Starting phenix.real_space_refine on Sat Jul 26 08:55:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9umh_64274/07_2025/9umh_64274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9umh_64274/07_2025/9umh_64274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9umh_64274/07_2025/9umh_64274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9umh_64274/07_2025/9umh_64274.map" model { file = "/net/cci-nas-00/data/ceres_data/9umh_64274/07_2025/9umh_64274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9umh_64274/07_2025/9umh_64274.cif" } resolution = 3.1 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): 0.02s 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: 4.84, per 1000 atoms: 0.57 Number of scatterers: 8421 At special positions: 0 Unit cell: (101.01, 58.83, 69.93, 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: 2.00 Conformation dependent library (CDL) restraints added in 712.1 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 6 sheets defined 0.0% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'AL' and resid 14 through 20 removed outlier: 6.115A pdb=" N HISAL 14 " --> pdb=" O GLNAN 15 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEUAN 17 " --> pdb=" O HISAL 14 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYSAL 16 " --> pdb=" O LEUAN 17 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHEAN 19 " --> pdb=" O LYSAL 16 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VALAL 18 " --> pdb=" O PHEAN 19 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEUAf 17 " --> pdb=" O HISAd 14 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYSAd 16 " --> pdb=" O LEUAf 17 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHEAf 19 " --> pdb=" O LYSAd 16 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VALAd 18 " --> pdb=" O PHEAf 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AL' and resid 30 through 32 removed outlier: 6.379A pdb=" N ILEAL 31 " --> pdb=" O ILEAN 32 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILEAN 31 " --> pdb=" O ILEAP 32 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILEAP 31 " --> pdb=" O ILEAR 32 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILEAR 31 " --> pdb=" O ILEAT 32 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILEAT 31 " --> pdb=" O ILEAV 32 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILEAV 31 " --> pdb=" O ILEAX 32 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILEAX 31 " --> pdb=" O ILEAZ 32 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILEAZ 31 " --> pdb=" O ILEAb 32 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILEAb 31 " --> pdb=" O ILEAd 32 " (cutoff:3.500A) removed outlier: 6.209A 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 'AL' and resid 35 through 37 removed outlier: 6.255A pdb=" N VALAL 36 " --> pdb=" O GLYAN 37 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VALAN 36 " --> pdb=" O GLYAP 37 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VALAP 36 " --> pdb=" O GLYAR 37 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VALAR 36 " --> pdb=" O GLYAT 37 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VALAT 36 " --> pdb=" O GLYAV 37 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VALAV 36 " --> pdb=" O GLYAX 37 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VALAX 36 " --> pdb=" O GLYAZ 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AM' and resid 14 through 20 removed outlier: 6.117A pdb=" N HISAM 14 " --> pdb=" O GLNAO 15 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEUAO 17 " --> pdb=" O HISAM 14 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYSAM 16 " --> pdb=" O LEUAO 17 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHEAO 19 " --> pdb=" O LYSAM 16 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VALAM 18 " --> pdb=" O PHEAO 19 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N HISAQ 14 " --> pdb=" O GLNAS 15 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEUAS 17 " --> pdb=" O HISAQ 14 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYSAQ 16 " --> pdb=" O LEUAS 17 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHEAS 19 " --> pdb=" O LYSAQ 16 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VALAQ 18 " --> pdb=" O PHEAS 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AM' and resid 30 through 37 removed outlier: 6.330A pdb=" N ILEAM 31 " --> pdb=" O ILEAO 32 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEUAO 34 " --> pdb=" O ILEAM 31 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLYAM 33 " --> pdb=" O LEUAO 34 " (cutoff:3.500A) removed outlier: 10.175A pdb=" N VALAO 36 " --> pdb=" O GLYAM 33 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N METAM 35 " --> pdb=" O VALAO 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILEAO 31 " --> pdb=" O ILEAQ 32 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILEAQ 31 " --> pdb=" O ILEAS 32 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILEAS 31 " --> pdb=" O ILEAU 32 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILEAU 31 " --> pdb=" O