Starting phenix.real_space_refine on Fri Aug 22 23:03:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m5q_63647/08_2025/9m5q_63647.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m5q_63647/08_2025/9m5q_63647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m5q_63647/08_2025/9m5q_63647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m5q_63647/08_2025/9m5q_63647.map" model { file = "/net/cci-nas-00/data/ceres_data/9m5q_63647/08_2025/9m5q_63647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m5q_63647/08_2025/9m5q_63647.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 21 5.16 5 C 2688 2.51 5 N 735 2.21 5 O 714 1.98 5 H 4263 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8421 Number of models: 1 Model: "" Number of chains: 21 Chain: "AL" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AM" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AN" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AO" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AP" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AQ" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AR" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AS" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AT" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AU" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AV" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AW" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AX" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AY" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "AZ" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "Aa" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "Ab" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "Ac" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "Ad" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "Ae" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "Af" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 401 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Time building chain proxies: 1.38, per 1000 atoms: 0.16 Number of scatterers: 8421 At special positions: 0 Unit cell: (101.01, 58.83, 71.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 O 714 8.00 N 735 7.00 C 2688 6.00 H 4263 1.00 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: 0.51 Conformation dependent library (CDL) restraints added in 238.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 44.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'AL' and resid 14 through 20 Processing sheet with id=AA2, first strand: chain 'AL' and resid 30 through 37 removed outlier: 6.157A pdb=" N ILEAL 31 " --> pdb=" O ILEAN 32 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEUAN 34 " --> pdb=" O ILEAL 31 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLYAL 33 " --> pdb=" O LEUAN 34 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N VALAN 36 " --> pdb=" O GLYAL 33 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N METAL 35 " --> pdb=" O VALAN 36 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILEAN 31 " --> pdb=" O ILEAP 32 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEUAP 34 " --> pdb=" O ILEAN 31 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLYAN 33 " --> pdb=" O LEUAP 34 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N VALAP 36 " --> pdb=" O GLYAN 33 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N METAN 35 " --> pdb=" O VALAP 36 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILEAP 31 " --> pdb=" O ILEAR 32 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEUAR 34 " --> pdb=" O ILEAP 31 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLYAP 33 " --> pdb=" O LEUAR 34 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N VALAR 36 " --> pdb=" O GLYAP 33 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N METAP 35 " --> pdb=" O VALAR 36 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILEAR 31 " --> pdb=" O ILEAT 32 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'AT' and resid 30 through 32 current: chain 'AX' and resid 30 through 37 removed outlier: 6.074A pdb=" N ILEAX 31 " --> pdb=" O ILEAZ 32 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEUAZ 34 " --> pdb=" O ILEAX 31 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLYAX 33 " --> pdb=" O LEUAZ 34 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N VALAZ 36 " --> pdb=" O GLYAX 33 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N METAX 35 " --> pdb=" O VALAZ 36 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILEAZ 31 " --> pdb=" O ILEAb 32 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEUAb 34 " --> pdb=" O ILEAZ 31 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLYAZ 33 " --> pdb=" O LEUAb 34 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N VALAb 36 " --> pdb=" O GLYAZ 33 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N METAZ 35 " --> pdb=" O VALAb 36 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILEAb 31 " --> pdb=" O ILEAd 32 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEUAd 34 " --> pdb=" O ILEAb 31 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLYAb 33 " --> pdb=" O LEUAd 34 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N VALAd 36 " --> pdb=" O GLYAb 33 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N METAb 35 " --> pdb=" O VALAd 36 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILEAd 31 " --> pdb=" O ILEAf 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'AM' and resid 14 through 20 Processing sheet with id=AA4, first strand: chain 'AM' and resid 30 through 37 removed outlier: 6.217A pdb=" N ILEAM 31 " --> pdb=" O ILEAO 32 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEUAO 34 " --> pdb=" O ILEAM 31 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLYAM 33 " --> pdb=" O LEUAO 34 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N VALAO 36 " --> pdb=" O GLYAM 33 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N METAM 35 " --> pdb=" O VALAO 36 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILEAO 31 " --> pdb=" O ILEAQ 