Starting phenix.real_space_refine on Wed Sep 17 03:16:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vps_21316/09_2025/6vps_21316.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vps_21316/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vps_21316/09_2025/6vps_21316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vps_21316/09_2025/6vps_21316.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vps_21316/09_2025/6vps_21316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vps_21316/09_2025/6vps_21316.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.89, per 1000 atoms: 0.33 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: 0.21 Conformation dependent library (CDL) restraints added in 138.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.08 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: 0.35 Time building geometry restraints manager: 0.28 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: 0.01 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' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.580 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.930 ------------------------------------------------------------------------------- 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= 0.768 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 : 18.26 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (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 Details of bonding type rmsd covalent geometry : bond 0.01109 ( 2844) covalent geometry : angle 1.13579 ( 3861) hydrogen bonds : bond 0.08426 ( 60) hydrogen bonds : angle 6.88455 ( 174) *********************** 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 : 0.089 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: 0.6789 time to fit residues: 15.2922 Evaluate side-chains 14 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 33 HIS B ** 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 33 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.116064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.093416 restraints weight = 36239.779| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.71 r_work: 0.3194 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- 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 = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2844 Z= 0.096 Angle : 0.435 5.243 3861 Z= 0.246 Chirality : 0.033 0.088 333 Planarity : 0.002 0.006 576 Dihedral : 4.339 11.617 324 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.98 % Allowed : 7.84 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (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 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 2844) covalent geometry : angle 0.43485 ( 3861) hydrogen bonds : bond 0.01961 ( 60) hydrogen bonds : angle 4.47482 ( 174) *********************** 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 39 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.105 Fit side-chains REVERT: C 35 GLN cc_start: 0.8538 (tt0) cc_final: 0.8270 (tt0) REVERT: F 52 LEU cc_start: 0.9131 (mp) cc_final: 0.8774 (mt) outliers start: 3 outliers final: 0 residues processed: 38 average time/residue: 0.7136 time to fit residues: 27.6118 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN C 33 HIS A C 35 GLN ** C 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN ** D 36 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 27 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 29 HIS A ** 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** ** I 29 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS A ** I 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.088611 restraints weight = 33630.399| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.66 r_work: 0.3139 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2844 Z= 0.177 Angle : 0.461 5.286 3861 Z= 0.260 Chirality : 0.033 0.083 333 Planarity : 0.002 0.006 576 Dihedral : 4.092 9.060 324 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.61 % Allowed : 9.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.77 (0.21), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.16), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 2844) covalent geometry : angle 0.46097 ( 3861) hydrogen bonds : bond 0.01916 ( 60) hydrogen bonds : angle 3.78100 ( 174) *********************** 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 35 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.094 Fit side-chains REVERT: F 52 LEU cc_start: 0.9122 (mp) cc_final: 0.8770 (mt) outliers start: 8 outliers final: 1 residues processed: 33 average time/residue: 0.7605 time to fit residues: 25.5754 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.0170 chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN ** A 33 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS B 35 GLN ** B 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN B 48 HIS C 29 HIS A C 36 HIS A C 48 HIS ** 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** 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 25 HIS H 33 HIS B H 36 HIS B H 38 GLN I 31 GLN I 36 HIS A I 48 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.104838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086039 restraints weight = 44406.874| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.44 r_work: 0.3111 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 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 = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2844 Z= 0.228 Angle : 0.486 5.463 3861 Z= 0.272 Chirality : 0.033 0.084 333 Planarity : 0.002 0.006 576 Dihedral : 4.202 9.667 324 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.27 % Allowed : 9.48 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.80 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.16), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 2844) covalent geometry : angle 0.48558 ( 3861) hydrogen bonds : bond 0.01943 ( 60) hydrogen bonds : angle 3.52533 ( 174) *********************** 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 38 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.077 Fit side-chains REVERT: F 52 LEU cc_start: 0.9097 (mp) cc_final: 0.8759 (mt) outliers start: 10 outliers final: 1 residues processed: 35 average time/residue: 0.7192 time to fit residues: 25.6588 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS A 36 HIS A A 48 HIS ** B 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN 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 ** 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 I 31 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.111201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089287 restraints weight = 38900.679| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.67 r_work: 0.3151 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2844 Z= 0.156 Angle : 0.438 4.808 3861 Z= 0.246 Chirality : 0.031 0.086 333 Planarity : 0.001 0.006 576 Dihedral : 3.951 10.250 324 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.96 % Allowed : 11.44 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.16), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2844) covalent geometry : angle 0.43774 ( 3861) hydrogen bonds : bond 0.01610 ( 60) hydrogen bonds : angle 3.38456 ( 174) *********************** 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 34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.100 Fit side-chains REVERT: F 52 LEU cc_start: 0.9122 (mp) cc_final: 0.8749 (mt) outliers start: 6 outliers final: 0 residues processed: 32 average time/residue: 0.8055 time to fit residues: 26.3361 Evaluate side-chains 27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN C 27 GLN 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.109543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087522 restraints weight = 34090.891| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.59 r_work: 0.3125 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- 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: 0.8446 moved from start: 0.2713 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= 0.217 Angle : 0.471 4.761 3861 Z= 0.264 Chirality : 0.032 0.088 333 Planarity : 0.002 0.006 576 Dihedral : 4.129 9.901 324 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.29 % Allowed : 10.