ILEAW 32 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILEAW 31 " --> pdb=" O ILEAY 32 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILEAY 31 " --> pdb=" O ILEAa 32 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILEAa 31 " --> pdb=" O ILEAc 32 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILEAc 31 " --> pdb=" O ILEAe 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'AM' and resid 30 through 37 removed outlier: 6.330A pdb=" N ILEAM 31 " --> pdb=" O ILEAO 32 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEUAO 34 " --> pdb=" O ILEAM 31 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLYAM 33 " --> pdb=" O LEUAO 34 " (cutoff:3.500A) removed outlier: 10.175A pdb=" N VALAO 36 " --> pdb=" O GLYAM 33 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N METAM 35 " --> pdb=" O VALAO 36 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N METAQ 35 " --> pdb=" O ILEAO 32 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEUAO 34 " --> pdb=" O METAQ 35 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLYAQ 37 " --> pdb=" O LEUAO 34 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VALAO 36 " --> pdb=" O GLYAQ 37 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VALAQ 36 " --> pdb=" O GLYAS 37 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VALAS 36 " --> pdb=" O GLYAU 37 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VALAU 36 " --> pdb=" O GLYAW 37 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VALAW 36 " --> pdb=" O GLYAY 37 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VALAY 36 " --> pdb=" O GLYAa 37 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VALAa 36 " --> pdb=" O GLYAc 37 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 285 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: 2.81 Time building geometry restraints manager: 2.50 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: 291 1.23 - 1.42: 1473 1.42 - 1.61: 2415 1.61 - 1.81: 42 Bond restraints: 8484 Sorted by residual: bond pdb=" N ALAAW 30 " pdb=" H ALAAW 30 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.66e+00 bond pdb=" N LYSAS 28 " pdb=" H LYSAS 28 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.64e+00 bond pdb=" N ALAAT 21 " pdb=" H ALAAT 21 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.63e+00 bond pdb=" N LYSAU 16 " pdb=" H LYSAU 16 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.62e+00 bond pdb=" N LYSAZ 28 " pdb=" H LYSAZ 28 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.62e+00 ... (remaining 8479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 12106 1.48 - 2.95: 1877 2.95 - 4.43: 436 4.43 - 5.90: 887 5.90 - 7.38: 24 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 112.60 116.83 -4.23 1.00e+00 1.00e+00 1.79e+01 angle pdb=" CA ASPAT 23 " pdb=" CB ASPAT 23 " pdb=" CG ASPAT 23 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA ASPAM 23 " pdb=" CB ASPAM 23 " pdb=" CG ASPAM 23 " ideal model delta sigma weight residual 112.60 116.74 -4.14 1.00e+00 1.00e+00 1.71e+01 angle pdb=" CA ASPAa 23 " pdb=" CB ASPAa 23 " pdb=" CG ASPAa 23 " ideal model delta sigma weight residual 112.60 116.66 -4.06 1.00e+00 1.00e+00 1.65e+01 angle pdb=" CA ASPAO 23 " pdb=" CB ASPAO 23 " pdb=" CG ASPAO 23 " ideal model delta sigma weight residual 112.60 116.65 -4.05 1.00e+00 1.00e+00 1.64e+01 ... (remaining 15325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.93: 3394 13.93 - 27.85: 180 27.85 - 41.78: 73 41.78 - 55.70: 42 55.70 - 69.63: 217 Dihedral angle restraints: 3906 sinusoidal: 2058 harmonic: 1848 Sorted by residual: 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 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 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 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+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 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 3903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 108 0.026 - 0.051: 175 0.051 - 0.077: 140 0.077 - 0.103: 153 0.103 - 0.128: 54 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 4.11e-01 chirality pdb=" CB VALAf 39 " pdb=" CA VALAf 39 " pdb=" CG1 VALAf 39 " pdb=" CG2 VALAf 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.12 2.00e-01 2.50e+01 3.90e-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 2.39 0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 627 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEAV 20 " 0.009 2.00e-02 2.50e+03 6.10e-03 1.12e+00 pdb=" CG PHEAV 20 " -0.019 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 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHEAV 20 " 0.001 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 HISAR 13 " -0.006 2.00e-02 2.50e+03 6.44e-03 1.04e+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 " -0.007 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 " -0.003 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 delta sigma weight rms_deltas residual plane pdb=" CB HISAZ 13 " -0.006 2.00e-02 2.50e+03 6.20e-03 9.61e-01 pdb=" CG HISAZ 13 " 