32 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEUAQ 34 " --> pdb=" O ILEAO 31 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLYAO 33 " --> pdb=" O LEUAQ 34 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N VALAQ 36 " --> pdb=" O GLYAO 33 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N METAO 35 " --> pdb=" O VALAQ 36 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILEAQ 31 " --> pdb=" O ILEAS 32 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEUAS 34 " --> pdb=" O ILEAQ 31 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLYAQ 33 " --> pdb=" O LEUAS 34 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N VALAS 36 " --> pdb=" O GLYAQ 33 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N METAQ 35 " --> pdb=" O VALAS 36 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILEAS 31 " --> pdb=" O ILEAU 32 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEUAU 34 " --> pdb=" O ILEAS 31 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLYAS 33 " --> pdb=" O LEUAU 34 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N VALAU 36 " --> pdb=" O GLYAS 33 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N METAS 35 " --> pdb=" O VALAU 36 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILEAU 31 " --> pdb=" O ILEAW 32 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEUAW 34 " --> pdb=" O ILEAU 31 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLYAU 33 " --> pdb=" O LEUAW 34 " (cutoff:3.500A) removed outlier: 10.183A pdb=" N VALAW 36 " --> pdb=" O GLYAU 33 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N METAU 35 " --> pdb=" O VALAW 36 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILEAW 31 " --> pdb=" O ILEAY 32 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEUAY 34 " --> pdb=" O ILEAW 31 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLYAW 33 " --> pdb=" O LEUAY 34 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N VALAY 36 " --> pdb=" O GLYAW 33 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N METAW 35 " --> pdb=" O VALAY 36 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILEAY 31 " --> pdb=" O ILEAa 32 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEUAa 34 " --> pdb=" O ILEAY 31 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLYAY 33 " --> pdb=" O LEUAa 34 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N VALAa 36 " --> pdb=" O GLYAY 33 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N METAY 35 " --> pdb=" O VALAa 36 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILEAa 31 " --> pdb=" O ILEAc 32 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEUAc 34 " --> pdb=" O ILEAa 31 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLYAa 33 " --> pdb=" O LEUAc 34 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N VALAc 36 " --> pdb=" O GLYAa 33 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N METAa 35 " --> pdb=" O VALAc 36 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILEAc 31 " --> pdb=" O ILEAe 32 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEUAe 34 " --> pdb=" O ILEAc 31 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLYAc 33 " --> pdb=" O LEUAe 34 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N VALAe 36 " --> pdb=" O GLYAc 33 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N METAc 35 " --> pdb=" O VALAe 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 114 hydrogen bonds defined for protein. 342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 4263 1.04 - 1.23: 237 1.23 - 1.42: 1526 1.42 - 1.61: 2416 1.61 - 1.81: 42 Bond restraints: 8484 Sorted by residual: bond pdb=" N PHEAT 19 " pdb=" H PHEAT 19 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" N VALAe 24 " pdb=" H VALAe 24 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.62e+00 bond pdb=" N GLNAT 15 " pdb=" H GLNAT 15 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" N METAT 35 " pdb=" H METAT 35 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" N METAS 35 " pdb=" H METAS 35 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.60e+00 ... (remaining 8479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 12118 1.50 - 3.01: 1866 3.01 - 4.51: 517 4.51 - 6.01: 815 6.01 - 7.52: 14 Bond angle restraints: 15330 Sorted by residual: angle pdb=" CA ASPAQ 23 " pdb=" CB ASPAQ 23 " pdb=" CG ASPAQ 23 " ideal model delta sigma weight residual 112.60 116.87 -4.27 1.00e+00 1.00e+00 1.83e+01 angle pdb=" CA ASPAT 23 " pdb=" CB ASPAT 23 " pdb=" CG ASPAT 23 " ideal model delta sigma weight residual 112.60 116.84 -4.24 1.00e+00 1.00e+00 1.80e+01 angle pdb=" CA ASPAN 23 " pdb=" CB ASPAN 23 " pdb=" CG ASPAN 23 " ideal model delta sigma weight residual 112.60 116.80 -4.20 1.00e+00 1.00e+00 1.76e+01 angle pdb=" CA PHEAV 20 " pdb=" CB PHEAV 20 " pdb=" CG PHEAV 20 " ideal model delta sigma weight residual 113.80 117.99 -4.19 1.00e+00 1.00e+00 1.75e+01 angle pdb=" CA ASPAM 23 " pdb=" CB ASPAM 23 " pdb=" CG ASPAM 23 " ideal model delta sigma weight residual 112.60 116.75 -4.15 1.00e+00 1.00e+00 1.72e+01 ... (remaining 15325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.91: 3395 13.91 - 27.82: 172 27.82 - 41.72: 82 41.72 - 55.63: 45 55.63 - 69.54: 212 Dihedral angle restraints: 3906 sinusoidal: 2058 harmonic: 1848 Sorted by residual: dihedral pdb=" CA ALAAb 21 " pdb=" C ALAAb 21 " pdb=" N GLUAb 22 " pdb=" CA GLUAb 22 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ALAAa 21 " pdb=" C ALAAa 21 " pdb=" N GLUAa 22 " pdb=" CA GLUAa 22 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ALAAW 21 " pdb=" C ALAAW 21 " pdb=" N GLUAW 22 " pdb=" CA GLUAW 22 " ideal model delta harmonic sigma weight residual 180.00 -151.50 -28.50 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 3903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 119 0.027 - 0.053: 182 0.053 - 0.080: 137 0.080 - 0.107: 169 0.107 - 0.133: 23 Chirality restraints: 630 Sorted by residual: chirality pdb=" CB VALAN 24 " pdb=" CA VALAN 24 " pdb=" CG1 VALAN 24 " pdb=" CG2 VALAN 24 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ASPAL 23 " pdb=" N