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.83 (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 0.005 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 2844) covalent geometry : angle 0.47109 ( 3861) hydrogen bonds : bond 0.01767 ( 60) hydrogen bonds : angle 3.34885 ( 174) *********************** 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: 7 poor density : 25 time to evaluate : 0.098 Fit side-chains REVERT: F 27 GLN cc_start: 0.8539 (pt0) cc_final: 0.8162 (tt0) REVERT: F 52 LEU cc_start: 0.9122 (mp) cc_final: 0.8753 (mt) outliers start: 7 outliers final: 2 residues processed: 29 average time/residue: 0.7567 time to fit residues: 22.3874 Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain H residue 27 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN E 27 GLN E 31 GLN E 33 HIS A E 33 HIS B ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.113565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091570 restraints weight = 32755.555| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.60 r_work: 0.3186 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2934 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= 0.109 Angle : 0.412 4.280 3861 Z= 0.231 Chirality : 0.030 0.085 333 Planarity : 0.001 0.005 576 Dihedral : 3.759 10.029 324 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.96 % Allowed : 11.76 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.15), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 2844) covalent geometry : angle 0.41153 ( 3861) hydrogen bonds : bond 0.01438 ( 60) hydrogen bonds : angle 3.28413 ( 174) *********************** 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 34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.097 Fit side-chains REVERT: F 27 GLN cc_start: 0.8542 (pt0) cc_final: 0.8189 (tt0) REVERT: F 52 LEU cc_start: 0.9103 (mp) cc_final: 0.8737 (mt) REVERT: H 40 GLN cc_start: 0.8973 (mp10) cc_final: 0.8579 (mp10) outliers start: 6 outliers final: 2 residues processed: 31 average time/residue: 0.8417 time to fit residues: 26.6033 Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain H residue 27 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN C 25 HIS E 27 GLN E 31 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.112758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090888 restraints weight = 35407.813| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.63 r_work: 0.3181 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2844 Z= 0.129 Angle : 0.426 5.652 3861 Z= 0.236 Chirality : 0.030 0.088 333 Planarity : 0.001 0.011 576 Dihedral : 3.762 9.784 324 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.63 % Allowed : 12.42 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.15), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2844) covalent geometry : angle 0.42642 ( 3861) hydrogen bonds : bond 0.01425 ( 60) hydrogen bonds : angle 3.20940 ( 174) *********************** 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 32 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.091 Fit side-chains REVERT: F 52 LEU cc_start: 0.9116 (mp) cc_final: 0.8738 (mt) outliers start: 5 outliers final: 1 residues processed: 30 average time/residue: 0.8002 time to fit residues: 24.4597 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS A 38 GLN B 25 HIS ** B 36 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN C 25 HIS E 27 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS ** 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 = 0.3653 r_free = 0.3653 target = 0.108594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086502 restraints weight = 38550.093| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.64 r_work: 0.3103 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 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 = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2844 Z= 0.286 Angle : 0.520 6.425 3861 Z= 0.288 Chirality : 0.034 0.095 333 Planarity : 0.002 0.010 576 Dihedral : 4.283 9.561 324 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.31 % Allowed : 12.42 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.20), residues: 306 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.15), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00629 ( 2844) covalent geometry : angle 0.51959 ( 3861) hydrogen bonds : bond 0.01834 ( 60) hydrogen bonds : angle 3.30674 ( 174) *********************** 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 31 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.102 Fit side-chains REVERT: F 52 LEU cc_start: 0.9115 (mp) cc_final: 0.8761 (mt) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.7868 time to fit residues: 24.0674 Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain H residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN B 27 GLN B 36 HIS A B 38 GLN C 27 GLN E 27 GLN E 31 GLN F 48 HIS ** 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.111574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089436 restraints weight = 36088.928| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.67 r_work: 0.3147 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2844 Z= 0.146 Angle : 0.441 6.670 3861 Z= 0.243 Chirality : 0.031 0.110 333 Planarity : 0.001 0.010 576 Dihedral : 3.995 9.954 324 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.29 % Allowed : 12.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.83 (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 0.004 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2844) covalent geometry : angle 0.44073 ( 3861) hydrogen bonds : bond 0.01470 ( 60) hydrogen bonds : angle 3.27230 ( 174) ********************** 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 33 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.060 Fit side-chains REVERT: E 27 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8216 (mt0) REVERT: F 52 LEU cc_start: 0.9112 (mp) cc_final: 0.8754 (mt) outliers start: 7 outliers final: 1 residues processed: 29 average time/residue: 0.8195 time to fit residues: 24.2202 Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain H residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 0 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN B 27 GLN B 36 HIS B B 38 GLN C 27 GLN E 29 HIS A F 36 HIS B ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.110829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 18)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.088669 restraints weight = 34110.783| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.65 r_work: 0.3144 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 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 = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2844 Z= 0.192 Angle : 0.460 6.328 3861 Z= 0.254 Chirality : 0.031 0.103 333 Planarity : 0.002 0.010 576 Dihedral : 4.034 9.751 324 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.63 % Allowed : 12.42 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 0.004 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 2844) covalent geometry : angle 0.45951 ( 3861) hydrogen bonds : bond 0.01548 ( 60) hydrogen bonds : angle 3.24921 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1163.99 seconds wall clock time: 20 minutes 46.97 seconds (1246.97 seconds total)