Starting phenix.real_space_refine on Fri May 9 20:53:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oqi_17111/05_2025/8oqi_17111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oqi_17111/05_2025/8oqi_17111.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/8oqi_17111/05_2025/8oqi_17111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oqi_17111/05_2025/8oqi_17111.map" model { file = "/net/cci-nas-00/data/ceres_data/8oqi_17111/05_2025/8oqi_17111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oqi_17111/05_2025/8oqi_17111.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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2370 2.51 5 N 660 2.21 5 O 780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3810 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 381 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.68, per 1000 atoms: 0.44 Number of scatterers: 3810 At special positions: 0 Unit cell: (90.1, 90.1, 41.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 780 8.00 N 660 7.00 C 2370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 485.4 milliseconds 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.834A pdb=" N VAL A 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS A 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL E 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS C 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL E 48 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL G 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS E 50 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL G 48 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL I 49 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS G 50 " --> pdb=" O VAL I 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.463A pdb=" N THR A 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLU C 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA A 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU E 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA C 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR E 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU G 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA E 56 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR G 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU I 57 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA G 56 " --> pdb=" O GLU I 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.410A pdb=" N ASN A 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN C 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN E 65 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN G 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 72 removed outlier: 6.364A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL E 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL G 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.638A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR C 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS A 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR E 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA E 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR G 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS E 80 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA G 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR I 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS G 80 " --> pdb=" O THR I 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.278A pdb=" N SER A 87 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER C 87 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER E 87 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER G 87 " --> pdb=" O ILE I 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 50 removed outlier: 6.834A pdb=" N VAL B 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL D 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS B 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL D 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL F 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS D 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL F 48 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL H 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS F 50 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL H 48 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL J 49 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS H 50 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 57 removed outlier: 6.463A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU D 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR D 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU F 57 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA D 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR F 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU H 57 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA F 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR H 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU J 57 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA H 56 " --> pdb=" O GLU J 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.410A pdb=" N ASN