ASPAL 23 " pdb=" C ASPAL 23 " pdb=" CB ASPAL 23 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CB VALAR 24 " pdb=" CA VALAR 24 " pdb=" CG1 VALAR 24 " pdb=" CG2 VALAR 24 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 627 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEAV 20 " 0.011 2.00e-02 2.50e+03 7.19e-03 1.55e+00 pdb=" CG PHEAV 20 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHEAV 20 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEAV 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEAV 20 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHEAV 20 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHEAV 20 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHEAV 20 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHEAV 20 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHEAV 20 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHEAV 20 " 0.000 2.00e-02 2.50e+03 pdb=" HZ PHEAV 20 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HISAZ 13 " -0.006 2.00e-02 2.50e+03 6.38e-03 1.02e+00 pdb=" CG HISAZ 13 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HISAZ 13 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HISAZ 13 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HISAZ 13 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HISAZ 13 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HISAZ 13 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 HISAZ 13 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 HISAZ 13 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 HISAZ 13 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HISAR 13 " -0.006 2.00e-02 2.50e+03 6.33e-03 1.00e+00 pdb=" CG HISAR 13 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HISAR 13 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HISAR 13 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HISAR 13 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HISAR 13 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HISAR 13 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HISAR 13 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 HISAR 13 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 HISAR 13 " -0.000 2.00e-02 2.50e+03 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 618 2.20 - 2.80: 16255 2.80 - 3.40: 21357 3.40 - 4.00: 32916 4.00 - 4.60: 46780 Nonbonded interactions: 117926 Sorted by model distance: nonbonded pdb=" OD1 ASPAZ 23 " pdb=" HG SERAZ 26 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASPAU 23 " pdb=" HG SERAU 26 " model vdw 1.624 2.450 nonbonded pdb=" OD1 ASPAP 23 " pdb=" HG SERAP 26 " model vdw 1.648 2.450 nonbonded pdb=" O GLUAR 22 " pdb=" H ASPAT 23 " model vdw 1.716 2.450 nonbonded pdb=" O GLUAM 22 " pdb=" H ASPAO 23 " model vdw 1.751 2.450 ... (remaining 117921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AR' selection = chain 'AS' selection = chain 'AT' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'AZ' selection = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' } 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=0.00 max=1.00 mean=0.99 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: 3.260 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.730 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.033 4221 Z= 0.521 Angle : 1.180 5.341 5628 Z= 0.741 Chirality : 0.066 0.133 630 Planarity : 0.002 0.009 714 Dihedral : 11.526 69.541 1428 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.90 % Favored : 89.71 % Rotamer: Outliers : 0.24 % Allowed : 0.71 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.29), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.003 PHEAV 20 HIS 0.010 0.002 HISAZ 13 Details of bonding type rmsd covalent geometry : bond 0.00852 ( 4221) covalent geometry : angle 1.17993 ( 5628) hydrogen bonds : bond 0.16727 ( 114) hydrogen bonds : angle 8.06968 ( 342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 16 LYS cc_start: 0.7548 (mttt) cc_final: 0.7188 (mttp) REVERT: AM 22 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7294 (mp0) REVERT: AN 22 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7021 (mp0) REVERT: AN 23 ASP cc_start: 0.7946 (t0) cc_final: 0.7368 (t0) REVERT: AO 16 LYS cc_start: 0.7535 (mttt) cc_final: 0.7333 (mttp) REVERT: AO 22 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7536 (mt-10) REVERT: AO 23 ASP cc_start: 0.8228 (t0) cc_final: 0.7803 (t0) REVERT: AP 16 LYS cc_start: 0.6995 (mttt) cc_final: 0.6147 (mmtm) REVERT: AP 28 LYS cc_start: 0.8350 (mttt) cc_final: 0.8048 (mttp) REVERT: AQ 23 ASP cc_start: 0.8245 (t0) cc_final: 0.7690 (t0) REVERT: AQ 28 LYS cc_start: 0.8247 (mttt) cc_final: 0.7982 (mttp) REVERT: AR 16 LYS cc_start: 0.7277 (mttt) cc_final: 0.6612 (mptt) REVERT: AR 23 ASP cc_start: 0.8136 (t0) cc_final: 0.7398 (t0) REVERT: AS 16 LYS cc_start: 0.7474 (mttt) cc_final: 0.6514 (mptt) REVERT: AU 16 LYS cc_start: 0.7623 (mttt) cc_final: 0.7153 (mttp) REVERT: AV 16 LYS cc_start: 0.7448 (mttt) cc_final: 0.7131 (mttp) REVERT: AW 22 GLU cc_start: 0.7791 (mt-10) cc_final: 0.6996 (mp0) REVERT: AW 23 ASP cc_start: 0.7814 (t0) cc_final: 0.7367 (t0) REVERT: AW 32 ILE cc_start: 0.8803 (mt) cc_final: 0.8555 (mm) REVERT: AX 16 LYS cc_start: 0.7399 (mttt) cc_final: 0.6927 (mttp) REVERT: AX 23 ASP cc_start: 0.7332 (t0) cc_final: 0.7065 (t0) REVERT: AY 16 LYS cc_start: 0.7637 (mttt) cc_final: 0.7043 (mttp) REVERT: AY 28 LYS cc_start: 0.8386 (mttt) cc_final: 0.8176 (mttm) REVERT: AZ 16 LYS cc_start: 0.7664 (mttt) cc_final: 0.6980 (mmtm) REVERT: AZ 28 LYS cc_start: 0.8542 (mttt) cc_final: 0.8218 (mttm) REVERT: Aa 22 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7044 (mp0) REVERT: Aa 23 ASP cc_start: 0.7710 (t0) cc_final: 0.7017 (t70) REVERT: Ab 23 ASP cc_start: 0.7705 (t0) cc_final: 0.7104 (t0) REVERT: Ac 23 ASP cc_start: 0.7319 (m-30) cc_final: 0.6927 (m-30) REVERT: Ac 28 LYS cc_start: 0.8321 (mttt) cc_final: 0.8091 (mttp) REVERT: Ae 16 LYS cc_start: 0.7651 (mttt) cc_final: 0.7442 (mmtm) REVERT: Ae 19 PHE cc_start: 0.7930 (t80) cc_final: 0.7626 (t80) REVERT: Ae 