Starting phenix.real_space_refine on Mon Feb 10 20:19:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2q_38863/02_2025/8y2q_38863.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2q_38863/02_2025/8y2q_38863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y2q_38863/02_2025/8y2q_38863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2q_38863/02_2025/8y2q_38863.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2q_38863/02_2025/8y2q_38863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2q_38863/02_2025/8y2q_38863.cif" } resolution = 2.8 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= 0.004 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 1368 2.51 5 N 390 2.21 5 O 456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2214 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 369 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.84, per 1000 atoms: 0.83 Number of scatterers: 2214 At special positions: 0 Unit cell: (77.19, 88.81, 30.71, 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 456 8.00 N 390 7.00 C 1368 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: 0.46 Conformation dependent library (CDL) restraints added in 283.9 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 69.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 66 removed outlier: 8.483A pdb=" N LYS A 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N GLU C 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N LYS A 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N VAL C 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY A 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N HIS C 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 10.404A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N LYS C 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N GLU A 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N LYS C 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR A 59 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N GLN C 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU A 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR C 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL C 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN A 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 44 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS D 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU A 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY D 47 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA D 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR A 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL D 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA A 56 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU D 57 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS A 58 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR D 59 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 69 through 72 removed outlier: 6.320A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 82 removed outlier: 6.862A pdb=" N ALA A 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR A 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N ALA D 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL A 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LYS D 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN A 79 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N VAL D 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A 81 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 87 through 92 removed outlier: 5.955A pdb=" N ILE A 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA C 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA A 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE D 88 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 43 through 66 removed outlier: 8.497A pdb=" N LYS B 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N GLU E 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LYS B 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N VAL E 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY B 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N HIS E 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL B 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL E 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLY B 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N THR E 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N ALA B 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N ALA E 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N VAL B 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N LYS E 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N GLU B 57 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N LYS E 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR B 59 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLN E 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU B 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N THR E 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL E 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR B 44 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS F 45 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU B 46 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY F 47 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA F 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B 54 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL F 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA B 56 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU F 57 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS B 58 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR F 59 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 69 through 72 removed outlier: 6.329A pdb=" N VAL B 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 75 through 