Starting phenix.real_space_refine on Sat Jul 26 08:36:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m5q_63647/07_2025/9m5q_63647.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m5q_63647/07_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_63647/07_2025/9m5q_63647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m5q_63647/07_2025/9m5q_63647.map" model { file = "/net/cci-nas-00/data/ceres_data/9m5q_63647/07_2025/9m5q_63647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m5q_63647/07_2025/9m5q_63647.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.87, per 1000 atoms: 0.70 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: 2.02 Conformation dependent library (CDL) restraints added in 707.5 milliseconds 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: 0.74 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: 3.05 Time building geometry restraints manager: 2.51 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: 3.030 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: 0.160 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.400 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.530 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (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 HIS 0.010 0.002 HISAZ 13 PHE 0.021 0.003 PHEAV 20 Details of bonding type rmsd hydrogen bonds : bond 0.16727 ( 114) hydrogen bonds : angle 8.06968 ( 342) covalent geometry : bond 0.00852 ( 4221) covalent geometry : angle 1.17993 ( 5628) *********************** 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 : 0.750 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: 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 22 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7535 (mt-10) REVERT: AO 23 ASP cc_start: 0.8228 (t0) cc_final: 0.7802 (t0) REVERT: AP 16 LYS cc_start: 0.6995 (mttt) cc_final: 0.6148 (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: 0.6611 (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: 0.6515 (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: 0.7366 (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: 0.6928 (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: 0.7046 (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: 0.6978 (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: 0.7016 (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: 0.6928 (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: 0.7406 (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: 0.7459 (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: 0.4310 time to fit residues: 86.9422 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 : 0.647 ------------------------------------------------------------------------------- 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 35 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 11 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 = 0.4418 r_free = 0.4418 target = 0.129752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.120484 restraints weight = 19598.413| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.93 r_work: 0.4161 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4221 Z= 0.166 Angle : 0.530 3.786 5628 Z= 0.294 Chirality : 0.052 0.138 630 Planarity : 0.002 0.008 714 Dihedral : 6.893 27.113 547 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HISAP 14 PHE 0.015 0.002 PHEAf 20 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 114) hydrogen bonds : angle 5.04355 ( 342) covalent geometry : bond 0.00330 ( 4221) covalent geometry : angle 0.52996 ( 5628) *********************** 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 123 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 16 LYS cc_start: 0.7576 (mttt) cc_final: 0.7141 (mttp) REVERT: AM 22 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7680 (pm20) REVERT: AN 22 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7171 (mp0) REVERT: AN 23 ASP cc_start: 0.7967 (t0) cc_final: 0.7731 (t0) REVERT: AO 22 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7837 (mt-10) REVERT: AO 23 ASP cc_start: 0.8443 (t0) cc_final: 0.8062 (t0) REVERT: AP 22 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8217 (mt-10) REVERT: AP 28 LYS cc_start: 0.8795 (mttt) cc_final: 0.8502 (mttp) REVERT: AQ 16 LYS cc_start: 0.7785 (mttt) cc_final: 0.6765 (mptt) REVERT: AQ 23 ASP cc_start: 0.7843 (t0) cc_final: 0.7259 (t70) REVERT: AQ 28 LYS cc_start: 0.8635 (mttt) cc_final: 0.8401 (mttp) REVERT: AR 16 LYS cc_start: 0.7667 (mttt) cc_final: 0.6719 (mptt) REVERT: AS 16 LYS cc_start: 0.7695 (mttt) cc_final: 0.7034 (mttp) REVERT: AS 22 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7928 (mp0) REVERT: AU 16 LYS cc_start: 0.7795 (mttt) cc_final: 0.7382 (mttp) REVERT: AW 22 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7471 (mp0) REVERT: AW 23 ASP cc_start: 0.8033 (t0) cc_final: 0.7648 (t0) REVERT: AX 16 LYS cc_start: 0.7565 (mttt) cc_final: 0.7027 (mttp) REVERT: AX 22 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7276 (mp0) REVERT: AY 16 LYS cc_start: 0.7931 (mttt) cc_final: 0.7474 (mttp) REVERT: AY 22 GLU cc_start: 0.7877 (mp0) cc_final: 0.7539 (pt0) REVERT: AY 23 ASP cc_start: 0.7980 (m-30) cc_final: 0.7319 (t70) REVERT: AZ 16 LYS cc_start: 0.7921 (mttt) cc_final: 0.7422 (mttp) REVERT: AZ 28 LYS cc_start: 0.8775 (mttt) cc_final: 0.8552 (mttm) REVERT: Aa 22 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6663 (mp0) REVERT: Aa 35 MET cc_start: 0.8549 (ttp) cc_final: 0.8341 (ttm) REVERT: Ab 22 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7220 (mp0) REVERT: Ad 22 GLU cc_start: 0.8019 (mp0) cc_final: 0.7774 (mp0) REVERT: Ae 19 PHE cc_start: 0.8122 (t80) cc_final: 0.7839 (t80) outliers start: 8 outliers final: 7 residues processed: 119 average time/residue: 0.3321 time to fit residues: 49.5623 Evaluate side-chains 110 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 26 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.123212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.114280 restraints weight = 20899.191| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 3.04 r_work: 0.4057 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 4221 Z= 0.272 Angle : 0.606 3.970 5628 Z= 0.337 Chirality : 0.053 0.134 630 Planarity : 0.003 0.010 714 Dihedral : 6.918 25.114 546 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 3.10 % Allowed : 12.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (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 HIS 0.006 0.002 HISAM 14 PHE 0.022 0.003 PHEAS 20 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 114) hydrogen bonds : angle 5.43482 ( 342) covalent geometry : bond 0.00546 ( 4221) covalent geometry : angle 0.60608 ( 5628) *********************** 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: 13 poor density : 105 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 16 LYS cc_start: 0.7804 (mttt) cc_final: 0.7373 (mttp) REVERT: AM 22 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7648 (mp0) REVERT: AN 22 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7291 (mp0) REVERT: AO 23 ASP cc_start: 0.8388 (t0) cc_final: 0.7945 (t0) REVERT: AP 28 LYS cc_start: 0.8801 (mttt) cc_final: 0.8520 (mttp) REVERT: AQ 23 ASP cc_start: 0.7984 (t0) cc_final: 0.7281 (t70) REVERT: AQ 28 LYS cc_start: 0.8586 (mttt) cc_final: 0.8320 (mttm) REVERT: AR 23 ASP cc_start: 0.8317 (t0) cc_final: 0.7744 (t0) REVERT: AS 16 LYS cc_start: 0.7903 (mttt) cc_final: 0.7327 (mttp) REVERT: AT 23 ASP cc_start: 0.8160 (t0) cc_final: 0.7749 (t0) REVERT: AU 16 LYS cc_start: 0.7801 (mttt) cc_final: 0.7426 (mttp) REVERT: AW 22 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7469 (mp0) REVERT: AW 23 ASP cc_start: 0.7947 (t0) cc_final: 0.7614 (t0) REVERT: AX 16 LYS cc_start: 0.7802 (mttt) cc_final: 0.7266 (mttp) REVERT: AX 22 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7321 (mp0) REVERT: AY 16 LYS cc_start: 0.8117 (mttt) cc_final: 0.7659 (mttp) REVERT: AY 22 GLU cc_start: 0.7947 (mp0) cc_final: 0.7287 (pt0) REVERT: AY 23 ASP cc_start: 0.8098 (m-30) cc_final: 0.7442 (t0) REVERT: AZ 16 LYS cc_start: 0.8094 (mttt) cc_final: 0.7508 (mttp) REVERT: AZ 28 LYS cc_start: 0.8868 (mttt) cc_final: 0.8602 (mttm) REVERT: Aa 22 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7095 (mp0) REVERT: Aa 35 MET cc_start: 0.8593 (ttp) cc_final: 0.8339 (ttm) REVERT: Ab 22 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7284 (mp0) REVERT: Ae 19 PHE cc_start: 0.8153 (t80) cc_final: 0.7898 (t80) outliers start: 13 outliers final: 11 residues processed: 113 average time/residue: 0.3184 time to fit residues: 45.8998 Evaluate side-chains 108 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.124974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.115993 restraints weight = 20622.911| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 3.04 r_work: 0.4079 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4221 Z= 0.200 Angle : 0.530 4.035 5628 Z= 0.294 Chirality : 0.054 0.143 630 Planarity : 0.002 0.007 714 Dihedral : 6.602 22.623 546 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.33 % Allowed : 13.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISAL 14 PHE 0.016 0.002 PHEAT 20 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 114) hydrogen bonds : angle 5.52382 ( 342) covalent geometry : bond 0.00404 ( 4221) covalent geometry : angle 0.52976 ( 5628) *********************** 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: 14 poor density : 100 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 16 LYS cc_start: 0.7813 (mttt) cc_final: 0.7534 (mttp) REVERT: AM 22 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7596 (mp0) REVERT: AN 22 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7254 (mp0) REVERT: AO 23 ASP cc_start: 0.8296 (t0) cc_final: 0.7969 (t0) REVERT: AP 22 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8147 (mt-10) REVERT: AQ 23 ASP cc_start: 0.7986 (t0) cc_final: 0.7390 (t0) REVERT: AQ 28 LYS cc_start: 0.8544 (mttt) cc_final: 0.8244 (mttp) REVERT: AR 23 ASP cc_start: 0.8203 (t0) cc_final: 0.7608 (t0) REVERT: AT 23 ASP cc_start: 0.8046 (t0) cc_final: 0.7673 (t0) REVERT: AU 16 LYS cc_start: 0.7781 (mttt) cc_final: 0.7395 (mttp) REVERT: AW 22 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7369 (mp0) REVERT: AW 23 ASP cc_start: 0.7912 (t0) cc_final: 0.7641 (t0) REVERT: AX 16 LYS cc_start: 0.7789 (mttt) cc_final: 0.7273 (mttp) REVERT: AX 22 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7614 (mp0) REVERT: AY 16 LYS cc_start: 0.8154 (mttt) cc_final: 0.7668 (mttp) REVERT: AY 23 ASP cc_start: 0.8115 (m-30) cc_final: 0.7419 (t70) REVERT: AZ 16 LYS cc_start: 0.8133 (mttt) cc_final: 0.7082 (mptt) REVERT: AZ 28 LYS cc_start: 0.8897 (mttt) cc_final: 0.8626 (mttm) REVERT: Aa 22 GLU cc_start: 0.7805 (mt-10) cc_final: 0.6875 (mp0) REVERT: Aa 23 ASP cc_start: 0.7669 (t70) cc_final: 0.7429 (t0) REVERT: Ac 22 GLU cc_start: 0.7874 (mp0) cc_final: 0.7468 (mp0) REVERT: Ae 19 PHE cc_start: 0.8161 (t80) cc_final: 0.7910 (t80) outliers start: 14 outliers final: 12 residues processed: 110 average time/residue: 0.2684 time to fit residues: 39.0182 Evaluate side-chains 105 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 