35 MET cc_start: 0.7691 (ttp) cc_final: 0.7460 (ttp) REVERT: Af 28 LYS cc_start: 0.8358 (mttt) cc_final: 0.8064 (mttp) outliers start: 1 outliers final: 1 residues processed: 168 average time/residue: 0.1788 time to fit residues: 35.9438 Evaluate side-chains 129 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 24 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.129232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.119852 restraints weight = 19754.560| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.96 r_work: 0.4145 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 4221 Z= 0.158 Angle : 0.528 3.918 5628 Z= 0.291 Chirality : 0.053 0.139 630 Planarity : 0.002 0.009 714 Dihedral : 6.885 27.677 547 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 1.90 % Allowed : 8.81 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHEAf 20 HIS 0.005 0.002 HISAP 14 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4221) covalent geometry : angle 0.52762 ( 5628) hydrogen bonds : bond 0.04820 ( 114) hydrogen bonds : angle 5.11165 ( 342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 16 LYS cc_start: 0.7598 (mttt) cc_final: 0.7215 (mttp) REVERT: AM 22 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7692 (pm20) REVERT: AN 22 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7197 (mp0) REVERT: AN 23 ASP cc_start: 0.7973 (t0) cc_final: 0.7715 (t0) REVERT: AO 22 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7840 (mt-10) REVERT: AO 23 ASP cc_start: 0.8394 (t0) cc_final: 0.8125 (t0) REVERT: AP 16 LYS cc_start: 0.7541 (mttt) cc_final: 0.6546 (mmtm) REVERT: AP 22 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8220 (mt-10) REVERT: AP 28 LYS cc_start: 0.8795 (mttt) cc_final: 0.8491 (mttp) REVERT: AQ 16 LYS cc_start: 0.7772 (mttt) cc_final: 0.6735 (mptt) REVERT: AQ 23 ASP cc_start: 0.7857 (t0) cc_final: 0.7373 (t0) REVERT: AQ 28 LYS cc_start: 0.8622 (mttt) cc_final: 0.8374 (mttp) REVERT: AR 16 LYS cc_start: 0.7661 (mttt) cc_final: 0.6689 (mptt) REVERT: AR 23 ASP cc_start: 0.8212 (t0) cc_final: 0.7810 (t0) REVERT: AS 16 LYS cc_start: 0.7696 (mttt) cc_final: 0.7029 (mttp) REVERT: AS 22 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7898 (mp0) REVERT: AU 16 LYS cc_start: 0.7790 (mttt) cc_final: 0.7375 (mttp) REVERT: AW 22 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7289 (mp0) REVERT: AW 23 ASP cc_start: 0.8010 (t0) cc_final: 0.7615 (t0) REVERT: AX 16 LYS cc_start: 0.7559 (mttt) cc_final: 0.7014 (mttp) REVERT: AX 19 PHE cc_start: 0.8021 (t80) cc_final: 0.7766 (t80) REVERT: AX 22 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7249 (mp0) REVERT: AX 23 ASP cc_start: 0.7523 (t0) cc_final: 0.7320 (t0) REVERT: AY 16 LYS cc_start: 0.7928 (mttt) cc_final: 0.7462 (mttp) REVERT: AY 23 ASP cc_start: 0.7918 (m-30) cc_final: 0.7124 (t70) REVERT: AY 28 LYS cc_start: 0.8663 (mttt) cc_final: 0.8341 (mttt) REVERT: AZ 16 LYS cc_start: 0.7903 (mttt) cc_final: 0.7412 (mttp) REVERT: AZ 28 LYS cc_start: 0.8781 (mttt) cc_final: 0.8553 (mttm) REVERT: Aa 22 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6618 (mp0) REVERT: Aa 35 MET cc_start: 0.8549 (ttp) cc_final: 0.8343 (ttm) REVERT: Ab 22 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7187 (mp0) REVERT: Ad 22 GLU cc_start: 0.8025 (mp0) cc_final: 0.7748 (mp0) REVERT: Ae 16 LYS cc_start: 0.8057 (mttt) cc_final: 0.7842 (mmtm) REVERT: Ae 19 PHE cc_start: 0.8090 (t80) cc_final: 0.7802 (t80) REVERT: Af 28 LYS cc_start: 0.8906 (mttt) cc_final: 0.8612 (mttt) outliers start: 8 outliers final: 7 residues processed: 120 average time/residue: 0.1340 time to fit residues: 20.5396 Evaluate side-chains 115 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AM residue 24 VAL Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AR residue 24 VAL Chi-restraints excluded: chain AS residue 24 VAL Chi-restraints excluded: chain AU residue 24 VAL Chi-restraints excluded: chain Ae residue 24 VAL Chi-restraints excluded: chain Af residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.121242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.112515 restraints weight = 20998.732| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 3.02 r_work: 0.4017 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 4221 Z= 0.324 Angle : 0.659 4.217 5628 Z= 0.365 Chirality : 0.053 0.136 630 Planarity : 0.003 0.011 714 Dihedral : 7.137 25.344 546 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 2.86 % Allowed : 12.38 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.004 PHEAS 20 HIS 0.006 0.002 HISAM 14 Details of bonding type rmsd covalent geometry : bond 0.00664 ( 4221) covalent geometry : angle 0.65878 ( 5628) hydrogen bonds : bond 0.04625 ( 114) hydrogen bonds : angle 5.62987 ( 342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 16 LYS cc_start: 0.7917 (mttt) cc_final: 0.7627 (mttp) REVERT: AM 22 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7562 (mp0) REVERT: AN 22 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7287 (mp0) REVERT: AO 22 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7905 (mt-10) REVERT: AO 23 ASP cc_start: 0.8364 (t0) cc_final: 0.8061 (t0) REVERT: AQ 23 ASP cc_start: 0.8136 (t0) cc_final: 0.7585 (t0) REVERT: AQ 28 LYS cc_start: 0.8553 (mttt) cc_final: 0.8259 (mttp) REVERT: AR 16 LYS cc_start: 0.7935 (mttt) cc_final: 0.7143 (mptt) REVERT: AR 23 ASP cc_start: 0.8324 (t0) cc_final: 0.7773 (t0) REVERT: AS 16 LYS cc_start: 0.7837 (mttt) cc_final: 0.7281 (mttp) REVERT: AT 23 ASP cc_start: 0.8230 (t0) cc_final: 0.7936 (t0) REVERT: AU 16 LYS cc_start: 0.7837 (mttt) cc_final: 0.7465 (mttp) REVERT: AW 22 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7506 (mp0) REVERT: AW 23 ASP cc_start: 0.7985 (t0) cc_final: 0.7399 (t0) REVERT: AX 16 LYS cc_start: 0.7831 (mttt) cc_final: 0.7329 (mttp) REVERT: AX 22 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7355 (mp0) REVERT: AX 23 ASP cc_start: 0.7639 (t0) cc_final: 0.7335 (t0) REVERT: AY 16 LYS cc_start: 0.8109 (mttt) cc_final: 0.7645 (mttp) REVERT: AY 22 GLU cc_start: 0.7942 (mp0) cc_final: 