B 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN D 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN F 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN H 65 " --> pdb=" O VAL J 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.364A pdb=" N VAL B 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL F 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL H 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 78 through 81 removed outlier: 6.638A pdb=" N ALA B 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR D 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS B 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA D 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR F 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS D 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA F 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR H 81 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS F 80 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA H 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR J 81 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS H 80 " --> pdb=" O THR J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 87 through 88 removed outlier: 6.278A pdb=" N SER B 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER D 87 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER F 87 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER H 87 " --> pdb=" O ILE J 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 92 24 hydrogen bonds defined for protein. 72 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 670 1.28 - 1.35: 610 1.35 - 1.41: 150 1.41 - 1.48: 205 1.48 - 1.54: 2195 Bond restraints: 3830 Sorted by residual: bond pdb=" N VAL E 63 " pdb=" CA VAL E 63 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.14e-02 7.69e+03 9.67e+00 bond pdb=" N VAL D 63 " pdb=" CA VAL D 63 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.14e-02 7.69e+03 9.65e+00 bond pdb=" N VAL B 49 " pdb=" CA VAL B 49 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.52e+00 bond pdb=" N VAL A 63 " pdb=" CA VAL A 63 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.14e-02 7.69e+03 9.52e+00 bond pdb=" N VAL J 74 " pdb=" CA VAL J 74 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.50e+00 ... (remaining 3825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 2450 1.12 - 2.25: 1223 2.25 - 3.37: 964 3.37 - 4.49: 431 4.49 - 5.62: 122 Bond angle restraints: 5190 Sorted by residual: angle pdb=" CA HIS H 50 " pdb=" CB HIS H 50 " pdb=" CG HIS H 50 " ideal model delta sigma weight residual 113.80 118.77 -4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" CA HIS C 50 " pdb=" CB HIS C 50 " pdb=" CG HIS C 50 " ideal model delta sigma weight residual 113.80 118.77 -4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" CA HIS A 50 " pdb=" CB HIS A 50 " pdb=" CG HIS A 50 " ideal model delta sigma weight residual 113.80 118.77 -4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" CA HIS E 50 " pdb=" CB HIS E 50 " pdb=" CG HIS E 50 " ideal model delta sigma weight residual 113.80 118.77 -4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" CA HIS I 50 " pdb=" CB HIS I 50 " pdb=" CG HIS I 50 " ideal model delta sigma weight residual 113.80 118.76 -4.96 1.00e+00 1.00e+00 2.46e+01 ... (remaining 5185 not shown) Histogram of dihedral angle deviations from ideal: 0.11 - 14.89: 1870 14.89 - 29.66: 220 29.66 - 44.43: 60 44.43 - 59.20: 30 59.20 - 73.97: 20 Dihedral angle restraints: 2200 sinusoidal: 700 harmonic: 1500 Sorted by residual: dihedral pdb=" CA GLU H 83 " pdb=" CB GLU H 83 " pdb=" CG GLU H 83 " pdb=" CD GLU H 83 " ideal model delta sinusoidal sigma weight residual -180.00 -124.94 -55.06 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CA GLU I 83 " pdb=" CB GLU I 83 " pdb=" CG GLU I 83 " pdb=" CD GLU I 83 " ideal model delta sinusoidal sigma weight residual -180.00 -124.94 -55.06 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " pdb=" CD GLU C 83 " ideal model delta sinusoidal sigma weight residual -180.00 -124.95 -55.05 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 2197 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.045: 100 0.045 - 0.087: 180 0.087 - 0.129: 220 0.129 - 0.171: 90 0.171 - 0.213: 90 Chirality restraints: 680 Sorted by residual: chirality pdb=" CA LYS D 45 " pdb=" N LYS D 45 " pdb=" C LYS D 45 " pdb=" CB LYS D 45 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA HIS I 50 " pdb=" N HIS I 50 " pdb=" C HIS I 50 " pdb=" CB HIS I 50 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA LYS C 45 " pdb=" N LYS C 45 " pdb=" C LYS C 45 " pdb=" CB LYS C 45 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 677 not shown) Planarity restraints: 650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 64 " -0.010 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C THR E 64 " 0.037 2.00e-02 2.50e+03 pdb=" O THR E 64 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN E 65 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 64 " 0.010 2.00e-02 2.50e+03 2.16e-02 4.64e+00 pdb=" C THR H 64 " -0.037 2.00e-02 2.50e+03 pdb=" O THR H 64 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN H 65 