24 VAL Chi-restraints excluded: chain AN residue 24 VAL 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 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 9 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AL 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.127017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.117970 restraints weight = 19435.138| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.69 r_work: 0.4067 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4221 Z= 0.226 Angle : 0.545 4.091 5628 Z= 0.301 Chirality : 0.054 0.137 630 Planarity : 0.002 0.009 714 Dihedral : 6.644 23.782 546 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 4.29 % Allowed : 15.00 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISAe 13 PHE 0.019 0.003 PHEAU 20 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 114) hydrogen bonds : angle 5.57217 ( 342) covalent geometry : bond 0.00467 ( 4221) covalent geometry : angle 0.54457 ( 5628) *********************** 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: 18 poor density : 94 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 16 LYS cc_start: 0.7789 (mttt) cc_final: 0.7505 (mttp) REVERT: AM 22 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7788 (mp0) REVERT: AN 22 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7192 (mp0) REVERT: AO 23 ASP cc_start: 0.8152 (t0) cc_final: 0.7612 (t70) REVERT: AQ 13 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6079 (m-70) REVERT: AQ 23 ASP cc_start: 0.7842 (t0) cc_final: 0.6927 (t70) REVERT: AQ 28 LYS cc_start: 0.8551 (mttt) cc_final: 0.8249 (mttm) REVERT: AR 23 ASP cc_start: 0.8248 (t0) cc_final: 0.7354 (t0) REVERT: AT 23 ASP cc_start: 0.7994 (t0) cc_final: 0.7730 (t0) REVERT: AW 22 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7348 (mp0) REVERT: AW 23 ASP cc_start: 0.8019 (t0) cc_final: 0.7353 (t0) REVERT: AX 13 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6092 (m-70) REVERT: AX 16 LYS cc_start: 0.7844 (mttt) cc_final: 0.7209 (mttp) REVERT: AX 22 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7162 (mp0) REVERT: AY 16 LYS cc_start: 0.8049 (mttt) cc_final: 0.7536 (mttp) REVERT: AY 23 ASP cc_start: 0.8097 (m-30) cc_final: 0.7008 (t70) REVERT: AY 28 LYS cc_start: 0.8703 (mttt) cc_final: 0.8386 (mttt) REVERT: AZ 16 LYS cc_start: 0.8089 (mttt) cc_final: 0.6950 (mptt) REVERT: AZ 28 LYS cc_start: 0.8942 (mttt) cc_final: 0.8693 (mttm) REVERT: Aa 22 GLU cc_start: 0.7790 (mt-10) cc_final: 0.6787 (mp0) REVERT: Ac 22 GLU cc_start: 0.7915 (mp0) cc_final: 0.7468 (mp0) REVERT: Ae 19 PHE cc_start: 0.8092 (t80) cc_final: 0.7782 (t80) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.2725 time to fit residues: 39.8637 Evaluate side-chains 105 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 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 11 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.124838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.115433 restraints weight = 19690.316| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.90 r_work: 0.4043 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4221 Z= 0.210 Angle : 0.517 4.132 5628 Z= 0.287 Chirality : 0.053 0.137 630 Planarity : 0.002 0.008 714 Dihedral : 6.515 22.368 546 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 4.52 % Allowed : 15.95 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISAT 13 PHE 0.018 0.002 PHEAU 20 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 114) hydrogen bonds : angle 5.45252 ( 342) covalent geometry : bond 0.00434 ( 4221) covalent geometry : angle 0.51688 ( 5628) *********************** 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 115 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 