0.7413 (pt0) REVERT: AY 23 ASP cc_start: 0.8158 (m-30) cc_final: 0.7395 (t70) REVERT: AY 28 LYS cc_start: 0.8698 (mttt) cc_final: 0.8423 (mttt) REVERT: AZ 16 LYS cc_start: 0.8239 (mttt) cc_final: 0.7620 (mttp) REVERT: AZ 28 LYS cc_start: 0.8888 (mttt) cc_final: 0.8657 (mttm) REVERT: Aa 22 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7106 (mp0) REVERT: Aa 35 MET cc_start: 0.8615 (ttp) cc_final: 0.8380 (ttm) REVERT: Ab 22 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7296 (mp0) REVERT: Ae 16 LYS cc_start: 0.8173 (mttt) cc_final: 0.7963 (mmtm) REVERT: Ae 19 PHE cc_start: 0.8193 (t80) cc_final: 0.7962 (t80) outliers start: 12 outliers final: 12 residues processed: 113 average time/residue: 0.1244 time to fit residues: 18.2107 Evaluate side-chains 112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 13 HIS Chi-restraints excluded: chain AL residue 24 VAL Chi-restraints excluded: chain AM residue 13 HIS Chi-restraints excluded: chain AM residue 24 VAL Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AR residue 24 VAL Chi-restraints excluded: chain AS residue 24 VAL Chi-restraints excluded: chain AU residue 24 VAL Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain AZ residue 24 VAL Chi-restraints excluded: chain Ae residue 24 VAL Chi-restraints excluded: chain Af residue 24 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.124310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.115348 restraints weight = 20822.201| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 3.02 r_work: 0.4101 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4221 Z= 0.161 Angle : 0.509 3.984 5628 Z= 0.281 Chirality : 0.054 0.141 630 Planarity : 0.002 0.007 714 Dihedral : 6.485 23.241 546 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 3.10 % Allowed : 13.81 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHEAT 20 HIS 0.003 0.001 HISAf 13 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4221) covalent geometry : angle 0.50925 ( 5628) hydrogen bonds : bond 0.03577 ( 114) hydrogen bonds : angle 5.50692 ( 342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 16 LYS cc_start: 0.7883 (mttt) cc_final: 0.7628 (mttp) REVERT: AM 22 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7710 (mp0) REVERT: AN 22 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7320 (mp0) REVERT: AO 22 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7741 (mt-10) REVERT: AO 23 ASP cc_start: 0.8379 (t0) cc_final: 0.8034 (t0) REVERT: AQ 23 ASP cc_start: 0.8073 (t0) cc_final: 0.7535 (t0) REVERT: AQ 28 LYS cc_start: 0.8532 (mttt) cc_final: 0.8235 (mttp) REVERT: AR 23 ASP cc_start: 0.8292 (t0) cc_final: 0.7700 (t0) REVERT: AT 23 ASP cc_start: 0.8002 (t0) cc_final: 0.7677 (t0) REVERT: AU 16 LYS cc_start: 0.7744 (mttt) cc_final: 0.7338 (mttp) REVERT: AW 22 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7353 (mp0) REVERT: AW 23 ASP cc_start: 0.7747 (t0) cc_final: 0.7237 (t0) REVERT: AX 16 LYS cc_start: 0.7763 (mttt) cc_final: 0.7252 (mttp) REVERT: AX 22 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7780 (mt-10) REVERT: AX 23 ASP cc_start: 0.7393 (t0) cc_final: 0.7122 (t0) REVERT: AY 16 LYS cc_start: 0.8024 (mttt) cc_final: 0.7570 (mttp) REVERT: AY 23 ASP cc_start: 0.8138 (m-30) cc_final: 0.7342 (t70) REVERT: AY 28 LYS cc_start: 0.8681 (mttt) cc_final: 0.8395 (mttt) REVERT: AZ 16 LYS cc_start: 0.8155 (mttt) cc_final: 0.7084 (mptt) REVERT: AZ 28 LYS cc_start: 0.8899 (mttt) cc_final: 0.8656 (mttm) REVERT: Aa 22 GLU cc_start: 0.7778 (mt-10) cc_final: 0.6922 (mp0) REVERT: Ac 22 GLU cc_start: 0.7859 (mp0) cc_final: 0.7484 (mp0) REVERT: Ae 19 PHE cc_start: 0.8141 (t80) cc_final: 0.7884 (t80) outliers start: 13 outliers final: 12 residues processed: 109 average time/residue: 0.1006 time to fit residues: 14.6489 Evaluate side-chains 106 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 24 VAL Chi-restraints excluded: chain AM residue 24 VAL Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AR residue 24 VAL Chi-restraints excluded: chain AS residue 24 VAL Chi-restraints excluded: chain AU residue 24 VAL Chi-restraints excluded: chain AW residue 24 VAL Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain AZ residue 24 VAL Chi-restraints excluded: chain Ab residue 13 HIS Chi-restraints excluded: chain Ab residue 24 VAL Chi-restraints excluded: chain Ae residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.122875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.114197 restraints weight = 21198.867| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 3.02 r_work: 0.4069 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4221 Z= 0.225 Angle : 0.545 4.463 5628 Z= 0.302 Chirality : 0.053 0.139 630 Planarity : 0.002 0.009 714 Dihedral : 6.650 23.881 546 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 3.81 % Allowed : 14.76 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.003 PHEAT 20 HIS 0.003 0.001 HISAM 14 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 4221) covalent geometry : angle 0.54490 ( 5628) hydrogen bonds : bond 0.03633 ( 114) hydrogen bonds : angle 5.52444 ( 342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 16 LYS cc_start: 0.7873 (mttt) cc_final: 0.7631 (mttp) REVERT: AM 22 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7534 (mp0) REVERT: AN 22 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7257 (mp0) REVERT: AN 23 ASP cc_start: 0.8045 (t0) cc_final: 0.7476 (t0) REVERT: AO 22 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7816 (mt-10) REVERT: AO 23 ASP cc_start: 0.8144 (t0) cc_final: 0.7588 (t70) REVERT: AQ 13 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6118 (m-70) REVERT: AQ 23 ASP cc_start: 0.7870 (t0) cc_final: 0.6914 (t70) REVERT: AQ 28 LYS cc_start: 0.8527 (mttt) cc_final: 0.8231 (mttp) REVERT: AR 23 ASP cc_start: 0.8247 (t0) cc_final: 0.7456 (t0) REVERT: AT 23 ASP cc_start: 0.8013 (t0) cc_final: 0.7758 (t0) REVERT: AU 16 LYS cc_start: 0.7795 (mttt) cc_final: 0.7374 (mttp) REVERT: AW 22 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7287 (mp0) REVERT: AW 23 ASP cc_start: 0.7884 (t0) cc_final: 0.7621 (t0) REVERT: AX 13 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.6143 (m-70) REVERT: AX 16 LYS cc_start: 0.7848 (mttt) cc_final: 0.7239 (mttp) REVERT: AX 22 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7686 (mt-10) REVERT: AX 23 ASP cc_start: 0.7404 (t0) cc_final: 0.7092 (t0) REVERT: AY 16 LYS cc_start: 0.8045 (mttt) cc_final: 0.7546 (mttp) REVERT: AY 23 ASP cc_start: 0.8162 (m-30) cc_final: 0.7936 (m-30) REVERT: AZ 16 LYS cc_start: 0.8138 (mttt) cc_final: 0.7016 (mptt) REVERT: AZ 28 LYS cc_start: 0.8918 (mttt) cc_final: 0.8648 (mttm) REVERT: Aa 22 GLU cc_start: 0.7746 (mt-10) cc_final: 0.6780 (mp0) REVERT: Ac 22 GLU cc_start: 0.7896 (mp0) cc_final: 0.7445 (mp0) REVERT: Ae 19 PHE cc_start: 0.8127 (t80) cc_final: 0.7836 (t80) outliers start: 16 outliers final: 12 residues processed: 110 average time/residue: 0.0964 time to fit residues: 14.2480 Evaluate side-chains 107 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 13 HIS Chi-restraints excluded: chain AL residue 24 VAL Chi-restraints excluded: chain AM residue 13 HIS Chi-restraints excluded: chain AM residue 24 VAL Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AQ residue 13 HIS Chi-restraints excluded: chain AR residue 24 VAL Chi-restraints excluded: chain AU residue 24 VAL Chi-restraints excluded: chain AW residue 24 VAL Chi-restraints excluded: chain AX residue 13 HIS Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain AZ residue 24 VAL Chi-restraints excluded: chain Ab residue 13 HIS Chi-restraints excluded: chain Ab residue 24 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.123602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.114992 restraints weight = 20880.541| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 3.00 r_work: 0.4086 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4221 Z= 0.185 Angle : 0.507 4.315 5628 Z= 0.280 Chirality : 0.053 0.136 630 Planarity : 0.002 0.007 714 Dihedral : 6.391 23.543 546 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 4.05 % Allowed : 15.48 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHEAT 20 HIS 0.002 0.001 HISAT 13 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4221) covalent geometry : angle 0.50704 ( 5628) hydrogen bonds : bond 0.03393 ( 114) hydrogen bonds : angle 5.40356 ( 342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AM 22 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7632 (mp0) REVERT: AN 22 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7285 (mp0) REVERT: AN 23 ASP cc_start: 0.7961 (t0) cc_final: 0.7401 (t0) REVERT: AO 22 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7825 (mt-10) REVERT: AO 23 ASP cc_start: 0.8315 (t0) cc_final: 0.7833 (t0) REVERT: AQ 13 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.6148 (m-70) REVERT: AQ 23 ASP cc_start: 0.7903 (t0) cc_final: 0.6986 (t70) REVERT: AQ 28 LYS cc_start: 0.8561 (mttt) cc_final: 0.8314 (mttp) REVERT: AR 23 ASP cc_start: 0.8081 (t0) cc_final: 0.7251 (t0) REVERT: AT 23 ASP cc_start: 0.7834 (t0) cc_final: 0.7420 (t0) REVERT: AW 22 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7203 (mp0) REVERT: AW 23 ASP cc_start: 0.7926 (t0) cc_final: 0.7662 (t0) REVERT: AX 13 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6116 (m-70) REVERT: AX 16 LYS cc_start: 0.7889 (mttt) cc_final: 0.7246 (mttp) REVERT: AX 22 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7164 (mp0) REVERT: AX 23 ASP cc_start: 0.7427 (t0) cc_final: 0.7150 (t0) REVERT: AY 16 LYS cc_start: 0.8063 (mttt) cc_final: 0.7585 (mttp) REVERT: AY 22 GLU cc_start: 0.7845 (mp0) cc_final: 0.7580 (pm20) REVERT: AZ 16 LYS cc_start: 0.8166 (mttt) cc_final: 0.7060 (mptt) REVERT: AZ 28 LYS cc_start: 0.8941 (mttt) cc_final: 0.8672 (mttm) REVERT: Aa 22 GLU cc_start: 0.7750 (mt-10) cc_final: 0.6799 (mp0) REVERT: Ac 22 GLU cc_start: 0.7823 (mp0) cc_final: 0.7486 (mp0) REVERT: Ae 19 PHE cc_start: 0.8154 (t80) cc_final: 0.7867 (t80) outliers start: 17 outliers final: 14 residues processed: 111 average time/residue: 0.0924 time to fit residues: 14.1938 Evaluate side-chains 108 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 13 HIS Chi-restraints excluded: chain AL residue 24 VAL Chi-restraints excluded: chain AM residue 13 HIS Chi-restraints excluded: chain AM residue 24 VAL Chi-restraints excluded: chain AN residue 13 HIS Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AQ residue 13 HIS Chi-restraints excluded: chain AR residue 24 VAL Chi-restraints excluded: chain AU residue 24 VAL Chi-restraints excluded: chain AV residue 13 HIS Chi-restraints excluded: chain AW residue 24 VAL Chi-restraints excluded: chain AX residue 13 HIS Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain Aa residue 24 VAL Chi-restraints excluded: chain Ab residue 13 HIS Chi-restraints excluded: chain Ab residue 24 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.126364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.117708 restraints weight = 20698.147| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 2.97 r_work: 0.4115 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4221 Z= 0.138 Angle : 0.463 4.722 5628 Z= 0.257 Chirality : 0.054 0.135 630 Planarity : 0.002 0.006 714 Dihedral : 6.069 23.798 546 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.67 % Favored : 89.14 % Rotamer: Outliers : 2.86 % Allowed : 17.38 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHEAU 20 HIS 0.002 0.001 HISAc 13 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4221) covalent geometry : angle 0.46325 ( 5628) hydrogen bonds : bond 0.03064 ( 114) hydrogen bonds : angle 5.25280 ( 342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: AM 22 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7590 (mp0) REVERT: AN 22 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7291 (mp0) REVERT: AN 23 ASP cc_start: 0.7933 (t0) cc_final: 0.7723 (t0) REVERT: AO 22 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7832 (mt-10) REVERT: AO 23 ASP cc_start: 0.8043 (t0) cc_final: 0.7588 (t70) REVERT: AQ 13 HIS cc_start: 0.7143 (OUTLIER) cc_final: 0.5995 (m-70) REVERT: AQ 23 ASP cc_start: 0.7830 (t0) cc_final: 0.6937 (t70) REVERT: AQ 28 LYS cc_start: 0.8584 (mttt) cc_final: 0.8326 (mttp) REVERT: AR 23 ASP cc_start: 0.7998 (t0) cc_final: 0.7146 (t0) REVERT: AT 23 ASP cc_start: 0.7871 (t0) cc_final: 0.7399 (t0) REVERT: AW 22 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7301 (mp0) REVERT: AW 23 ASP cc_start: 0.7989 (t0) cc_final: 0.7682 (t0) REVERT: AX 16 LYS cc_start: 0.7923 (mttt) cc_final: 0.7249 (mttp) REVERT: AX 22 GLU cc_start: 0.7846 (mt-10) cc_final: 0.6981 (mp0) REVERT: AY 16 LYS cc_start: 0.8033 (mttt) cc_final: 0.7546 (mttp) REVERT: AY 23 ASP cc_start: 0.8226 (m-30) cc_final: 0.7884 (t0) REVERT: AZ 16 LYS cc_start: 0.8119 (mttt) cc_final: 0.7055 (mptt) REVERT: AZ 22 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7327 (mp0) REVERT: AZ 28 LYS cc_start: 0.8935 (mttt) cc_final: 0.8619 (mttm) REVERT: Aa 22 GLU cc_start: 0.7809 (mt-10) cc_final: 0.6861 (mp0) REVERT: Ab 22 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7216 (mp0) REVERT: Ac 22 GLU cc_start: 0.7860 (mp0) cc_final: 0.7535 (mp0) REVERT: Ae 19 PHE cc_start: 0.8139 (t80) cc_final: 0.7887 (t80) REVERT: Ae 35 MET cc_start: 0.7854 (ttp) cc_final: 0.7148 (ptm) REVERT: Af 23 ASP cc_start: 0.7804 (m-30) cc_final: 0.7510 (t0) outliers start: 12 outliers final: 8 residues processed: 110 average time/residue: 0.0963 time to fit residues: 14.5008 Evaluate side-chains 104 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 24 VAL Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AQ residue 13 HIS Chi-restraints excluded: chain AR residue 24 VAL Chi-restraints excluded: chain AW residue 24 VAL Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain Aa residue 24 VAL Chi-restraints excluded: chain Ab residue 13 HIS Chi-restraints excluded: chain Ab residue 24 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.123641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.115324 restraints weight = 20941.056| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.92 r_work: 0.4075 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4221 Z= 0.216 Angle : 0.530 4.508 5628 Z= 0.293 Chirality : 0.053 0.137 630 Planarity : 0.002 0.014 714 Dihedral : 6.393 22.729 546 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 3.57 % Allowed : 17.38 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.003 PHEAc 19 HIS 0.003 0.001 HISAT 13 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 4221) covalent geometry : angle 0.53004 ( 5628) hydrogen bonds : bond 0.03515 ( 114) hydrogen bonds : angle 5.33283 ( 342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: AM 22 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7632 (mp0) REVERT: AN 22 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7283 (mp0) REVERT: AO 23 ASP cc_start: 0.8287 (t0) cc_final: 0.7726 (t70) REVERT: AQ 13 HIS cc_start: 0.7114 (OUTLIER) cc_final: 0.5929 (m-70) REVERT: AQ 23 ASP cc_start: 0.7968 (t0) cc_final: 0.7107 (t70) REVERT: AQ 28 LYS cc_start: 0.8549 (mttt) cc_final: 0.8273 (mttp) REVERT: AR 23 ASP cc_start: 0.8159 (t0) cc_final: 0.7292 (t0) REVERT: AT 23 ASP cc_start: 0.7925 (t0) cc_final: 0.7377 (t0) REVERT: AW 22 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7434 (mp0) REVERT: AW 23 ASP cc_start: 0.8164 (t0) cc_final: 0.7794 (t0) REVERT: AX 13 HIS cc_start: 0.7094 (OUTLIER) cc_final: 0.5999 (m-70) REVERT: AX 16 LYS cc_start: 0.7884 (mttt) cc_final: 0.7212 (mttp) REVERT: AX 22 GLU cc_start: 0.7859 (mt-10) cc_final: 0.6926 (mp0) REVERT: AY 16 LYS cc_start: 0.7871 (mttt) cc_final: 0.7355 (mttp) REVERT: AY 23 ASP cc_start: 0.8349 (m-30) cc_final: 0.7783 (t0) REVERT: AZ 16 LYS cc_start: 0.8162 (mttt) cc_final: 0.7035 (mptt) REVERT: AZ 22 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7440 (mp0) REVERT: AZ 28 LYS cc_start: 0.8919 (mttt) cc_final: 0.8590 (mttm) REVERT: Aa 22 GLU cc_start: 0.7723 (mt-10) cc_final: 0.6720 (mp0) REVERT: Ab 22 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7174 (mp0) REVERT: Ac 22 GLU cc_start: 0.7900 (mp0) cc_final: 0.7485 (mp0) REVERT: Ad 19 PHE cc_start: 0.8042 (t80) cc_final: 0.7802 (t80) REVERT: Ae 19 PHE cc_start: 0.8185 (t80) cc_final: 0.7876 (t80) REVERT: Ae 35 MET cc_start: 0.7941 (ttp) cc_final: 0.7201 (ptm) REVERT: Af 23 ASP cc_start: 0.7837 (m-30) cc_final: 0.7576 (t0) outliers start: 15 outliers final: 10 residues processed: 104 average time/residue: 0.0991 time to fit residues: 14.1532 Evaluate side-chains 102 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 24 VAL Chi-restraints excluded: chain AN residue 13 HIS Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AQ residue 13 HIS Chi-restraints excluded: chain AR residue 24 VAL Chi-restraints excluded: chain AV residue 13 HIS Chi-restraints excluded: chain AW residue 24 VAL Chi-restraints excluded: chain AX residue 13 HIS Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain Aa residue 24 VAL Chi-restraints excluded: chain Ab residue 13 HIS Chi-restraints excluded: chain Ab residue 24 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.121350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.112990 restraints weight = 21482.859| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.96 r_work: 0.4048 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 4221 Z= 0.267 Angle : 0.575 4.334 5628 Z= 0.316 Chirality : 0.053 0.139 630 Planarity : 0.002 0.012 714 Dihedral : 6.737 23.553 546 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 4.05 % Allowed : 17.14 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.003 PHEAU 20 HIS 0.004 0.001 HISAR 13 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 4221) covalent geometry : angle 0.57515 ( 5628) hydrogen bonds : bond 0.03818 ( 114) hydrogen bonds : angle 5.52317 ( 342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AM 22 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7552 (mp0) REVERT: AN 22 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7311 (mp0) REVERT: AN 23 ASP cc_start: 0.8018 (t0) cc_final: 