Starting phenix.real_space_refine on Tue Feb 11 04:16:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az3_15731/02_2025/8az3_15731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az3_15731/02_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_15731/02_2025/8az3_15731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az3_15731/02_2025/8az3_15731.map" model { file = "/net/cci-nas-00/data/ceres_data/8az3_15731/02_2025/8az3_15731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az3_15731/02_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 1.94, per 1000 atoms: 0.48 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: 0.98 Conformation dependent library (CDL) restraints added in 483.0 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: 0.77 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: 0.98 Time building geometry restraints manager: 1.12 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.850 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- 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 : 0.005 0.037 4080 Z= 0.370 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 *********************** 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 : 0.397 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: 0.0880 time to fit residues: 6.7987 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 : 0.426 ------------------------------------------------------------------------------- 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: 6.9990 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: 9.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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** D 35 ASN 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 18 HIS ** 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 ASN ** 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 22 ASN ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 ASN S 35 ASN T 35 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.128954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081219 restraints weight = 4245.914| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.47 r_work: 0.3228 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 4080 Z= 0.465 Angle : 0.547 4.568 5520 Z= 0.308 Chirality : 0.048 0.143 640 Planarity : 0.003 0.013 720 Dihedral : 5.779 20.404 560 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.23 % Allowed : 3.64 % Favored : 96.14 % 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: -3.60 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS N 18 PHE 0.015 0.002 PHE B 15 TYR 0.011 0.003 TYR F 37 ARG 0.001 0.000 ARG B 11 *********************** 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 44 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.452 Fit side-chains REVERT: C 37 TYR cc_start: 0.8040 (p90) cc_final: 0.7687 (p90) REVERT: G 23 PHE cc_start: 0.7912 (m-80) cc_final: 0.7517 (m-80) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.0977 time to fit residues: 6.4849 Evaluate side-chains 42 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.128726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081747 restraints weight = 4296.320| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.43 r_work: 0.3219 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 4080 Z= 0.487 Angle : 0.548 3.100 5520 Z= 0.311 Chirality : 0.046 0.124 640 Planarity : 0.003 0.012 720 Dihedral : 6.077 22.215 560 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.36 % Allowed : 6.36 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.98 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS N 18 PHE 0.011 0.002 PHE A 23 TYR 0.011 0.003 TYR F 37 ARG 0.001 0.000 ARG B 11 *********************** 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 54 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.410 Fit side-chains REVERT: G 37 TYR cc_start: 0.8114 (p90) cc_final: 0.7593 (p90) REVERT: H 37 TYR cc_start: 0.7962 (p90) cc_final: 0.7565 (p90) REVERT: K 37 TYR cc_start: 0.7796 (p90) cc_final: 0.7455 (p90) REVERT: L 37 TYR cc_start: 0.7820 (p90) cc_final: 0.7508 (p90) REVERT: O 37 TYR cc_start: 0.8017 (p90) cc_final: 0.7662 (p90) REVERT: P 37 TYR cc_start: 0.7963 (p90) cc_final: 0.7571 (p90) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.0923 time to fit residues: 6.7805 Evaluate side-chains 53 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 12 optimal weight: 40.0000 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.134856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.086497 restraints weight = 4251.877| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.52 r_work: 0.3318 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4080 Z= 0.171 Angle : 0.432 3.405 5520 Z= 0.240 Chirality : 0.044 0.129 640 Planarity : 0.001 0.005 720 Dihedral : 4.906 18.066 560 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.91 % Allowed : 8.18 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.04 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 18 PHE 0.009 0.001 PHE T 23 