22 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7708 (mp0) REVERT: AN 22 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7068 (mp0) REVERT: AN 23 ASP cc_start: 0.7729 (t0) cc_final: 0.7332 (t0) REVERT: AO 23 ASP cc_start: 0.8067 (t0) cc_final: 0.7557 (t0) REVERT: AQ 13 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.5904 (m-70) REVERT: AQ 23 ASP cc_start: 0.7807 (t0) cc_final: 0.6961 (t70) REVERT: AQ 28 LYS cc_start: 0.8491 (mttt) cc_final: 0.8184 (mttm) REVERT: AR 23 ASP cc_start: 0.8013 (t0) cc_final: 0.7091 (t0) REVERT: AT 23 ASP cc_start: 0.7868 (t0) cc_final: 0.7377 (t0) REVERT: AV 22 GLU cc_start: 0.7491 (mp0) cc_final: 0.7203 (mp0) REVERT: AW 22 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7284 (mp0) REVERT: AW 23 ASP cc_start: 0.7970 (t0) cc_final: 0.7338 (t0) REVERT: AX 13 HIS cc_start: 0.6917 (OUTLIER) cc_final: 0.5975 (m-70) REVERT: AX 16 LYS cc_start: 0.7743 (mttt) cc_final: 0.7016 (mttp) REVERT: AY 16 LYS cc_start: 0.7948 (mttt) cc_final: 0.7427 (mttp) REVERT: AY 23 ASP cc_start: 0.8227 (m-30) cc_final: 0.7154 (t70) REVERT: AZ 16 LYS cc_start: 0.8013 (mttt) cc_final: 0.6828 (mptt) REVERT: AZ 28 LYS cc_start: 0.8891 (mttt) cc_final: 0.8607 (mttm) REVERT: Aa 22 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6650 (mp0) REVERT: Ac 22 GLU cc_start: 0.7774 (mp0) cc_final: 0.7370 (mp0) REVERT: Ae 19 PHE cc_start: 0.8031 (t80) cc_final: 0.7698 (t80) REVERT: Ae 35 MET cc_start: 0.7975 (ttp) cc_final: 0.7309 (ptm) outliers start: 19 outliers final: 14 residues processed: 112 average time/residue: 0.2504 time to fit residues: 37.7976 Evaluate side-chains 109 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 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 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 29 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 1.1980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 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 = 0.4369 r_free = 0.4369 target = 0.126256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.116787 restraints weight = 19771.537| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.87 r_work: 0.4081 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4221 Z= 0.187 Angle : 0.494 4.150 5628 Z= 0.275 Chirality : 0.053 0.137 630 Planarity : 0.002 0.008 714 Dihedral : 6.380 23.962 546 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 4.76 % Allowed : 16.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISAR 13 PHE 0.017 0.002 PHEAU 20 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 114) hydrogen bonds : angle 5.38247 ( 342) covalent geometry : bond 0.00383 ( 4221) covalent geometry : angle 0.49376 ( 5628) *********************** 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 118 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AM 22 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7601 (mp0) REVERT: AN 22 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7060 (mp0) REVERT: AN 23 ASP cc_start: 0.7773 (t0) cc_final: 0.7297 (t0) REVERT: AO 23 ASP cc_start: 0.7940 (t0) cc_final: 0.7347 (t70) REVERT: AQ 13 HIS cc_start: 0.6815 (OUTLIER) cc_final: 0.5778 (m-70) REVERT: AQ 23 ASP cc_start: 0.7773 (t0) cc_final: 0.6870 (t70) REVERT: AQ 28 LYS cc_start: 0.8426 (mttt) cc_final: 0.8107 (mttm) REVERT: AR 23 ASP cc_start: 0.7885 (t0) cc_final: 0.6920 (t0) REVERT: AS 28 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.7893 (mtmm) REVERT: AT 23 ASP cc_start: 0.7777 (t0) cc_final: 0.7205 (t0) REVERT: AW 22 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7226 (mp0) REVERT: AW 23 ASP cc_start: 0.7939 (t0) cc_final: 0.7268 (t0) REVERT: AX 13 HIS cc_start: 0.6778 (OUTLIER) cc_final: 0.5864 (m-70) REVERT: AX 16 