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 64 " -0.010 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C THR G 64 " 0.037 2.00e-02 2.50e+03 pdb=" O THR G 64 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN G 65 " -0.013 2.00e-02 2.50e+03 ... (remaining 647 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 1772 2.95 - 3.44: 3537 3.44 - 3.93: 6175 3.93 - 4.41: 6924 4.41 - 4.90: 13698 Nonbonded interactions: 32106 Sorted by model distance: nonbonded pdb=" ND2 ASN G 65 " pdb=" O GLY G 68 " model vdw 2.465 3.120 nonbonded pdb=" ND2 ASN D 65 " pdb=" O GLY D 68 " model vdw 2.465 3.120 nonbonded pdb=" ND2 ASN C 65 " pdb=" O GLY C 68 " model vdw 2.465 3.120 nonbonded pdb=" ND2 ASN B 65 " pdb=" O GLY B 68 " model vdw 2.465 3.120 nonbonded pdb=" ND2 ASN J 65 " pdb=" O GLY J 68 " model vdw 2.465 3.120 ... (remaining 32101 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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=1.00 max=1.00 mean=1.00 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: 0.690 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.140 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.013 0.039 3830 Z= 0.988 Angle : 2.008 5.618 5190 Z= 1.508 Chirality : 0.115 0.213 680 Planarity : 0.007 0.022 650 Dihedral : 18.286 73.975 1260 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.63 % Allowed : 18.42 % Favored : 78.95 % 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: 0.22 (0.36), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.18 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.007 HIS D 50 PHE 0.002 0.001 PHE G 94 TYR 0.008 0.002 TYR J 39 Details of bonding type rmsd hydrogen bonds : bond 0.16975 ( 24) hydrogen bonds : angle 8.70612 ( 72) covalent geometry : bond 0.01311 ( 3830) covalent geometry : angle 2.00804 ( 5190) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.435 Fit side-chains REVERT: C 80 LYS cc_start: 0.9030 (tttp) cc_final: 0.8598 (tttm) REVERT: D 60 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7510 (mttp) REVERT: E 60 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7582 (mttp) REVERT: E 80 LYS cc_start: 0.9021 (tttp) cc_final: 0.8763 (tttp) REVERT: H 60 LYS cc_start: 0.7810 (ttmt) cc_final: 0.7436 (mttt) outliers start: 10 outliers final: 2 residues processed: 88 average time/residue: 0.1993 time to fit residues: 20.8983 Evaluate side-chains 80 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.132006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.114480 restraints weight = 4971.063| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.33 r_work: 0.3510 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3830 Z= 0.105 Angle : 0.435 2.557 5190 Z= 0.266 Chirality : 0.051 0.119 680 Planarity : 0.002 0.009 650 Dihedral : 5.591 40.925 562 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.63 % Allowed : 17.89 % Favored : 79.47 % 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: -0.64 (0.35), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.48 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 50 PHE 0.009 0.002 PHE F 94 TYR 0.001 0.000 TYR H 39 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 24) hydrogen bonds : angle 6.70864 ( 72) covalent geometry : bond 0.00233 ( 3830) covalent geometry : angle 0.43521 ( 5190) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.452 Fit side-chains REVERT: A 43 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8320 (mtpt) REVERT: F 43 LYS cc_start: 0.8387 (mtpp) cc_final: 0.8095 (mttm) REVERT: J 43 LYS cc_start: 0.8525 (mtpt) cc_final: 0.8073 (mttp) outliers start: 10 outliers final: 5 residues processed: 71 average time/residue: 0.1960 time to fit residues: 16.6401 Evaluate side-chains 59 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.2980 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.126560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108401 restraints weight = 5079.266| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.36 r_work: 0.3400 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3830 Z= 0.159 Angle : 0.430 2.510 5190 Z= 0.266 Chirality : 0.052 0.121 680 Planarity : 0.002 0.011 650 Dihedral : 5.244 32.656 562 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.32 % Allowed : 20.26 % Favored : 78.42 % 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: -1.19 (0.36), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS H 50 PHE 0.006 0.002 PHE H 94 TYR 0.002 0.001 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 24) hydrogen bonds : angle 6.33666 ( 72) covalent geometry : bond 0.00374 ( 3830) covalent geometry : angle 0.43024 ( 5190) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.434 Fit side-chains REVERT: C 54 THR cc_start: 0.8927 (m) cc_final: 0.8697 (p) REVERT: F 43 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8257 (mttm) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.1888 time to fit residues: 14.4674 Evaluate side-chains 59 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain H residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 0.0670 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.123632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.106033 restraints weight = 