Starting phenix.real_space_refine on Wed Mar 5 16:25:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vps_21316/03_2025/6vps_21316.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vps_21316/03_2025/6vps_21316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vps_21316/03_2025/6vps_21316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vps_21316/03_2025/6vps_21316.map" model { file = "/net/cci-nas-00/data/ceres_data/6vps_21316/03_2025/6vps_21316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vps_21316/03_2025/6vps_21316.cif" } resolution = 2.6 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= 0.001 sd= 0.007 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 1611 2.51 5 N 648 2.21 5 O 477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2736 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Conformer: "B" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} bond proxies already assigned to first conformer: 256 Chain: "B" Number of atoms: 304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Conformer: "B" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} bond proxies already assigned to first conformer: 256 Chain: "C" Number of atoms: 304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Conformer: "B" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} bond proxies already assigned to first conformer: 256 Chain: "D" Number of atoms: 304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Conformer: "B" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} bond proxies already assigned to first conformer: 256 Chain: "E" Number of atoms: 304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Conformer: "B" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} bond proxies already assigned to first conformer: 256 Chain: "F" Number of atoms: 304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Conformer: "B" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} bond proxies already assigned to first conformer: 256 Chain: "G" Number of atoms: 304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Conformer: "B" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} bond proxies already assigned to first conformer: 256 Chain: "H" Number of atoms: 304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Conformer: "B" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} bond proxies already assigned to first conformer: 256 Chain: "I" Number of atoms: 304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Conformer: "B" Number of residues, atoms: 31, 280 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} bond proxies already assigned to first conformer: 256 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AHIS A 36 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 36 " occ=0.50 residue: pdb=" N AHIS B 36 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 36 " occ=0.50 residue: pdb=" N AHIS C 36 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 36 " occ=0.50 residue: pdb=" N AHIS D 36 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 36 " occ=0.50 residue: pdb=" N AHIS E 36 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 36 " occ=0.50 residue: pdb=" N AHIS F 36 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 36 " occ=0.50 residue: pdb=" N AHIS G 36 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS G 36 " occ=0.50 residue: pdb=" N AHIS H 36 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS H 36 " occ=0.50 residue: pdb=" N AHIS I 36 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS I 36 " occ=0.50 Time building chain proxies: 2.49, per 1000 atoms: 0.91 Number of scatterers: 2736 At special positions: 0 Unit cell: (86.72, 88.888, 31.436, 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 477 8.00 N 648 7.00 C 1611 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=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 461.8 milliseconds 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 612 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 67.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 24 through 38 removed outlier: 6.811A pdb=" N GLN A 37 " --> pdb=" O AHIS D 36 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN D 38 " --> pdb=" O GLN A 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 24 " --> pdb=" O HIS E 25 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 27 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN A 26 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N HIS E 29 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN A 28 " --> pdb=" O HIS E 29 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLN E 31 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN A 30 " --> pdb=" O GLN E 31 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N HIS E 33 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN A 32 " --> pdb=" O HIS E 33 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLN E 35 " --> pdb=" O GLN A 32 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN A 34 " --> pdb=" O GLN E 35 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLN E 37 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N AHIS A 36 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 44 through 51 removed outlier: 6.145A pdb=" N GLN A 44 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN D 47 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS A 46 " --> pdb=" O GLN D 47 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N GLN D 49 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS A 48 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N GLN D 51 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN A 50 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 24 through 38 removed outlier: 6.800A pdb=" N GLN B 37 " --> pdb=" O AHIS F 36 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN F 38 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 24 " --> pdb=" O HIS G 25 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLN G 27 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN B 26 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N HIS G 29 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN B 28 " --> pdb=" O HIS G 29 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLN G 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN B 30 " --> pdb=" O GLN G 31 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N HIS G 33 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN B 32 " --> pdb=" O HIS G 33 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLN G 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN B 34 " --> pdb=" O GLN G 35 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN G 37 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N AHIS B 36 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 44 through 51 removed outlier: 6.144A pdb=" N GLN B 44 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLN F 47 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS B 46 " --> pdb=" O GLN F 47 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLN F 49 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N HIS B 48 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N GLN F 51 " --> pdb=" O HIS B 48 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN B 50 " --> pdb=" O GLN F 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 38 removed outlier: 6.788A pdb=" N GLN C 37 " --> pdb=" O AHIS H 36 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN H 38 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU C 24 " --> pdb=" O HIS I 25 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLN I 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN C 26 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N HIS I 29 " --> pdb=" O GLN C 26 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLN C 28 " --> pdb=" O HIS I 29 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLN I 31 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN C 30 " --> pdb=" O GLN I 31 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N HIS I 33 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN C 32 " --> pdb=" O HIS I 33 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLN I 35 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN C 34 " --> pdb=" O GLN I 35 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN I 37 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N AHIS C 36 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 44 through 51 removed outlier: 6.122A pdb=" N GLN C 44 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN H 47 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS C 46 " --> pdb=" O GLN H 47 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N GLN H 49 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS C 48 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N GLN H 51 " --> pdb=" O HIS C 48 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN C 50 " --> pdb=" O GLN H 51 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 174 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: 0.56 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 468 1.28 - 1.35: 628 1.35 - 1.42: 299 1.42 - 1.49: 330 1.49 - 1.55: 1119 Bond restraints: 2844 Sorted by residual: bond pdb=" CE1 HIS A 48 " pdb=" NE2 HIS A 48 " ideal model delta sigma weight residual 1.321 1.351 -0.030 1.00e-02 1.00e+04 9.26e+00 bond pdb=" CE1 HIS F 48 " pdb=" NE2 HIS F 48 " ideal model delta sigma weight residual 1.321 1.351 -0.030 1.00e-02 1.00e+04 9.23e+00 bond pdb=" CE1 HIS E 48 " pdb=" NE2 HIS E 48 " ideal model delta sigma weight residual 1.321 1.351 -0.030 1.00e-02 1.00e+04 8.79e+00 bond pdb=" CE1 HIS F 39 " pdb=" NE2 HIS F 39 " ideal model delta sigma weight residual 1.321 1.350 -0.029 1.00e-02 1.00e+04 8.27e+00 bond pdb=" CE1 HIS C 48 " pdb=" NE2 HIS C 48 " ideal model delta sigma weight residual 1.321 1.350 -0.029 1.00e-02 1.00e+04 8.25e+00 ... (remaining 2839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 3356 1.45 - 2.89: 377 2.89 - 4.34: 102 4.34 - 5.78: 17 5.78 - 7.23: 9 Bond angle restraints: 3861 Sorted by residual: angle pdb=" C GLN H 31 " pdb=" CA GLN H 31 " pdb=" CB GLN H 31 " ideal model delta sigma weight residual 109.35 116.58 -7.23 1.98e+00 2.55e-01 1.33e+01 angle pdb=" C GLN C 31 " pdb=" CA GLN C 31 " pdb=" CB GLN C 31 " ideal model delta sigma weight residual 109.35 116.15 -6.80 1.98e+00 2.55e-01 1.18e+01 angle pdb=" C GLN G 31 " pdb=" CA GLN G 31 " pdb=" CB GLN G 31 " ideal model delta sigma weight residual 109.35 116.01 -6.66 1.98e+00 2.55e-01 1.13e+01 angle pdb=" C GLN F 31 " pdb=" CA GLN F 31 " pdb=" CB GLN F 31 " ideal model delta sigma weight residual 109.35 115.93 -6.58 1.98e+00 2.55e-01 1.10e+01 angle pdb=" C GLN D 31 " pdb=" CA GLN D 31 " pdb=" CB GLN D 31 " ideal model delta sigma weight residual 109.35 115.72 -6.37 1.98e+00 2.55e-01 1.03e+01 ... (remaining 3856 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.66: 1331 15.66 - 31.30: 252 31.30 - 46.94: 84 46.94 - 62.59: 41 62.59 - 78.23: 11 Dihedral angle restraints: 1719 sinusoidal: 783 harmonic: 936 Sorted by residual: dihedral pdb=" C GLN H 31 " pdb=" N GLN H 31 " pdb=" CA GLN H 31 " pdb=" CB GLN H 31 " ideal model delta harmonic sigma weight residual -122.60 -134.19 11.59 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" C GLN G 31 " pdb=" N GLN G 31 " pdb=" CA GLN G 31 " pdb=" CB GLN G 31 " ideal model delta harmonic sigma weight residual -122.60 -133.59 10.99 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" C GLN C 31 " pdb=" N GLN C 31 " pdb=" CA GLN C 31 " pdb=" CB GLN C 31 " ideal model delta harmonic sigma weight residual -122.60 -133.50 10.90 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 1716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 209 0.091 - 0.181: 94 0.181 - 0.271: 12 0.271 - 0.361: 0 0.361 - 0.452: 18 Chirality restraints: 333 Sorted by residual: chirality pdb=" CA GLN G 31 " pdb=" N GLN G 31 " pdb=" C GLN G 31 " pdb=" CB GLN G 31 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CA GLN H 31 " pdb=" N GLN H 31 " pdb=" C GLN H 31 " pdb=" CB GLN H 31 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA GLN D 27 " pdb=" N GLN D 27 " pdb=" C GLN D 27 " pdb=" CB GLN D 27 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 ... (remaining 330 not shown) Planarity restraints: 576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 45 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C LEU A 45 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU A 45 " 0.026 2.00e-02 2.50e+03 pdb=" N HIS A 46 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 45 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C LEU G 45 " 0.067 2.00e-02 2.50e+03 pdb=" O LEU G 45 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS G 46 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 45 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C LEU E 45 " -0.067 2.00e-02 