TYR 0.012 0.002 TYR R 37 ARG 0.001 0.000 ARG F 11 *********************** 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 54 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.409 Fit side-chains REVERT: G 37 TYR cc_start: 0.7993 (p90) cc_final: 0.7420 (p90) REVERT: H 37 TYR cc_start: 0.7789 (p90) cc_final: 0.7396 (p90) REVERT: K 37 TYR cc_start: 0.7694 (p90) cc_final: 0.7303 (p90) REVERT: L 37 TYR cc_start: 0.7717 (p90) cc_final: 0.7369 (p90) REVERT: O 37 TYR cc_start: 0.7956 (p90) cc_final: 0.7588 (p90) REVERT: P 37 TYR cc_start: 0.7857 (p90) cc_final: 0.7431 (p90) REVERT: T 23 PHE cc_start: 0.7876 (m-80) cc_final: 0.7500 (m-80) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.0909 time to fit residues: 6.7917 Evaluate side-chains 53 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain Q 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: 8.9990 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.131421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082263 restraints weight = 4772.010| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.64 r_work: 0.3250 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4080 Z= 0.351 Angle : 0.477 3.262 5520 Z= 0.271 Chirality : 0.044 0.124 640 Planarity : 0.002 0.008 720 Dihedral : 5.351 20.644 560 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.14 % Allowed : 7.27 % Favored : 91.59 % 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: -4.25 (0.22), 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 HIS 0.007 0.003 HIS B 18 PHE 0.009 0.002 PHE L 15 TYR 0.015 0.002 TYR R 37 ARG 0.001 0.000 ARG E 11 *********************** 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 63 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.590 Fit side-chains REVERT: G 37 TYR cc_start: 0.8063 (p90) cc_final: 0.7475 (p90) REVERT: H 37 TYR cc_start: 0.7791 (p90) cc_final: 0.7435 (p90) REVERT: K 37 TYR cc_start: 0.7658 (p90) cc_final: 0.7308 (p90) REVERT: P 37 TYR cc_start: 0.7937 (p90) cc_final: 0.7699 (p90) REVERT: S 37 TYR cc_start: 0.7752 (p90) cc_final: 0.7509 (p90) REVERT: T 23 PHE cc_start: 0.7983 (m-80) cc_final: 0.7591 (m-80) outliers start: 5 outliers final: 5 residues processed: 59 average time/residue: 0.0953 time to fit residues: 8.4541 Evaluate side-chains 60 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 Q 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: 30.0000 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.132622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083207 restraints weight = 4531.529| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.61 r_work: 0.3243 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4080 Z= 0.396 Angle : 0.505 3.223 5520 Z= 0.285 Chirality : 0.045 0.122 640 Planarity : 0.002 0.009 720 Dihedral : 5.420 20.812 560 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.82 % Allowed : 9.09 % Favored : 89.09 % 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: -4.40 (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 A 18 PHE 0.008 0.002 PHE I 23 TYR 0.015 0.003 TYR R 37 ARG 0.001 0.000 ARG F 11 *********************** 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 66 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.536 Fit side-chains REVERT: D 37 TYR cc_start: 0.7687 (p90) cc_final: 0.6952 (p90) REVERT: G 23 PHE cc_start: 0.8038 (m-80) cc_final: 0.7764 (m-80) REVERT: G 37 TYR cc_start: 0.8111 (p90) cc_final: 0.7904 (p90) REVERT: K 37 TYR cc_start: 0.7610 (p90) cc_final: 0.7259 (p90) REVERT: O 37 TYR cc_start: 0.7852 (p90) cc_final: 0.7543 (p90) REVERT: T 23 PHE cc_start: 0.7989 (m-80) cc_final: 0.7580 (m-80) outliers start: 8 outliers final: 8 residues processed: 59 average time/residue: 0.0934 time to fit residues: 8.2227 Evaluate side-chains 61 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 29 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 16 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 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: 1.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.132871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082965 restraints weight = 4490.561| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.62 r_work: 0.3248 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4080 Z= 0.416 Angle : 0.517 3.217 5520 Z= 0.291 Chirality : 0.045 0.122 640 Planarity : 0.002 0.011 720 Dihedral : 5.420 21.460 560 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.82 % Allowed : 9.09 % Favored : 89.09 % 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: -4.47 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 18 PHE 0.009 0.002 PHE L 23 TYR 0.025 0.003 TYR P 37 ARG 0.001 0.000 ARG B 11 *********************** 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 63 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.424 Fit side-chains REVERT: G 23 PHE cc_start: 0.8056 (m-80) cc_final: 0.7778 (m-80) REVERT: G 37 TYR cc_start: 0.8153 (p90) cc_final: 0.7952 (p90) REVERT: O 37 TYR cc_start: 0.7855 (p90) cc_final: 0.7627 (p90) REVERT: T 23 PHE