4850.992| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.24 r_work: 0.3402 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3830 Z= 0.226 Angle : 0.471 2.546 5190 Z= 0.289 Chirality : 0.052 0.120 680 Planarity : 0.002 0.009 650 Dihedral : 5.366 15.443 560 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.32 % Allowed : 20.26 % Favored : 78.42 % 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: -1.49 (0.35), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS H 50 PHE 0.007 0.001 PHE A 94 TYR 0.004 0.002 TYR J 39 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 24) hydrogen bonds : angle 6.13411 ( 72) covalent geometry : bond 0.00534 ( 3830) covalent geometry : angle 0.47072 ( 5190) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.427 Fit side-chains REVERT: C 54 THR cc_start: 0.8928 (m) cc_final: 0.8719 (p) REVERT: F 43 LYS cc_start: 0.8567 (mtpp) cc_final: 0.8239 (mttm) REVERT: F 57 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8822 (mt-10) REVERT: I 79 GLN cc_start: 0.9455 (tt0) cc_final: 0.9245 (tt0) outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 0.1654 time to fit residues: 13.0905 Evaluate side-chains 64 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain H residue 81 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.125292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107832 restraints weight = 4936.458| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.26 r_work: 0.3431 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3830 Z= 0.159 Angle : 0.420 2.118 5190 Z= 0.258 Chirality : 0.051 0.123 680 Planarity : 0.002 0.007 650 Dihedral : 4.920 14.184 560 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.11 % Allowed : 20.26 % Favored : 77.63 % 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: -1.46 (0.35), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.004 0.001 PHE A 94 TYR 0.003 0.001 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 24) hydrogen bonds : angle 5.94023 ( 72) covalent geometry : bond 0.00367 ( 3830) covalent geometry : angle 0.42016 ( 5190) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.446 Fit side-chains REVERT: C 54 THR cc_start: 0.8978 (m) cc_final: 0.8775 (p) REVERT: F 57 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8821 (mt-10) REVERT: I 79 GLN cc_start: 0.9432 (tt0) cc_final: 0.9211 (tt0) outliers start: 8 outliers final: 7 residues processed: 64 average time/residue: 0.1923 time to fit residues: 14.9695 Evaluate side-chains 61 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.120672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.102218 restraints weight = 5090.314| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.35 r_work: 0.3317 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 3830 Z= 0.294 Angle : 0.495 2.621 5190 Z= 0.304 Chirality : 0.054 0.125 680 Planarity : 0.002 0.010 650 Dihedral : 5.456 16.126 560 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.68 % Allowed : 19.74 % Favored : 76.58 % 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: -1.68 (0.34), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS H 50 PHE 0.009 0.002 PHE B 94 TYR 0.006 0.002 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 24) hydrogen bonds : angle 6.07591 ( 72) covalent geometry : bond 0.00691 ( 3830) covalent geometry : angle 0.49511 ( 5190) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.436 Fit side-chains REVERT: C 54 THR cc_start: 0.8971 (m) cc_final: 0.8719 (p) REVERT: F 43 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8211 (mttm) REVERT: F 54 THR cc_start: 0.8923 (m) cc_final: 0.8713 (p) REVERT: F 57 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8812 (mt-10) outliers start: 14 outliers final: 13 residues processed: 69 average time/residue: 0.1607 time to fit residues: 13.7788 Evaluate side-chains 71 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.122170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104796 restraints weight = 4875.891| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.20 r_work: 0.3384 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 3830 Z= 0.237 Angle : 0.459 2.397 5190 Z= 0.282 Chirality : 0.053 0.124 680 Planarity : 0.002 0.009 650 Dihedral : 5.255 15.149 560 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.47 % Allowed : 20.26 % Favored : 75.26 % 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: -1.71 (0.33), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS H 50 PHE 0.005 0.002 PHE B 94 TYR 0.004 0.001 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 24) hydrogen bonds : angle 5.99552 ( 72) covalent geometry : bond 0.00553 ( 3830) covalent geometry : angle 0.45938 ( 5190) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.381 Fit side-chains REVERT: B 94 PHE cc_start: 0.7505 (m-10) cc_final: 0.6956 (t80) REVERT: C 54 THR cc_start: 0.8966 (m) cc_final: 0.8709 (p) REVERT: F 57 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8823 (mt-10) outliers start: 17 outliers final: 17 residues processed: 71 average time/residue: 0.1569 time to fit residues: 13.7540 Evaluate side-chains 75 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 39 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 