0.017 2.00e-02 2.50e+03 pdb=" ND1 HISAZ 13 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HISAZ 13 " -0.006 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 " -0.002 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 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 623 2.21 - 2.81: 16125 2.81 - 3.40: 20366 3.40 - 4.00: 31657 4.00 - 4.60: 45075 Nonbonded interactions: 113846 Sorted by model distance: nonbonded pdb=" OD1 ASPAZ 23 " pdb=" HG SERAZ 26 " model vdw 1.610 2.450 nonbonded pdb=" OD1 ASPAU 23 " pdb=" HG SERAU 26 " model vdw 1.637 2.450 nonbonded pdb=" OD1 ASPAP 23 " pdb=" HG SERAP 26 " model vdw 1.656 2.450 nonbonded pdb=" O ASNAc 27 " pdb=" H LYSAe 28 " model vdw 1.760 2.450 nonbonded pdb=" O ASNAa 27 " pdb=" H LYSAc 28 " model vdw 1.772 2.450 ... (remaining 113841 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: 2.340 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: 0.140 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.570 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 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 : 0.008 0.033 4221 Z= 0.518 Angle : 1.169 7.380 5628 Z= 0.729 Chirality : 0.067 0.128 630 Planarity : 0.002 0.008 714 Dihedral : 11.425 69.626 1428 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.10 % Favored : 89.52 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % 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: -2.39 (0.29), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HISAR 13 PHE 0.018 0.003 PHEAV 20 Details of bonding type rmsd hydrogen bonds : bond 0.20266 ( 95) hydrogen bonds : angle 7.85729 ( 285) covalent geometry : bond 0.00849 ( 4221) covalent geometry : angle 1.16911 ( 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 139 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.591 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: AL 23 ASP cc_start: 0.7895 (p0) cc_final: 0.7046 (p0) REVERT: AL 28 LYS cc_start: 0.8598 (mttt) cc_final: 0.8283 (mttp) REVERT: AN 22 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6407 (pt0) REVERT: AO 23 ASP cc_start: 0.8227 (t0) cc_final: 0.7901 (t0) REVERT: AP 23 ASP cc_start: 0.7824 (t70) cc_final: 0.7097 (t0) REVERT: AP 28 LYS cc_start: 0.8255 (mttt) cc_final: 0.7937 (mttp) REVERT: AR 28 LYS cc_start: 0.8293 (mttt) cc_final: 0.8069 (mttp) REVERT: AV 22 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6843 (mm-30) REVERT: AW 28 LYS cc_start: 0.8246 (mttt) cc_final: 0.8021 (mttp) REVERT: AX 23 ASP cc_start: 0.8099 (t0) cc_final: 0.7887 (t0) REVERT: AX 28 LYS cc_start: 0.7977 (mttt) cc_final: 0.7770 (mttp) REVERT: AY 23 ASP cc_start: 0.7666 (m-30) cc_final: 0.7428 (m-30) REVERT: AY 28 LYS cc_start: 0.8304 (mttt) cc_final: 0.8025 (mttt) REVERT: AZ 15 GLN cc_start: 0.5815 (mt0) cc_final: 0.5494 (mt0) REVERT: AZ 23 ASP cc_start: 0.7832 (t70) cc_final: 0.7487 (t0) REVERT: Aa 23 ASP cc_start: 0.8262 (t0) cc_final: 0.7146 (t0) REVERT: Ab 23 ASP cc_start: 0.8286 (t0) cc_final: 0.8060 (t0) REVERT: Ac 23 ASP cc_start: 0.7593 (m-30) cc_final: 0.7346 (m-30) REVERT: Ac 28 LYS cc_start: 0.8587 (mttt) cc_final: 0.8157 (mttp) REVERT: Ae 28 LYS cc_start: 0.8668 (mttt) cc_final: 0.8440 (mtmt) REVERT: Af 28 LYS cc_start: 0.8603 (mttt) cc_final: 0.8345 (mttt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.5478 time to fit residues: 88.2728 Evaluate side-chains 80 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.128457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.108148 restraints weight = 16954.154| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 3.53 r_work: 0.3970 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4221 Z= 0.156 Angle : 0.549 3.957 5628 Z= 0.286 Chirality : 0.054 0.132 630 Planarity : 0.002 0.009 714 Dihedral : 6.083 25.004 546 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.71 % Allowed : 4.52 % Favored : 94.76 % 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: -1.91 (0.31), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISAX 14 PHE 0.014 0.001 PHEAS 19 Details of bonding type rmsd hydrogen bonds : bond 0.02811 ( 95) hydrogen bonds : angle 4.54255 ( 285) covalent geometry : bond 0.00330 ( 4221) covalent geometry : angle 0.54858 ( 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 113 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AL 23 ASP cc_start: 0.7912 (p0) cc_final: 0.7055 (p0) REVERT: AL 28 LYS cc_start: 0.8939 (mttt) cc_final: 0.8545 (mttp) REVERT: AM 22 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6834 (pm20) REVERT: AM 23 ASP cc_start: 0.8455 (t0) cc_final: 0.8079 (t0) REVERT: AM 28 LYS cc_start: 0.8766 (mttt) cc_final: 0.8561 (mttt) REVERT: AN 15 GLN cc_start: 0.5875 (mt0) cc_final: 0.5599 (mt0) REVERT: AO 23 ASP cc_start: 0.8448 (t0) cc_final: 0.8187 (t0) REVERT: AP 15 GLN cc_start: 0.5784 (mt0) cc_final: 0.5496 (mt0) REVERT: AP 23 ASP cc_start: 0.8181 (t0) cc_final: 0.7737 (t0) REVERT: AP 28 LYS cc_start: 0.8864 (mttt) cc_final: 0.8578 (mttp) REVERT: AR 28 LYS cc_start: 0.8805 (mttt) cc_final: 0.8569 (mtmt) REVERT: AS 15 GLN cc_start: 