0.7601 (t0) REVERT: AO 23 ASP cc_start: 0.8271 (t0) cc_final: 0.7742 (t70) REVERT: AQ 13 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.5982 (m-70) REVERT: AQ 23 ASP cc_start: 0.8093 (t0) cc_final: 0.7181 (t70) REVERT: AQ 28 LYS cc_start: 0.8574 (mttt) cc_final: 0.8296 (mttp) REVERT: AR 23 ASP cc_start: 0.8083 (t0) cc_final: 0.7275 (t0) REVERT: AT 23 ASP cc_start: 0.8065 (t0) cc_final: 0.7401 (t0) REVERT: AW 22 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7402 (mp0) REVERT: AX 13 HIS cc_start: 0.7183 (OUTLIER) cc_final: 0.6225 (m-70) REVERT: AX 22 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7071 (mp0) REVERT: AY 16 LYS cc_start: 0.7955 (mttt) cc_final: 0.7427 (mttp) REVERT: AY 23 ASP cc_start: 0.8406 (m-30) cc_final: 0.7767 (t0) REVERT: AZ 16 LYS cc_start: 0.8126 (mttt) cc_final: 0.7742 (mttp) REVERT: AZ 28 LYS cc_start: 0.8937 (mttt) cc_final: 0.8619 (mttm) REVERT: Aa 22 GLU cc_start: 0.7868 (mt-10) cc_final: 0.6947 (mp0) REVERT: Ac 22 GLU cc_start: 0.7955 (mp0) cc_final: 0.7519 (mp0) REVERT: Ad 19 PHE cc_start: 0.8117 (t80) cc_final: 0.7903 (t80) REVERT: Ae 19 PHE cc_start: 0.8199 (t80) cc_final: 0.7905 (t80) REVERT: Ae 35 MET cc_start: 0.8043 (ttp) cc_final: 0.7228 (ptm) REVERT: Af 22 GLU cc_start: 0.8089 (mp0) cc_final: 0.7783 (mp0) outliers start: 17 outliers final: 13 residues processed: 103 average time/residue: 0.1007 time to fit residues: 14.5028 Evaluate side-chains 106 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 24 VAL Chi-restraints excluded: chain AM residue 13 HIS Chi-restraints excluded: chain AN residue 13 HIS Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AO residue 24 VAL Chi-restraints excluded: chain AQ residue 13 HIS Chi-restraints excluded: chain AQ residue 24 VAL Chi-restraints excluded: chain AR residue 24 VAL Chi-restraints excluded: chain AV residue 13 HIS Chi-restraints excluded: chain AW residue 24 VAL Chi-restraints excluded: chain AX residue 13 HIS Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain Aa residue 24 VAL Chi-restraints excluded: chain Ab residue 13 HIS Chi-restraints excluded: chain Ab residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.125176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.116361 restraints weight = 19676.108| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.68 r_work: 0.4092 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4221 Z= 0.151 Angle : 0.484 4.146 5628 Z= 0.266 Chirality : 0.053 0.138 630 Planarity : 0.002 0.012 714 Dihedral : 6.216 22.759 546 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.81 % Favored : 88.00 % Rotamer: Outliers : 3.33 % Allowed : 17.62 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHEAc 19 HIS 0.002 0.001 HISAR 13 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4221) covalent geometry : angle 0.48358 ( 5628) hydrogen bonds : bond 0.03307 ( 114) hydrogen bonds : angle 5.31353 ( 342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AM 22 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7539 (mp0) REVERT: AN 22 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7171 (mp0) REVERT: AN 23 ASP cc_start: 0.7767 (t0) cc_final: 0.7376 (t0) REVERT: AO 23 ASP cc_start: 0.8120 (t0) cc_final: 0.7499 (t70) REVERT: AQ 13 HIS cc_start: 0.6700 (OUTLIER) cc_final: 0.5598 (m-70) REVERT: AQ 23 ASP cc_start: 0.7805 (t0) cc_final: 0.6889 (t70) REVERT: AQ 28 LYS cc_start: 0.8577 (mttt) cc_final: 0.8264 (mttp) REVERT: AR 23 ASP cc_start: 0.7906 (t0) cc_final: 0.7046 (t0) REVERT: AT 23 ASP cc_start: 0.7728 (t0) cc_final: 0.7189 (t0) REVERT: AW 22 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7351 (mp0) REVERT: AY 16 LYS cc_start: 0.7739 (mttt) cc_final: 0.7215 (mttp) REVERT: AY 23 ASP cc_start: 0.8400 (m-30) cc_final: 0.7852 (t0) REVERT: AZ 16 LYS cc_start: 0.8057 (mttt) cc_final: 0.6895 (mptt) REVERT: AZ 22 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7406 (mp0) REVERT: Aa 22 GLU cc_start: 0.7753 (mt-10) cc_final: 0.6671 (mp0) REVERT: Ab 22 GLU cc_start: 0.7693 (mt-10) cc_final: 0.6888 (mp0) REVERT: Ac 22 GLU cc_start: 0.7867 (mp0) cc_final: 0.7453 (mp0) REVERT: Ad 19 PHE cc_start: 0.7957 (t80) cc_final: 0.7752 (t80) REVERT: Ad 22 GLU cc_start: 0.7843 (mp0) cc_final: 0.7594 (mp0) REVERT: Ae 19 PHE cc_start: 0.8052 (t80) cc_final: 0.7700 (t80) REVERT: Ae 35 MET cc_start: 0.7885 (ttp) cc_final: 0.7039 (ptm) REVERT: Af 23 ASP cc_start: 0.7598 (m-30) cc_final: 0.7253 (t0) outliers start: 14 outliers final: 12 residues processed: 105 average time/residue: 0.0921 time to fit residues: 13.5271 Evaluate side-chains 102 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 24 VAL Chi-restraints excluded: chain AM residue 13 HIS Chi-restraints excluded: chain AN residue 13 HIS Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AQ residue 13 HIS Chi-restraints excluded: chain AQ residue 24 VAL Chi-restraints excluded: chain AR residue 24 VAL Chi-restraints excluded: chain AV residue 13 HIS Chi-restraints excluded: chain AW residue 24 VAL Chi-restraints excluded: chain AX residue 24 VAL Chi-restraints excluded: chain Aa residue 24 VAL Chi-restraints excluded: chain Ab residue 13 HIS Chi-restraints excluded: chain Ab residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.126362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.117125 restraints weight = 19494.544| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.80 r_work: 0.4092 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4221 Z= 0.171 Angle : 0.490 3.947 5628 Z= 0.272 Chirality : 0.053 0.139 630 Planarity : 0.002 0.012 714 Dihedral : 6.255 23.406 546 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 3.33 % Allowed : 17.62 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEAc 19 HIS 0.002 0.001 HISAR 13 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4221) covalent geometry : angle 0.48994 ( 5628) hydrogen bonds : bond 0.03328 ( 114) hydrogen bonds : angle 5.23105 ( 342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1962.43 seconds wall clock time: 33 minutes 55.21 seconds (2035.21 seconds total)