LYS cc_start: 0.7672 (mttt) cc_final: 0.6929 (mttp) REVERT: AX 22 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7308 (pt0) REVERT: AY 16 LYS cc_start: 0.7880 (mttt) cc_final: 0.7351 (mttp) REVERT: AY 23 ASP cc_start: 0.8142 (m-30) cc_final: 0.7002 (t70) REVERT: AY 28 LYS cc_start: 0.8704 (mttt) cc_final: 0.8336 (mttt) REVERT: AZ 16 LYS cc_start: 0.7910 (mttt) cc_final: 0.6726 (mptt) REVERT: AZ 28 LYS cc_start: 0.8835 (mttt) cc_final: 0.8499 (mttm) REVERT: Aa 22 GLU cc_start: 0.7764 (mt-10) cc_final: 0.6788 (mp0) REVERT: Ab 22 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6796 (mp0) REVERT: Ac 19 PHE cc_start: 0.7535 (t80) cc_final: 0.7287 (t80) REVERT: Ac 22 GLU cc_start: 0.7785 (mp0) cc_final: 0.7391 (mp0) REVERT: Ad 19 PHE cc_start: 0.7875 (t80) cc_final: 0.7593 (t80) REVERT: Ad 22 GLU cc_start: 0.7872 (mp0) cc_final: 0.7620 (mp0) REVERT: Ae 19 PHE cc_start: 0.7957 (t80) cc_final: 0.7665 (t80) REVERT: Ae 35 MET cc_start: 0.7888 (ttp) cc_final: 0.7191 (ptm) REVERT: Af 35 MET cc_start: 0.7912 (ttp) cc_final: 0.7708 (ttp) outliers start: 20 outliers final: 13 residues processed: 116 average time/residue: 0.2639 time to fit residues: 40.7131 Evaluate side-chains 113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 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 AS residue 28 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4361 r_free = 0.4361 target = 0.125849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.116449 restraints weight = 19838.382| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.89 r_work: 0.4074 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.4895 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= 0.194 Angle : 0.496 4.093 5628 Z= 0.276 Chirality : 0.053 0.140 630 Planarity : 0.002 0.007 714 Dihedral : 6.363 22.671 546 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 5.00 % Allowed : 15.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (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 HIS 0.003 0.001 HISAR 13 PHE 0.016 0.002 PHEAU 20 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 114) hydrogen bonds : angle 5.36932 ( 342) covalent geometry : bond 0.00400 ( 4221) covalent geometry : angle 0.49567 ( 5628) *********************** 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 117 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 22 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7633 (mp0) REVERT: AN 22 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7047 (mp0) REVERT: AN 23 ASP cc_start: 0.7661 (t0) cc_final: 0.7232 (t0) REVERT: AO 23 ASP cc_start: 0.8003 (t0) cc_final: 0.7389 (t70) REVERT: AQ 13 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.5675 (m-70) REVERT: AQ 23 ASP cc_start: 0.7776 (t0) cc_final: 0.6926 (t70) REVERT: AQ 28 LYS cc_start: 0.8428 (mttt) cc_final: 0.8103 (mttm) REVERT: AR 23 ASP cc_start: 0.7828 (t0) cc_final: 0.6941 (t0) REVERT: AT 23 ASP cc_start: 0.7713 (t0) cc_final: 0.7104 (t0) REVERT: AW 22 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7298 (mp0) REVERT: AW 23 ASP cc_start: 0.8029 (t0) cc_final: 0.7359 (t0) REVERT: AX 13 HIS cc_start: 0.6796 (OUTLIER) cc_final: 0.5862 (m-70) REVERT: AX 16 LYS cc_start: 0.7654 (mttt) cc_final: 0.6917 (mttp) REVERT: AX 22 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7371 (pt0) REVERT: AY 16 LYS cc_start: 0.7862 (mttt) cc_final: 0.7329 (mttp) REVERT: AY 23 ASP cc_start: 0.8188 (m-30) cc_final: 0.7143 (t70) REVERT: AY 28 LYS cc_start: 0.8697 (mttt) cc_final: 0.8341 (mttt) REVERT: AZ 16 LYS cc_start: 0.7918 (mttt) cc_final: 0.6720 (mptt) REVERT: AZ 28 LYS cc_start: 0.8832 (mttt) cc_final: 0.8523 (mttm) REVERT: Aa 22 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6681 (mp0) REVERT: Ac 