0.6100 (mt0) cc_final: 0.5876 (mt0) REVERT: AS 22 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7041 (mt-10) REVERT: AU 22 GLU cc_start: 0.7967 (tp30) cc_final: 0.7663 (tp30) REVERT: AU 23 ASP cc_start: 0.8364 (t70) cc_final: 0.7964 (t0) REVERT: AW 23 ASP cc_start: 0.8430 (t0) cc_final: 0.7764 (t0) REVERT: AW 28 LYS cc_start: 0.8740 (mttt) cc_final: 0.8381 (mttp) REVERT: AX 23 ASP cc_start: 0.8125 (t0) cc_final: 0.7807 (t0) REVERT: AX 28 LYS cc_start: 0.8725 (mttt) cc_final: 0.8461 (mtmt) REVERT: AY 28 LYS cc_start: 0.8720 (mttt) cc_final: 0.8409 (mttt) REVERT: Aa 23 ASP cc_start: 0.8150 (t0) cc_final: 0.7448 (t0) REVERT: Ab 23 ASP cc_start: 0.8334 (t0) cc_final: 0.7766 (t0) REVERT: Ac 28 LYS cc_start: 0.8917 (mttt) cc_final: 0.8391 (mttp) REVERT: Ad 22 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7617 (tp30) REVERT: Ae 23 ASP cc_start: 0.8470 (m-30) cc_final: 0.8238 (m-30) REVERT: Ae 28 LYS cc_start: 0.8854 (mttt) cc_final: 0.8608 (mttt) outliers start: 3 outliers final: 0 residues processed: 112 average time/residue: 0.3258 time to fit residues: 46.3011 Evaluate side-chains 93 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 22 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.103455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.083723 restraints weight = 18351.404| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.26 r_work: 0.3627 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.6484 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= 0.252 Angle : 0.621 4.766 5628 Z= 0.324 Chirality : 0.054 0.132 630 Planarity : 0.002 0.010 714 Dihedral : 6.347 24.266 546 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.33 % Allowed : 7.14 % Favored : 89.52 % 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: -1.80 (0.32), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HISAe 14 PHE 0.021 0.002 PHEAf 20 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 95) hydrogen bonds : angle 4.99446 ( 285) covalent geometry : bond 0.00550 ( 4221) covalent geometry : angle 0.62085 ( 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 101 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: AL 23 ASP cc_start: 0.8103 (p0) cc_final: 0.7241 (p0) REVERT: AL 28 LYS cc_start: 0.8840 (mttt) cc_final: 0.8424 (mttp) REVERT: AM 19 PHE cc_start: 0.8379 (t80) cc_final: 0.8166 (t80) REVERT: AN 23 ASP cc_start: 0.8188 (t0) cc_final: 0.7852 (t0) REVERT: AO 23 ASP cc_start: 0.7991 (t0) cc_final: 0.7687 (t0) REVERT: AP 23 ASP cc_start: 0.7819 (t0) cc_final: 0.7251 (t0) REVERT: AP 28 LYS cc_start: 0.8770 (mttt) cc_final: 0.8449 (mttp) REVERT: AR 16 LYS cc_start: 0.7786 (mttt) cc_final: 0.7497 (mttm) REVERT: AR 23 ASP cc_start: 0.8507 (t0) cc_final: 0.8246 (t0) REVERT: AR 28 LYS cc_start: 0.8703 (mttt) cc_final: 0.8449 (mttp) REVERT: AS 23 ASP cc_start: 0.8078 (m-30) cc_final: 0.7718 (m-30) REVERT: AU 23 ASP cc_start: 0.8602 (t70) cc_final: 0.7983 (t0) REVERT: AV 23 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7591 (t0) REVERT: AW 28 LYS cc_start: 0.8664 (mttt) cc_final: 0.8335 (mttp) REVERT: AX 28 LYS cc_start: 0.8603 (mttt) cc_final: 0.8322 (mtmt) REVERT: AX 35 MET cc_start: 0.8687 (ttp) cc_final: 0.8445 (ttm) REVERT: AZ 23 ASP cc_start: 0.8072 (t0) cc_final: 0.7635 (t0) REVERT: Aa 23 ASP cc_start: 0.7885 (t0) cc_final: 0.7640 (t0) REVERT: Ac 28 LYS cc_start: 0.8710 (mttt) cc_final: 0.8365 (mttp) REVERT: Ae 28 LYS cc_start: 0.8844 (mttt) cc_final: 0.8617 (mttp) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 0.3687 time to fit residues: 43.5707 Evaluate side-chains 92 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 24 VAL Chi-restraints excluded: chain AO residue 39 VAL Chi-restraints excluded: chain AQ residue 39 VAL Chi-restraints excluded: chain AV residue 23 ASP Chi-restraints excluded: chain AW residue 39 VAL Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AY residue 39 VAL Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ad residue 39 VAL Chi-restraints excluded: chain Ae residue 23 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 10 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.102976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.081224 restraints weight = 18411.358| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.39 r_work: 0.3539 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.6910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 4221 Z= 0.154 Angle : 0.472 5.198 5628 Z= 0.250 Chirality : 0.053 0.130 630 Planarity : 0.001 0.005 714 Dihedral : 5.725 22.213 546 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 1.43 % Allowed : 10.71 % Favored : 87.86 % 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: -1.57 (0.33), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HISAe 14 PHE 0.009 0.001 PHEAL 20 Details of bonding type rmsd hydrogen bonds : bond 0.02607 ( 95) hydrogen bonds : angle 4.73016 ( 285) covalent geometry : bond 0.00319 ( 4221) covalent geometry : angle 0.47247 ( 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 84 