cc_start: 0.7994 (m-80) cc_final: 0.7583 (m-80) outliers start: 8 outliers final: 8 residues processed: 56 average time/residue: 0.0950 time to fit residues: 7.8033 Evaluate side-chains 62 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q 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: 10.0000 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 18 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.135345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085963 restraints weight = 4273.762| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.58 r_work: 0.3303 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4080 Z= 0.242 Angle : 0.453 3.420 5520 Z= 0.252 Chirality : 0.044 0.126 640 Planarity : 0.002 0.012 720 Dihedral : 4.910 19.202 560 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.59 % Allowed : 9.55 % 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: -4.44 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 18 PHE 0.009 0.001 PHE L 23 TYR 0.029 0.003 TYR P 37 ARG 0.001 0.000 ARG N 11 *********************** 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 63 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.430 Fit side-chains REVERT: T 23 PHE cc_start: 0.8032 (m-80) cc_final: 0.7627 (m-80) outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.0893 time to fit residues: 7.3815 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 : 0.465 ------------------------------------------------------------------------------- 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 Q 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 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.136295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.086752 restraints weight = 4342.707| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.61 r_work: 0.3307 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4080 Z= 0.190 Angle : 0.433 3.444 5520 Z= 0.240 Chirality : 0.043 0.126 640 Planarity : 0.001 0.011 720 Dihedral : 4.663 18.342 560 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.14 % Allowed : 10.00 % 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: -4.41 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 18 PHE 0.008 0.001 PHE L 23 TYR 0.026 0.003 TYR O 37 ARG 0.001 0.000 ARG F 11 *********************** 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 59 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.439 Fit side-chains REVERT: L 37 TYR cc_start: 0.7919 (p90) cc_final: 0.7590 (p90) REVERT: T 23 PHE cc_start: 0.7995 (m-80) cc_final: 0.7642 (m-80) outliers start: 5 outliers final: 5 residues processed: 54 average time/residue: 0.0944 time to fit residues: 7.5419 Evaluate side-chains 59 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain Q 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: 10.0000 chunk 29 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 14 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 = 0.3950 r_free = 0.3950 target = 0.132401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082625 restraints weight = 4427.563| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.61 r_work: 0.3246 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4080 Z= 0.436 Angle : 0.522 4.366 5520 Z= 0.296 Chirality : 0.045 0.120 640 Planarity : 0.003 0.015 720 Dihedral : 5.354 21.369 560 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.59 % Allowed : 9.77 % Favored : 88.64 % 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: -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 HIS 0.008 0.003 HIS A 18 PHE 0.014 0.002 PHE P 15 TYR 0.034 0.004 TYR P 37 ARG 0.002 0.000 ARG F 11 ********************** 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: 7 poor density : 53 time to evaluate : 0.469 Fit side-chains REVERT: F 28 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8559 (m) REVERT: G 23 PHE cc_start: 0.8080 (m-80) cc_final: 0.7774 (m-80) REVERT: T 23 PHE cc_start: 0.8019 (m-80) cc_final: 0.7606 (m-80) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.0926 time to fit residues: 7.5372 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 : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q 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: 5.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.136176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.087023 restraints weight = 4311.792| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.60 r_work: 0.3313 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4080 Z= 0.194 Angle : 0.443 4.267 5520 Z= 0.246 Chirality : 0.043 0.126 640 Planarity : 0.001 0.010 720 Dihedral : 4.697 18.410 560 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.82 % Allowed : 9.77 % Favored : 88.41 % 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: -4.51 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 18 PHE 0.009 0.001 PHE O 23 TYR 0.024 0.002 TYR P 37 ARG 0.001 0.000 ARG N 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1984.78 seconds wall clock time: 36 minutes 6.03 seconds (2166.03 seconds total)