0.0030 chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.123224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.106012 restraints weight = 4894.462| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.19 r_work: 0.3405 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3830 Z= 0.171 Angle : 0.422 2.183 5190 Z= 0.259 Chirality : 0.051 0.124 680 Planarity : 0.001 0.007 650 Dihedral : 4.950 14.089 560 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.21 % Allowed : 20.00 % Favored : 75.79 % 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: -1.67 (0.34), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.004 0.001 PHE B 94 TYR 0.003 0.001 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 24) hydrogen bonds : angle 5.83897 ( 72) covalent geometry : bond 0.00395 ( 3830) covalent geometry : angle 0.42196 ( 5190) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.513 Fit side-chains REVERT: B 94 PHE cc_start: 0.7529 (m-10) cc_final: 0.6996 (t80) REVERT: C 54 THR cc_start: 0.8992 (m) cc_final: 0.8760 (p) REVERT: F 57 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8820 (mt-10) outliers start: 16 outliers final: 15 residues processed: 68 average time/residue: 0.1696 time to fit residues: 14.2372 Evaluate side-chains 69 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain C residue 39 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 0.0570 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.0170 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.134043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.117823 restraints weight = 4739.595| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.22 r_work: 0.3592 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 3830 Z= 0.061 Angle : 0.356 1.998 5190 Z= 0.216 Chirality : 0.050 0.126 680 Planarity : 0.001 0.004 650 Dihedral : 3.848 10.742 560 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.37 % Allowed : 21.84 % Favored : 75.79 % 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: -1.47 (0.35), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.002 0.000 PHE B 94 TYR 0.001 0.000 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02351 ( 24) hydrogen bonds : angle 5.13887 ( 72) covalent geometry : bond 0.00119 ( 3830) covalent geometry : angle 0.35648 ( 5190) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.401 Fit side-chains REVERT: B 94 PHE cc_start: 0.7338 (m-10) cc_final: 0.6736 (t80) REVERT: E 46 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7800 (mt-10) REVERT: F 54 THR cc_start: 0.8841 (m) cc_final: 0.8638 (p) REVERT: G 43 LYS cc_start: 0.8542 (mttp) cc_final: 0.8314 (mttp) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.1842 time to fit residues: 14.7034 Evaluate side-chains 64 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 39 TYR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 0.3980 chunk 44 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.121580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.104013 restraints weight = 4930.737| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.21 r_work: 0.3371 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 3830 Z= 0.266 Angle : 0.466 2.567 5190 Z= 0.286 Chirality : 0.053 0.120 680 Planarity : 0.002 0.012 650 Dihedral : 5.030 14.275 560 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.95 % Allowed : 20.53 % Favored : 75.53 % 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: -1.62 (0.34), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS H 50 PHE 0.005 0.002 PHE B 94 TYR 0.005 0.002 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 24) hydrogen bonds : angle 5.87543 ( 72) covalent geometry : bond 0.00620 ( 3830) covalent geometry : angle 0.46609 ( 5190) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.452 Fit side-chains REVERT: B 94 PHE cc_start: 0.7542 (m-10) cc_final: 0.6950 (t80) REVERT: I 57 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8680 (mt-10) REVERT: I 60 LYS cc_start: 0.8359 (ttmt) cc_final: 0.7500 (tptp) outliers start: 15 outliers final: 14 residues processed: 71 average time/residue: 0.1948 time to fit residues: 16.8634 Evaluate side-chains 75 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 39 TYR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.121719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104557 restraints weight = 4882.235| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.18 r_work: 0.3381 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 3830 Z= 0.238 Angle : 0.456 2.377 5190 Z= 0.279 Chirality : 0.053 0.124 680 Planarity : 0.002 0.011 650 Dihedral : 5.121 14.271 560 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.68 % Allowed : 20.79 % Favored : 75.53 % 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: -1.71 (0.33), residues: 540 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS H 50 PHE 0.005 0.002 PHE E 94 TYR 0.004 0.001 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 24) hydrogen bonds : angle 5.88510 ( 72) covalent geometry : bond 0.00556 ( 3830) covalent geometry : angle 0.45592 ( 5190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.14 seconds wall clock time: 38 minutes 0.14 seconds (2280.14 seconds total)