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: AL 23 ASP cc_start: 0.8225 (p0) cc_final: 0.7350 (p0) REVERT: AL 28 LYS cc_start: 0.8743 (mttt) cc_final: 0.8331 (mttp) REVERT: AM 22 GLU cc_start: 0.7746 (tt0) cc_final: 0.7221 (tp30) REVERT: AM 23 ASP cc_start: 0.8725 (t0) cc_final: 0.8494 (t0) REVERT: AN 23 ASP cc_start: 0.8147 (t0) cc_final: 0.7859 (t0) REVERT: AO 23 ASP cc_start: 0.8009 (t0) cc_final: 0.7646 (t70) REVERT: AP 28 LYS cc_start: 0.8719 (mttt) cc_final: 0.8475 (mttp) REVERT: AQ 16 LYS cc_start: 0.8041 (mttt) cc_final: 0.7644 (mttp) REVERT: AR 23 ASP cc_start: 0.8332 (t0) cc_final: 0.8098 (t0) REVERT: AR 28 LYS cc_start: 0.8714 (mttt) cc_final: 0.8475 (mttp) REVERT: AS 23 ASP cc_start: 0.7991 (m-30) cc_final: 0.7518 (m-30) REVERT: AU 23 ASP cc_start: 0.8523 (t0) cc_final: 0.8045 (t0) REVERT: AW 28 LYS cc_start: 0.8593 (mttt) cc_final: 0.8261 (mttp) REVERT: AX 28 LYS cc_start: 0.8494 (mttt) cc_final: 0.8185 (mtmt) REVERT: AZ 23 ASP cc_start: 0.8204 (t0) cc_final: 0.7751 (t0) REVERT: Aa 23 ASP cc_start: 0.7870 (t0) cc_final: 0.7556 (t0) REVERT: Ac 28 LYS cc_start: 0.8627 (mttt) cc_final: 0.8213 (mttp) REVERT: Ad 22 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: Ae 28 LYS cc_start: 0.8909 (mttt) cc_final: 0.8441 (mttt) outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.4258 time to fit residues: 42.6822 Evaluate side-chains 80 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AQ residue 39 VAL Chi-restraints excluded: chain AV residue 23 ASP Chi-restraints excluded: chain Ad residue 22 GLU Chi-restraints excluded: chain Ad residue 39 VAL Chi-restraints excluded: chain Ae residue 23 ASP 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: 0.9980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 12 optimal weight: 0.4980 chunk 5 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.102693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.082279 restraints weight = 19330.522| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.39 r_work: 0.3506 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.7207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4221 Z= 0.170 Angle : 0.474 4.566 5628 Z= 0.253 Chirality : 0.052 0.127 630 Planarity : 0.001 0.006 714 Dihedral : 5.673 22.810 546 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.86 % Allowed : 9.52 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.34), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HISAe 14 PHE 0.009 0.001 PHEAM 20 Details of bonding type rmsd hydrogen bonds : bond 0.02820 ( 95) hydrogen bonds : angle 4.80668 ( 285) covalent geometry : bond 0.00359 ( 4221) covalent geometry : angle 0.47444 ( 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 89 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.634 Fit side-chains REVERT: AL 23 ASP cc_start: 0.8262 (p0) cc_final: 0.7391 (p0) REVERT: AL 28 LYS cc_start: 0.8736 (mttt) cc_final: 0.8260 (mttp) REVERT: AN 23 ASP cc_start: 0.8057 (t0) cc_final: 0.7779 (t0) REVERT: AO 23 ASP cc_start: 0.8023 (t0) cc_final: 0.7646 (t70) REVERT: AP 28 LYS cc_start: 0.8627 (mttt) cc_final: 0.8395 (mttp) REVERT: AQ 16 LYS cc_start: 0.8089 (mttt) cc_final: 0.7711 (mttp) REVERT: AR 23 ASP cc_start: 0.8384 (t0) cc_final: 0.8167 (t0) REVERT: AR 28 LYS cc_start: 0.8703 (mttt) cc_final: 0.8467 (mttp) REVERT: AS 23 ASP cc_start: 0.8170 (m-30) cc_final: 0.7576 (m-30) REVERT: AU 23 ASP cc_start: 0.8644 (t0) cc_final: 0.7638 (t0) REVERT: AV 23 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7905 (t0) REVERT: AW 16 LYS cc_start: 0.8093 (mttt) cc_final: 0.7625 (mttp) REVERT: AW 28 LYS cc_start: 0.8584 (mttt) cc_final: 0.8252 (mttp) REVERT: AZ 23 ASP cc_start: 0.8051 (t0) cc_final: 0.7511 (t0) REVERT: Aa 23 ASP cc_start: 0.7796 (t0) cc_final: 0.7458 (t0) REVERT: Ac 28 LYS cc_start: 0.8623 (mttt) cc_final: 0.8192 (mttp) REVERT: Ad 22 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: Ae 28 LYS cc_start: 0.8888 (mttt) cc_final: 0.8457 (mttt) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.3548 time to fit residues: 36.7426 Evaluate side-chains 86 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 39 VAL Chi-restraints excluded: chain AQ residue 23 ASP Chi-restraints excluded: chain AQ residue 39 VAL Chi-restraints excluded: chain AS residue 39 VAL Chi-restraints excluded: chain AV residue 23 ASP Chi-restraints excluded: chain AW residue 39 VAL Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain Ac residue 23 ASP Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ad residue 22 GLU Chi-restraints excluded: chain Ad residue 39 VAL Chi-restraints excluded: chain Ae residue 23 ASP 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: 0.9990 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 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 = 0.4032 r_free = 0.4032 target = 0.101464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.080553 restraints weight = 18474.278| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.17 r_work: 0.3504 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.7558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4221 