22 GLU cc_start: 0.7777 (mp0) cc_final: 0.7360 (mp0) REVERT: Ad 19 PHE cc_start: 0.7897 (t80) cc_final: 0.7629 (t80) REVERT: Ae 19 PHE cc_start: 0.7946 (t80) cc_final: 0.7657 (t80) REVERT: Ae 35 MET cc_start: 0.7842 (ttp) cc_final: 0.7156 (ptm) REVERT: Af 35 MET cc_start: 0.7901 (ttp) cc_final: 0.7692 (ttp) outliers start: 21 outliers final: 16 residues processed: 113 average time/residue: 0.2702 time to fit residues: 40.4172 Evaluate side-chains 112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 AN residue 13 HIS Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AO residue 13 HIS 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 AS residue 28 LYS 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 35 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4308 r_free = 0.4308 target = 0.122243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.113154 restraints weight = 20326.747| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.85 r_work: 0.4021 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4221 Z= 0.305 Angle : 0.601 4.342 5628 Z= 0.332 Chirality : 0.053 0.152 630 Planarity : 0.003 0.011 714 Dihedral : 6.938 23.743 546 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 5.48 % Allowed : 16.19 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISAR 13 PHE 0.025 0.003 PHEAU 20 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 114) hydrogen bonds : angle 5.49075 ( 342) covalent geometry : bond 0.00636 ( 4221) covalent geometry : angle 0.60122 ( 5628) *********************** 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 115 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 22 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7605 (mp0) REVERT: AN 22 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7099 (mp0) REVERT: AN 23 ASP cc_start: 0.7836 (t0) cc_final: 0.7323 (t0) REVERT: AO 23 ASP cc_start: 0.8142 (t0) cc_final: 0.7551 (t70) REVERT: AQ 13 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.5704 (m-70) REVERT: AQ 23 ASP cc_start: 0.7954 (t0) cc_final: 0.7053 (t70) REVERT: AQ 28 LYS cc_start: 0.8423 (mttt) cc_final: 0.8091 (mttp) REVERT: AR 23 ASP cc_start: 0.8007 (t0) cc_final: 0.7355 (t0) REVERT: AT 23 ASP cc_start: 0.7912 (t0) cc_final: 0.7667 (t0) REVERT: AW 22 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7276 (mp0) REVERT: AW 23 ASP cc_start: 0.8255 (t0) cc_final: 0.7800 (t0) REVERT: AX 13 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.6049 (m-70) REVERT: AX 22 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7378 (pt0) REVERT: AY 16 LYS cc_start: 0.7942 (mttt) cc_final: 0.7373 (mttp) REVERT: AZ 28 LYS cc_start: 0.8851 (mttt) cc_final: 0.8536 (mttm) REVERT: Aa 22 GLU cc_start: 0.7744 (mt-10) cc_final: 0.6899 (mp0) REVERT: Ab 22 GLU cc_start: 0.7655 (mt-10) cc_final: 0.6893 (mp0) REVERT: Ad 19 PHE cc_start: 0.7904 (t80) cc_final: 0.7650 (t80) REVERT: Ae 19 PHE cc_start: 0.8004 (t80) cc_final: 0.7649 (t80) REVERT: Ae 35 MET cc_start: 0.7912 (ttp) cc_final: 0.7089 (ptm) REVERT: Af 22 GLU cc_start: 0.8290 (mp0) cc_final: 0.8064 (mp0) REVERT: Af 35 MET cc_start: 0.7953 (ttp) cc_final: 0.7736 (ttp) outliers start: 23 outliers final: 16 residues processed: 112 average time/residue: 0.3828 time to fit residues: 57.0826 Evaluate side-chains 109 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 AN residue 13 HIS Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AO residue 13 HIS 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 AS residue 28 LYS 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 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.123658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.114499 restraints weight = 19946.899| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 