2.50e+03 pdb=" O LEU E 45 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS E 46 " 0.023 2.00e-02 2.50e+03 ... (remaining 573 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1153 2.98 - 3.46: 2478 3.46 - 3.94: 5600 3.94 - 4.42: 5649 4.42 - 4.90: 10376 Nonbonded interactions: 25256 Sorted by model distance: nonbonded pdb=" CD2AHIS C 36 " pdb=" ND1AHIS H 36 " model vdw 2.501 3.340 nonbonded pdb=" CD2AHIS B 36 " pdb=" ND1AHIS F 36 " model vdw 2.538 3.340 nonbonded pdb=" CD2AHIS A 36 " pdb=" ND1AHIS D 36 " model vdw 2.565 3.340 nonbonded pdb=" ND1AHIS C 36 " pdb=" CD2AHIS I 36 " model vdw 2.591 3.340 nonbonded pdb=" OE1 GLN A 34 " pdb=" NE2 GLN E 34 " model vdw 2.599 3.120 ... (remaining 25251 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' } 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=0.50 max=1.00 mean=0.92 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.200 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.047 2844 Z= 0.788 Angle : 1.136 7.229 3861 Z= 0.683 Chirality : 0.128 0.452 333 Planarity : 0.012 0.040 576 Dihedral : 20.445 78.235 1107 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 3.27 % 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: -3.61 (0.21), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.16), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.024 0.007 HIS C 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.271 Fit side-chains REVERT: F 52 LEU cc_start: 0.9142 (mp) cc_final: 0.8853 (mt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 1.5162 time to fit residues: 34.2718 Evaluate side-chains 13 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS A ** B 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** C 29 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 27 GLN ** E 29 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 HIS ** G 29 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS A ** G 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 27 GLN ** I 29 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.115838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.093115 restraints weight = 35444.649| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.71 r_work: 0.3170 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2844 Z= 0.148 Angle : 0.435 5.490 3861 Z= 0.246 Chirality : 0.033 0.087 333 Planarity : 0.002 0.006 576 Dihedral : 4.366 11.724 324 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.65 % Allowed : 7.84 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.21), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.16), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.274 Fit side-chains REVERT: C 35 GLN cc_start: 0.8557 (tt0) cc_final: 0.8291 (tt0) REVERT: F 52 LEU cc_start: 0.9135 (mp) cc_final: 0.8779 (mt) outliers start: 2 outliers final: 0 residues processed: 36 average time/residue: 1.7822 time to fit residues: 65.4058 Evaluate side-chains 26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A A 33 HIS B ** A 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 29 HIS A B 33 HIS B ** B 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS A C 35 GLN C 36 HIS A ** D 36 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 29 HIS A E 31 GLN ** E 33 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS G 27 GLN G 29 HIS A ** G 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 HIS B H 36 HIS B I 29 HIS A I 33 HIS A I 36 HIS A ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.117531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095495 restraints weight = 32095.033| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.63 r_work: 0.3230 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2844 Z= 0.122 Angle : 0.403 5.388 3861 Z= 0.228 Chirality : 0.030 0.080 333 Planarity : 0.001 0.005 576 Dihedral : 3.619 9.906 324 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.63 % Allowed : 10.13 % Favored : 88.24 % 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: -3.70 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.16), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.278 Fit side-chains REVERT: F 52 LEU cc_start: 0.9125 (mp) cc_final: 0.8778 (mt) REVERT: H 27 GLN cc_start: 0.8537 (pt0) cc_final: 0.8285 (tt0) REVERT: H 40 GLN cc_start: 0.8980 (mp10) cc_final: 0.8644 (mp-120) outliers start: 5 outliers final: 0 residues processed: 41 average time/residue: 1.6248 time to fit residues: 67.9262 Evaluate side-chains 31 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 6.9990 chunk 23 optimal weight: 0.0030 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS ** A 33 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS ** B 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS ** C 29 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.109425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.087093 restraints weight = 37077.386| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.72 r_work: 0.3118 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2844 Z= 0.442 Angle : 0.520 5.092 3861 Z= 0.292 Chirality : 0.035 0.085 333 Planarity : 0.002 0.011 576 Dihedral : 4.278 9.401 324 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.31 % Allowed : 11.76 % Favored : 86.93 % 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: -3.83 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.16), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.281 Fit side-chains REVERT: F 52 LEU cc_start: 0.9114 (mp) cc_final: 0.8766 (mt) outliers start: 4 outliers final: 1 residues processed: 29 average time/residue: 1.4702 time to fit residues: 43.8967 Evaluate side-chains 27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A A 48 HIS B 36 HIS A B 36 HIS B ** C 29 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 HIS B E 27 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 HIS A ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 HIS B ** G 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 HIS A ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 48 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.088875 restraints weight = 37625.870| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.75 r_work: 0.3138 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2844 Z= 0.328 Angle : 0.476 4.848 3861 Z= 0.267 Chirality : 0.032 0.083 333 Planarity : 0.002 0.010 576 Dihedral : 4.132 8.911 324 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.96 % Allowed : 12.75 % Favored : 85.29 % 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: -3.87 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.15), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.299 Fit side-chains REVERT: F 52 LEU cc_start: 0.9107 (mp) cc_final: 0.8754 (mt) outliers start: 6 outliers final: 1 residues processed: 29 average time/residue: 1.4838 time to fit residues: 44.1070 Evaluate side-chains 26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 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 38 GLN C 27 GLN ** C 29 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.108616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086430 restraints weight = 32229.676| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.61 r_work: 0.3115 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 2844 Z= 0.472 Angle : 0.529 4.838 3861 Z= 0.296 Chirality : 0.035 0.085 333 Planarity : 0.002 0.011 576 Dihedral : 4.382 10.051 324 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.61 % Allowed : 11.76 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.16), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.272 Fit side-chains REVERT: F 27 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8413 (mt0) REVERT: F 52 LEU cc_start: 0.9113 (mp) cc_final: 0.8754 (mt) outliers start: 8 outliers final: 1 residues processed: 29 average time/residue: 1.5901 time to fit residues: 47.1756 Evaluate side-chains 26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 27 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN C 29 HIS A E 27 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS A ** E 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 29 HIS A I 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.089586 restraints weight = 33120.220| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.68 r_work: 0.3153 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2844 Z= 0.263 Angle : 0.452 5.033 3861 Z= 0.253 Chirality : 0.031 0.087 333 Planarity : 0.001 0.010 576 Dihedral : 4.064 10.829 324 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.63 % Allowed : 13.07 % Favored : 85.29 % 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: -3.87 (0.21), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.16), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.295 Fit side-chains REVERT: F 27 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8423 (mt0) REVERT: F 52 LEU cc_start: 0.9106 (mp) cc_final: 0.8729 (mt) outliers start: 5 outliers final: 1 residues processed: 29 average time/residue: 1.6110 time to fit residues: 47.8133 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 27 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 HIS E 27 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.110077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087860 restraints weight = 36651.821| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.72 r_work: 0.3133 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2844 Z= 0.319 Angle : 0.478 5.296 3861 Z= 0.266 Chirality : 0.032 0.089 333 Planarity : 0.002 0.009 576 Dihedral : 4.110 10.569 324 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.31 % Allowed : 13.73 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.15), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.282 Fit side-chains REVERT: F 27 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8409 (mt0) REVERT: F 52 LEU cc_start: 0.9113 (mp) cc_final: 0.8750 (mt) outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 1.6238 time to fit residues: 46.5486 Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain H residue 35 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.1980 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 27 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS ** G 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089752 restraints weight = 32973.785| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.63 r_work: 0.3160 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2844 Z= 0.230 Angle : 0.444 4.736 3861 Z= 0.248 Chirality : 0.031 0.086 333 Planarity : 0.001 0.009 576 Dihedral : 3.960 10.890 324 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.31 % Allowed : 13.73 % Favored : 84.97 % 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: -3.88 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.15), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.275 Fit side-chains REVERT: E 37 GLN cc_start: 0.9086 (pt0) cc_final: 0.8884 (pt0) REVERT: F 27 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: F 52 LEU cc_start: 0.9107 (mp) cc_final: 0.8740 (mt) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 1.5980 time to fit residues: 45.8013 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 HIS C 25 HIS E 27 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.109458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087206 restraints weight = 36505.236| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.71 r_work: 0.3117 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2844 Z= 0.430 Angle : 0.508 4.969 3861 Z= 0.283 Chirality : 0.033 0.094 333 Planarity : 0.002 0.009 576 Dihedral : 4.185 10.439 324 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.98 % Allowed : 14.05 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.15), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 612 Ramachandran restraints generated. 306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.270 Fit side-chains REVERT: F 27 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8429 (mt0) REVERT: F 52 LEU cc_start: 0.9118 (mp) cc_final: 0.8758 (mt) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 1.4484 time to fit residues: 41.5870 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 27 GLN E 27 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.109973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.087726 restraints weight = 34485.405| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.69 r_work: 0.3129 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2844 Z= 0.358 Angle : 0.485 5.024 3861 Z= 0.271 Chirality : 0.032 0.095 333 Planarity : 0.002 0.009 576 Dihedral : 4.174 10.570 324 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.63 % Allowed : 13.73 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.15), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.63 seconds wall clock time: 40 minutes 34.83 seconds (2434.83 seconds total)