Z= 0.208 Angle : 0.497 4.732 5628 Z= 0.264 Chirality : 0.052 0.129 630 Planarity : 0.001 0.006 714 Dihedral : 5.777 22.216 546 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.86 % Allowed : 10.95 % Favored : 86.19 % 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: -1.66 (0.35), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAM 14 PHE 0.011 0.001 PHEAL 20 Details of bonding type rmsd hydrogen bonds : bond 0.02904 ( 95) hydrogen bonds : angle 5.02011 ( 285) covalent geometry : bond 0.00442 ( 4221) covalent geometry : angle 0.49745 ( 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 88 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.715 Fit side-chains REVERT: AL 16 LYS cc_start: 0.8205 (mttt) cc_final: 0.7913 (mttp) REVERT: AL 23 ASP cc_start: 0.8375 (p0) cc_final: 0.7527 (p0) REVERT: AL 28 LYS cc_start: 0.8805 (mttt) cc_final: 0.8444 (mttp) REVERT: AM 16 LYS cc_start: 0.8059 (mttt) cc_final: 0.7742 (mttm) REVERT: AN 23 ASP cc_start: 0.8227 (t0) cc_final: 0.7870 (t0) REVERT: AO 23 ASP cc_start: 0.8299 (t0) cc_final: 0.8030 (t0) REVERT: AP 28 LYS cc_start: 0.8700 (mttt) cc_final: 0.8464 (mttp) REVERT: AQ 16 LYS cc_start: 0.8202 (mttt) cc_final: 0.7840 (mttp) REVERT: AR 23 ASP cc_start: 0.8510 (t0) cc_final: 0.8270 (t0) REVERT: AR 28 LYS cc_start: 0.8793 (mttt) cc_final: 0.8554 (mttp) REVERT: AS 23 ASP cc_start: 0.8420 (m-30) cc_final: 0.7688 (m-30) REVERT: AU 23 ASP cc_start: 0.8738 (t0) cc_final: 0.7699 (t0) REVERT: AV 23 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8113 (t0) REVERT: AW 16 LYS cc_start: 0.8164 (mttt) cc_final: 0.7727 (mttp) REVERT: AW 28 LYS cc_start: 0.8684 (mttt) cc_final: 0.8370 (mttp) REVERT: AZ 23 ASP cc_start: 0.8254 (t0) cc_final: 0.7714 (t0) REVERT: Aa 23 ASP cc_start: 0.8052 (t0) cc_final: 0.7622 (t0) REVERT: Ac 28 LYS cc_start: 0.8639 (mttt) cc_final: 0.8226 (mttp) REVERT: Ad 22 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: Ae 23 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: Ae 28 LYS cc_start: 0.8991 (mttt) cc_final: 0.8570 (mttt) outliers start: 12 outliers final: 8 residues processed: 82 average time/residue: 0.5705 time to fit residues: 61.1785 Evaluate side-chains 87 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AQ residue 23 ASP Chi-restraints excluded: chain AQ residue 39 VAL Chi-restraints excluded: chain AS residue 39 VAL Chi-restraints excluded: chain AV residue 23 ASP Chi-restraints excluded: chain AW residue 39 VAL Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain Ac residue 23 ASP Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ad residue 22 GLU Chi-restraints excluded: chain Ad residue 39 VAL Chi-restraints excluded: chain Ae residue 23 ASP 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: 0.9980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 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 = 0.3981 r_free = 0.3981 target = 0.099298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.078657 restraints weight = 18782.607| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.06 r_work: 0.3482 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.7788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4221 Z= 0.205 Angle : 0.489 4.701 5628 Z= 0.260 Chirality : 0.052 0.130 630 Planarity : 0.001 0.005 714 Dihedral : 5.736 23.165 546 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 2.86 % Allowed : 10.95 % Favored : 86.19 % 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: -1.75 (0.35), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAe 14 PHE 0.009 0.001 PHEAL 20 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 95) hydrogen bonds : angle 5.00044 ( 285) covalent geometry : bond 0.00437 ( 4221) covalent geometry : angle 0.48937 ( 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 93 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: AL 23 ASP cc_start: 0.8359 (p0) cc_final: 0.7494 (p0) REVERT: AL 28 LYS cc_start: 0.8822 (mttt) cc_final: 0.8453 (mttp) REVERT: AM 16 LYS cc_start: 0.8095 (mttt) cc_final: 0.7803 (mttm) REVERT: AN 23 ASP cc_start: 0.8002 (t0) cc_final: 0.7722 (t0) REVERT: AQ 16 LYS cc_start: 0.8143 (mttt) cc_final: 0.7777 (mttp) REVERT: AR 23 ASP cc_start: 0.8516 (t0) cc_final: 0.8300 (t70) REVERT: AR 28 LYS cc_start: 0.8766 (mttt) cc_final: 0.8545 (mttp) REVERT: AS 23 ASP cc_start: 0.8379 (m-30) cc_final: 0.7694 (m-30) REVERT: AU 23 ASP cc_start: 0.8788 (t0) cc_final: 0.7785 (t0) REVERT: AV 23 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8038 (t0) REVERT: AW 16 LYS cc_start: 0.8073 (mttt) cc_final: 0.7645 (mttp) REVERT: AW 28 LYS cc_start: 0.8651 (mttt) cc_final: 0.8341 (mttp) REVERT: AZ 23 ASP cc_start: 0.8178 (t0) cc_final: 0.7639 (t0) REVERT: Aa 23 ASP cc_start: 0.7989 (t0) cc_final: 0.7569 (t0) REVERT: Ac 28 LYS cc_start: 0.8600 (mttt) cc_final: 0.8209 (mttp) REVERT: Ad 16 LYS cc_start: 0.8387 (mttt) cc_final: 0.8051 (mttm) REVERT: Ad 22 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7274 (mp0) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.4320 