2.84 r_work: 0.4044 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4221 Z= 0.225 Angle : 0.532 4.291 5628 Z= 0.294 Chirality : 0.053 0.148 630 Planarity : 0.002 0.008 714 Dihedral : 6.595 23.210 546 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 4.29 % Allowed : 17.62 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISAT 13 PHE 0.018 0.003 PHEAU 20 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 114) hydrogen bonds : angle 5.36393 ( 342) covalent geometry : bond 0.00468 ( 4221) covalent geometry : angle 0.53186 ( 5628) ********************** 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 112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AM 22 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7708 (mp0) REVERT: AN 22 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7123 (mp0) REVERT: AN 23 ASP cc_start: 0.7762 (t0) cc_final: 0.7303 (t0) REVERT: AO 23 ASP cc_start: 0.8032 (t0) cc_final: 0.7401 (t70) REVERT: AQ 13 HIS cc_start: 0.6650 (OUTLIER) cc_final: 0.5645 (m-70) REVERT: AQ 23 ASP cc_start: 0.7919 (t0) cc_final: 0.7041 (t70) REVERT: AQ 28 LYS cc_start: 0.8490 (mttt) cc_final: 0.8170 (mttp) REVERT: AR 22 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7336 (mp0) REVERT: AR 23 ASP cc_start: 0.8059 (t0) cc_final: 0.7163 (t0) REVERT: AT 23 ASP cc_start: 0.7801 (t0) cc_final: 0.7210 (t0) REVERT: AW 22 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7371 (mp0) REVERT: AW 23 ASP cc_start: 0.8189 (t0) cc_final: 0.7710 (t0) REVERT: AX 13 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.5940 (m-70) REVERT: AX 22 GLU cc_start: 0.7610 (mt-10) cc_final: 0.6882 (mp0) REVERT: AY 16 LYS cc_start: 0.7927 (mttt) cc_final: 0.7393 (mttp) REVERT: AY 22 GLU cc_start: 0.7658 (mp0) cc_final: 0.7032 (pt0) REVERT: AZ 16 LYS cc_start: 0.7936 (mttt) cc_final: 0.6810 (mptt) REVERT: Aa 22 GLU cc_start: 0.7689 (mt-10) cc_final: 0.6843 (mp0) REVERT: Ad 19 PHE cc_start: 0.7885 (t80) cc_final: 0.7626 (t80) REVERT: Ae 19 PHE cc_start: 0.8009 (t80) cc_final: 0.7650 (t80) REVERT: Ae 35 MET cc_start: 0.7831 (ttp) cc_final: 0.7048 (ptm) REVERT: Af 22 GLU cc_start: 0.8206 (mp0) cc_final: 0.7789 (mp0) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 0.2851 time to fit residues: 42.4308 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 : 0.783 ------------------------------------------------------------------------------- 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 AN residue 13 HIS Chi-restraints excluded: chain AN residue 24 VAL Chi-restraints excluded: chain AO residue 13 HIS Chi-restraints excluded: chain AP residue 13 HIS 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 AS residue 28 LYS 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 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 2 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.122143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.113410 restraints weight = 20397.106| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.71 r_work: 0.4030 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4221 Z= 0.240 Angle : 0.552 5.508 5628 Z= 0.306 Chirality : 0.053 0.143 630 Planarity : 0.002 0.017 714 Dihedral : 6.666 23.676 546 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.71 % Favored : 86.29 % Rotamer: Outliers : 4.05 % Allowed : 18.10 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISAR 13 PHE 0.020 0.003 PHEAU 20 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 114) hydrogen bonds : angle 5.31223 ( 342) covalent geometry : bond 0.00500 ( 4221) covalent geometry : angle 0.55205 ( 5628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4811.87 seconds wall clock time: 85 minutes 15.45 seconds (5115.45 seconds total)