmsd covalent geometry : bond 0.00893 ( 4080) covalent geometry : angle 0.59605 ( 5520) hydrogen bonds : bond 0.03548 ( 71) hydrogen bonds : angle 4.50368 ( 213) Misc. bond : bond 0.00183 ( 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 60 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.157 Fit side-chains REVERT: G 23 PHE cc_start: 0.7970 (m-80) cc_final: 0.7638 (m-80) REVERT: G 37 TYR cc_start: 0.8042 (p90) cc_final: 0.7598 (p90) REVERT: O 37 TYR cc_start: 0.8068 (p90) cc_final: 0.7714 (p90) REVERT: P 37 TYR cc_start: 0.8059 (p90) cc_final: 0.7670 (p90) REVERT: S 18 HIS cc_start: 0.7759 (t-170) cc_final: 0.7541 (t-90) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.0354 time to fit residues: 2.9121 Evaluate side-chains 57 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 29 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 19 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 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 14 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.132030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085363 restraints weight = 4219.930| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.43 r_work: 0.3294 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3240 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= 0.173 Angle : 0.457 3.297 5520 Z= 0.258 Chirality : 0.044 0.127 640 Planarity : 0.002 0.007 720 Dihedral : 5.214 19.515 560 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.23 % Allowed : 7.27 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.79 (0.25), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 11 TYR 0.014 0.002 TYR R 37 PHE 0.008 0.001 PHE S 23 HIS 0.006 0.003 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 4080) covalent geometry : angle 0.45675 ( 5520) hydrogen bonds : bond 0.02090 ( 71) hydrogen bonds : angle 4.35668 ( 213) Misc. bond : bond 0.00076 ( 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: 1 poor density : 52 time to evaluate : 0.123 Fit side-chains REVERT: G 37 TYR cc_start: 0.8004 (p90) cc_final: 0.7522 (p90) REVERT: H 37 TYR cc_start: 0.7932 (p90) cc_final: 0.7582 (p90) REVERT: K 37 TYR cc_start: 0.7615 (p90) cc_final: 0.7357 (p90) REVERT: L 37 TYR cc_start: 0.7850 (p90) cc_final: 0.7443 (p90) REVERT: O 37 TYR cc_start: 0.7992 (p90) cc_final: 0.7613 (p90) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.0420 time to fit residues: 3.1980 Evaluate side-chains 51 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 30.0000 chunk 36 optimal weight: 30.0000 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 14 ASN ** 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 = 0.3921 r_free = 0.3921 target = 0.129401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.080305 restraints weight = 4546.703| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.61 r_work: 0.3220 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 4100 Z= 0.421 Angle : 0.609 3.210 5520 Z= 0.347 Chirality : 0.048 0.123 640 Planarity : 0.004 0.012 720 Dihedral : 6.234 22.923 560 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.91 % Allowed : 8.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.25 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 11 TYR 0.018 0.004 TYR R 37 PHE 0.013 0.002 PHE N 23 HIS 0.012 0.004 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00911 ( 4080) covalent geometry : angle 0.60859 ( 5520) hydrogen bonds : bond 0.03901 ( 71) hydrogen bonds : angle 4.44452 ( 213) Misc. bond : bond 0.00193 ( 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 66 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.111 Fit side-chains REVERT: G 23 PHE cc_start: 0.8049 (m-80) cc_final: 0.7770 (m-80) REVERT: G 37 TYR cc_start: 0.8119 (p90) cc_final: 0.7637 (p90) REVERT: H 37 TYR cc_start: 0.7836 (p90) cc_final: 0.7574 (p90) REVERT: L 37 TYR cc_start: 0.7805 (p90) cc_final: 0.7570 (p90) REVERT: O 37 TYR cc_start: 0.8034 (p90) cc_final: 0.7714 (p90) REVERT: S 37 TYR cc_start: 0.7760 (p90) cc_final: 0.7478 (p90) REVERT: T 18 HIS cc_start: 0.7963 (t-90) cc_final: 0.7729 (t-90) REVERT: T 37 TYR cc_start: 0.7746 (p90) cc_final: 0.7511 (p90) outliers start: 4 outliers final: 4 residues processed: 63 average time/residue: 0.0318 time to fit residues: 3.0499 Evaluate side-chains 64 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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 29 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 34 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 14 ASN ** 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 = 0.3990 r_free = 0.3990 target = 0.136060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.085301 restraints weight = 5239.271| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.80 r_work: 0.3286 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4100 Z= 0.124 Angle : 0.446 3.669 5520 Z= 0.250 Chirality : 0.044 0.130 640 Planarity : 0.001 0.007 720 Dihedral : 4.883 18.370 560 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.68 % Allowed : 11.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.28 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 11 TYR 0.016 0.002 TYR K 37 PHE 0.008 0.001 PHE P 23 HIS 0.004 0.001 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4080) covalent geometry : angle 0.44633 ( 5520) hydrogen bonds : bond 0.01748 ( 71) hydrogen bonds : angle 4.31872 ( 213) Misc. bond : bond 0.00057 ( 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 62 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.099 Fit side-chains REVERT: G 37 TYR cc_start: 0.8073 (p90) cc_final: 0.7483 (p90) REVERT: P 37 TYR cc_start: 0.8118 (p90) cc_final: 0.7794 (p90) REVERT: T 23 PHE cc_start: 0.8026 (m-80) cc_final: 0.7632 (m-80) outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 0.0368 time to fit residues: 3.2741 Evaluate side-chains 57 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 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 = 0.3939 r_free = 0.3939 target = 0.131753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081859 restraints weight = 4518.259| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.63 r_work: 0.3241 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4100 Z= 0.298 Angle : 0.521 3.078 5520 Z= 0.295 Chirality : 0.045 0.123 640 Planarity : 0.003 0.011 720 Dihedral : 5.563 21.591 560 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.68 % Allowed : 11.