time to fit residues: 47.7150 Evaluate side-chains 85 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AQ residue 23 ASP Chi-restraints excluded: chain AQ residue 39 VAL Chi-restraints excluded: chain AS residue 39 VAL Chi-restraints excluded: chain AV residue 23 ASP Chi-restraints excluded: chain AW residue 39 VAL Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain Ac residue 23 ASP Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ad residue 22 GLU Chi-restraints excluded: chain Ad residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 24 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 = 0.3954 r_free = 0.3954 target = 0.098165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.077848 restraints weight = 19010.550| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.04 r_work: 0.3457 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.8024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 4221 Z= 0.253 Angle : 0.527 4.828 5628 Z= 0.278 Chirality : 0.052 0.128 630 Planarity : 0.002 0.006 714 Dihedral : 5.965 23.112 546 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 2.86 % Allowed : 11.19 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.82 (0.35), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HISAa 14 PHE 0.010 0.001 PHEAL 20 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 95) hydrogen bonds : angle 4.83031 ( 285) covalent geometry : bond 0.00543 ( 4221) covalent geometry : angle 0.52701 ( 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 88 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AL 23 ASP cc_start: 0.8397 (p0) cc_final: 0.7525 (p0) REVERT: AL 28 LYS cc_start: 0.8819 (mttt) cc_final: 0.8441 (mttp) REVERT: AN 23 ASP cc_start: 0.8126 (t0) cc_final: 0.7766 (t0) REVERT: AQ 16 LYS cc_start: 0.8123 (mttt) cc_final: 0.7702 (mttp) REVERT: AR 23 ASP cc_start: 0.8495 (t0) cc_final: 0.8199 (t0) REVERT: AR 28 LYS cc_start: 0.8733 (mttt) cc_final: 0.8524 (mttp) REVERT: AS 23 ASP cc_start: 0.8536 (m-30) cc_final: 0.8090 (m-30) REVERT: AU 23 ASP cc_start: 0.8728 (t0) cc_final: 0.8005 (t0) REVERT: AV 23 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8061 (t0) REVERT: AW 16 LYS cc_start: 0.7994 (mttt) cc_final: 0.7582 (mttp) REVERT: AW 28 LYS cc_start: 0.8642 (mttt) cc_final: 0.8310 (mttp) REVERT: AZ 23 ASP cc_start: 0.8269 (t0) cc_final: 0.7667 (t0) REVERT: Aa 23 ASP cc_start: 0.7993 (t0) cc_final: 0.7499 (t0) REVERT: Ac 28 LYS cc_start: 0.8619 (mttt) cc_final: 0.8213 (mttp) REVERT: Ad 16 LYS cc_start: 0.8373 (mttt) cc_final: 0.8019 (mttm) REVERT: Ad 22 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7351 (tp30) outliers start: 12 outliers final: 9 residues processed: 82 average time/residue: 0.3262 time to fit residues: 34.2734 Evaluate side-chains 85 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AL residue 24 VAL Chi-restraints excluded: chain AQ residue 23 ASP Chi-restraints excluded: chain AQ residue 39 VAL Chi-restraints excluded: chain AS residue 39 VAL Chi-restraints excluded: chain AV residue 23 ASP Chi-restraints excluded: chain AW residue 39 VAL Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain Ac residue 23 ASP Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ad residue 22 GLU Chi-restraints excluded: chain Ad residue 39 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.099482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.079963 restraints weight = 18852.312| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.94 r_work: 0.3510 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.8107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 4221 Z= 0.177 Angle : 0.458 4.216 5628 Z= 0.247 Chirality : 0.052 0.130 630 Planarity : 0.001 0.005 714 Dihedral : 5.630 22.829 546 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 2.14 % Allowed : 12.38 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.79 (0.36), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HISAP 14 PHE 0.007 0.001 PHEAL 20 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 95) hydrogen bonds : angle 4.64544 ( 285) covalent geometry : bond 0.00376 ( 4221) covalent geometry : angle 0.45848 ( 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 87 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: AL 23 ASP cc_start: 0.8351 (p0) cc_final: 0.7504 (p0) REVERT: AL 28 LYS cc_start: 0.8858 (mttt) cc_final: 0.8472 (mttp) REVERT: AM 16 LYS cc_start: 0.8303 (mttt) cc_final: 0.7980 (mttm) REVERT: AN 23 ASP cc_start: 0.8135 (t0) cc_final: 0.7872 (t0) REVERT: AO 23 ASP cc_start: 0.8582 (t0) cc_final: 0.8228 (t0) REVERT: AQ 16 LYS cc_start: 0.8273 (mttt) cc_final: 0.7876 (mttp) REVERT: AR 23 ASP cc_start: 0.8507 (t0) cc_final: 0.8300 (t70) REVERT: AR 28 LYS cc_start: 0.8777 (mttt) cc_final: 0.8551 (mttp) REVERT: AS 23 ASP cc_start: 0.8428 (m-30) cc_final: 0.8061 (m-30) REVERT: AU 23 ASP cc_start: 0.8792 (t0) cc_final: 0.8087 (t0) REVERT: AV 16 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7585 (mttp) REVERT: AV 23 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8038 (t0) REVERT: AW 16 LYS cc_start: 0.8183 (mttt) cc_final: 0.7796 (mttp) REVERT: AW 28 LYS cc_start: 0.8666 (mttt) cc_final: 0.8364 (mttp) REVERT: AX 16 LYS cc_start: 0.8191 (mttt) cc_final: 0.7897 (mttm) REVERT: AZ 23 ASP cc_start: 0.8236 (t0) cc_final: 0.7690 (t0) REVERT: Aa 23 ASP cc_start: 0.8066 (t0) cc_final: 0.7569 (t0) REVERT: Ac 28 LYS cc_start: 0.8602 (mttt) cc_final: 0.8209 (mttp) REVERT: Ad 16 LYS cc_start: 0.8542 (mttt) cc_final: 0.8184 (mttm) REVERT: Ad 22 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7343 (tp30) outliers start: 9 outliers final: 7 residues processed: 83 average time/residue: 0.3743 time to fit residues: 40.2155 Evaluate side-chains 87 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AQ residue 23 ASP Chi-restraints excluded: chain AQ residue 39 VAL Chi-restraints excluded: chain AS residue 39 VAL Chi-restraints excluded: chain AV residue 23 ASP Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain Ac residue 23 ASP Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ad residue 22 GLU Chi-restraints excluded: chain Ad residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 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: 0.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.099335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.079469 restraints weight = 18670.219| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.03 r_work: 0.3487 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.8196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 4221 Z= 0.204 Angle : 0.479 4.437 5628 Z= 0.256 Chirality : 0.052 0.127 630 Planarity : 0.001 0.005 714 Dihedral : 5.728 22.417 546 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.52 % Favored : 86.48 % Rotamer: Outliers : 2.14 % Allowed : 12.86 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.36), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HISAQ 13 PHE 0.008 0.001 PHEAL 20 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 95) hydrogen bonds : angle 4.49420 ( 285) covalent geometry : bond 0.00434 ( 4221) covalent geometry : angle 0.47929 ( 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 91 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AL 23 ASP cc_start: 0.8355 (p0) cc_final: 0.7565 (p0) REVERT: AL 28 LYS cc_start: 0.8835 (mttt) cc_final: 0.8456 (mttp) REVERT: AM 16 LYS cc_start: 0.8298 (mttt) cc_final: 0.7984 (mttm) REVERT: AN 23 ASP cc_start: 0.8166 (t0) cc_final: 0.7864 (t0) REVERT: AO 23 ASP cc_start: 0.8621 (t0) cc_final: 0.8165 (t0) REVERT: AQ 16 LYS cc_start: 0.8280 (mttt) cc_final: 0.7881 (mttp) REVERT: AR 23 ASP cc_start: 0.8548 (t0) cc_final: 0.8318 (t0) REVERT: AR 28 LYS cc_start: 0.8812 (mttt) cc_final: 0.8592 (mttp) REVERT: AS 23 ASP cc_start: 0.8563 (m-30) cc_final: 0.8167 (m-30) REVERT: AU 23 ASP cc_start: 0.8731 (t0) cc_final: 0.8037 (t0) REVERT: AV 23 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8068 (t0) REVERT: AW 16 LYS cc_start: 0.8109 (mttt) cc_final: 0.7714 (mttm) REVERT: AW 28 LYS cc_start: 0.8686 (mttt) cc_final: 0.8381 (mttp) REVERT: AX 16 LYS cc_start: 0.8238 (mttt) cc_final: 0.7912 (mttm) REVERT: AZ 23 ASP cc_start: 0.8285 (t0) cc_final: 0.7700 (t0) REVERT: Aa 23 ASP cc_start: 0.8074 (t0) cc_final: 0.7553 (t0) REVERT: Ac 28 LYS cc_start: 0.8645 (mttt) cc_final: 0.8246 (mttp) REVERT: Ad 14 HIS cc_start: 0.6863 (m170) cc_final: 0.6388 (t-170) outliers start: 9 outliers final: 7 residues processed: 86 average time/residue: 0.3281 time to fit residues: 36.1176 Evaluate side-chains 90 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AQ residue 23 ASP Chi-restraints excluded: chain AQ residue 39 VAL Chi-restraints excluded: chain AS residue 39 VAL Chi-restraints excluded: chain AV residue 23 ASP Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain Ac residue 23 ASP Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ad residue 39 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: 0.9980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 overall best weight: 0.7978 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.099378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.079477 restraints weight = 18960.146| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.99 r_work: 0.3489 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.8311 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= 0.216 Angle : 0.487 4.462 5628 Z= 0.261 Chirality : 0.052 0.128 630 Planarity : 0.001 0.005 714 Dihedral : 5.728 23.093 546 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 2.14 % Allowed : 13.33 % Favored : 84.52 % 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: -1.73 (0.36), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HISAP 14 PHE 0.008 0.001 PHEAL 20 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 95) hydrogen bonds : angle 4.44145 ( 285) covalent geometry : bond 0.00462 ( 4221) covalent geometry : angle 0.48708 ( 5628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5314.69 seconds wall clock time: 93 minutes 22.36 seconds (5602.36 seconds total)