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.40 (0.23), 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 ARG 0.002 0.000 ARG F 11 TYR 0.026 0.003 TYR O 37 PHE 0.009 0.002 PHE N 23 HIS 0.008 0.003 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00648 ( 4080) covalent geometry : angle 0.52090 ( 5520) hydrogen bonds : bond 0.03069 ( 71) hydrogen bonds : angle 4.37368 ( 213) Misc. bond : bond 0.00147 ( 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 61 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.161 Fit side-chains REVERT: C 37 TYR cc_start: 0.7701 (p90) cc_final: 0.7320 (p90) REVERT: G 23 PHE cc_start: 0.8044 (m-80) cc_final: 0.7779 (m-80) outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 0.0395 time to fit residues: 3.5785 Evaluate side-chains 56 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.133625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.083592 restraints weight = 4307.052| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.63 r_work: 0.3258 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4100 Z= 0.269 Angle : 0.514 3.124 5520 Z= 0.289 Chirality : 0.045 0.123 640 Planarity : 0.002 0.016 720 Dihedral : 5.390 20.734 560 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.14 % Allowed : 10.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.40 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 11 TYR 0.038 0.004 TYR O 37 PHE 0.008 0.001 PHE B 23 HIS 0.007 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 4080) covalent geometry : angle 0.51439 ( 5520) hydrogen bonds : bond 0.02870 ( 71) hydrogen bonds : angle 4.34139 ( 213) Misc. bond : bond 0.00142 ( 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 57 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.146 Fit side-chains REVERT: D 37 TYR cc_start: 0.7865 (p90) cc_final: 0.7450 (p90) REVERT: G 23 PHE cc_start: 0.8088 (m-80) cc_final: 0.7826 (m-80) REVERT: T 23 PHE cc_start: 0.8061 (m-80) cc_final: 0.7686 (m-80) outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 0.0384 time to fit residues: 3.1282 Evaluate side-chains 56 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 N residue 29 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 39 optimal weight: 9.9990 chunk 14 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 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 = 0.3948 r_free = 0.3948 target = 0.131894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082057 restraints weight = 4526.475| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.65 r_work: 0.3244 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 4100 Z= 0.343 Angle : 0.561 3.518 5520 Z= 0.317 Chirality : 0.046 0.121 640 Planarity : 0.003 0.017 720 Dihedral : 5.716 21.975 560 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.14 % Allowed : 10.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.50 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 11 TYR 0.040 0.004 TYR O 37 PHE 0.009 0.002 PHE I 23 HIS 0.009 0.003 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00747 ( 4080) covalent geometry : angle 0.56133 ( 5520) hydrogen bonds : bond 0.03429 ( 71) hydrogen bonds : angle 4.47660 ( 213) Misc. bond : bond 0.00186 ( 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 58 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.105 Fit side-chains REVERT: D 37 TYR cc_start: 0.7875 (p90) cc_final: 0.7470 (p90) REVERT: G 23 PHE cc_start: 0.8093 (m-80) cc_final: 0.7847 (m-80) outliers start: 5 outliers final: 5 residues processed: 54 average time/residue: 0.0357 time to fit residues: 2.9639 Evaluate side-chains 58 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 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 18 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 30.0000 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 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 = 0.3965 r_free = 0.3965 target = 0.133184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083589 restraints weight = 4355.901| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.63 r_work: 0.3281 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4100 Z= 0.222 Angle : 0.494 3.291 5520 Z= 0.276 Chirality : 0.044 0.125 640 Planarity : 0.002 0.013 720 Dihedral : 5.227 20.224 560 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.91 % Allowed : 11.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.53 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 11 TYR 0.032 0.003 TYR O 37 PHE 0.009 0.001 PHE P 23 HIS 0.006 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 4080) covalent geometry : angle 0.49380 ( 5520) hydrogen bonds : bond 0.02580 ( 71) hydrogen bonds : angle 4.37494 ( 213) Misc. bond : bond 0.00121 ( 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 56 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.110 Fit side-chains REVERT: D 37 TYR cc_start: 0.7842 (p90) cc_final: 0.7423 (p90) REVERT: G 23 PHE cc_start: 0.8092 (m-80) cc_final: 0.7844 (m-80) REVERT: L 37 TYR cc_start: 0.8119 (p90) cc_final: 0.7762 (p90) REVERT: T 23 PHE cc_start: 0.8072 (m-80) cc_final: 0.7693 (m-80) outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 0.0380 time to fit residues: 2.9874 Evaluate side-chains 56 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 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 = 0.3955 r_free = 0.3955 target = 0.132143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.082749 restraints weight = 4420.752| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.62 r_work: 0.3251 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 4100 Z= 0.304 Angle : 0.540 3.604 5520 Z= 0.303 Chirality : 0.045 0.122 640 Planarity : 0.003 0.021 720 Dihedral : 5.529 21.416 560 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.14 % Allowed : 11.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.58 (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 ARG 0.002 0.000 ARG F 11 TYR 0.051 0.004 TYR O 37 PHE 0.013 0.002 PHE D 23 HIS 0.008 0.003 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 4080) covalent geometry : angle 0.53994 ( 5520) hydrogen bonds : bond 0.03186 ( 71) hydrogen bonds : angle 4.46311 ( 213) Misc. bond : bond 0.00171 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 965.23 seconds wall clock time: 17 minutes 18.57 seconds (1038.57 seconds total)