82 removed outlier: 6.874A pdb=" N ALA B 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N THR B 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ALA F 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LYS F 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN B 79 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N VAL F 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR B 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 87 through 92 removed outlier: 5.973A pdb=" N ILE B 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA E 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA B 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE F 88 " --> pdb=" O SER B 87 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 144 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: 0.49 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 396 1.29 - 1.35: 354 1.35 - 1.42: 55 1.42 - 1.48: 392 1.48 - 1.54: 1023 Bond restraints: 2220 Sorted by residual: bond pdb=" CB VAL F 74 " pdb=" CG1 VAL F 74 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.31e-01 bond pdb=" CB VAL A 74 " pdb=" CG1 VAL A 74 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.27e-01 bond pdb=" CB VAL E 74 " pdb=" CG1 VAL E 74 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.17e-01 bond pdb=" CB VAL D 74 " pdb=" CG1 VAL D 74 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 5.99e-01 bond pdb=" CB VAL C 74 " pdb=" CG1 VAL C 74 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.96e-01 ... (remaining 2215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.77: 2571 0.77 - 1.54: 356 1.54 - 2.30: 51 2.30 - 3.07: 22 3.07 - 3.84: 6 Bond angle restraints: 3006 Sorted by residual: angle pdb=" CA GLU F 83 " pdb=" CB GLU F 83 " pdb=" CG GLU F 83 " ideal model delta sigma weight residual 114.10 117.94 -3.84 2.00e+00 2.50e-01 3.68e+00 angle pdb=" CA GLU D 83 " pdb=" CB GLU D 83 " pdb=" CG GLU D 83 " ideal model delta sigma weight residual 114.10 117.92 -3.82 2.00e+00 2.50e-01 3.65e+00 angle pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " ideal model delta sigma weight residual 114.10 117.92 -3.82 2.00e+00 2.50e-01 3.64e+00 angle pdb=" CA GLU B 83 " pdb=" CB GLU B 83 " pdb=" CG GLU B 83 " ideal model delta sigma weight residual 114.10 117.92 -3.82 2.00e+00 2.50e-01 3.64e+00 angle pdb=" CA GLU A 83 " pdb=" CB GLU A 83 " pdb=" CG GLU A 83 " ideal model delta sigma weight residual 114.10 117.90 -3.80 2.00e+00 2.50e-01 3.61e+00 ... (remaining 3001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 1230 15.37 - 30.74: 42 30.74 - 46.11: 6 46.11 - 61.47: 0 61.47 - 76.84: 6 Dihedral angle restraints: 1284 sinusoidal: 408 harmonic: 876 Sorted by residual: dihedral pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " pdb=" CD GLU C 83 " pdb=" OE1 GLU C 83 " ideal model delta sinusoidal sigma weight residual 0.00 -76.84 76.84 1 3.00e+01 1.11e-03 8.24e+00 dihedral pdb=" CB GLU E 83 " pdb=" CG GLU E 83 " pdb=" CD GLU E 83 " pdb=" OE1 GLU E 83 " ideal model delta sinusoidal sigma weight residual 0.00 -76.84 76.84 1 3.00e+01 1.11e-03 8.24e+00 dihedral pdb=" CB GLU F 83 " pdb=" CG GLU F 83 " pdb=" CD GLU F 83 " pdb=" OE1 GLU F 83 " ideal model delta sinusoidal sigma weight residual 0.00 -76.79 76.79 1 3.00e+01 1.11e-03 8.23e+00 ... (remaining 1281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 142 0.024 - 0.048: 153 0.048 - 0.072: 30 0.072 - 0.096: 29 0.096 - 0.120: 48 Chirality restraints: 402 Sorted by residual: chirality pdb=" CB THR A 75 " pdb=" CA THR A 75 " pdb=" OG1 THR A 75 " pdb=" CG2 THR A 75 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CB THR C 75 " pdb=" CA THR C 75 " pdb=" OG1 THR C 75 " pdb=" CG2 THR C 75 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CB THR D 75 " pdb=" CA THR D 75 " pdb=" OG1 THR D 75 " pdb=" CG2 THR D 75 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 399 not shown) Planarity restraints: 378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 50 " -0.007 2.00e-02 2.50e+03 5.86e-03 5.15e-01 pdb=" CG HIS C 50 " 0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS C 50 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS C 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 50 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS C 50 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.007 2.00e-02 2.50e+03 5.84e-03 5.12e-01 pdb=" CG HIS A 50 " -0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " -0.007 2.00e-02 2.50e+03 5.75e-03 4.97e-01 pdb=" CG HIS B 50 " 0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " -0.002 2.00e-02 2.50e+03 ... (remaining 375 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 454 2.80 - 3.33: 1855 3.33 - 3.85: 3471 3.85 - 4.38: 3707 4.38 - 4.90: 7810 Nonbonded interactions: 17297 Sorted by model distance: nonbonded pdb=" OE1 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.276 3.120 nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.276 3.120 nonbonded pdb=" OE1 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.276 3.120 nonbonded pdb=" OE1 GLU B 46 " pdb=" NZ LYS B 80 " model vdw 2.276 3.120 nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.277 3.120 ... (remaining 17292 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 2.610 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.340 Find NCS groups from input model: 0.050 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.006 0.026 2220 Z= 0.401 Angle : 0.615 3.839 3006 Z= 0.356 Chirality : 0.052 0.120 402 Planarity : 0.002 0.006 378 Dihedral : 10.801 76.843 732 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.99 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.006 0.003 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.229 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.5935 time to fit residues: 21.7220 Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN B 79 GLN C 79 GLN E 79 GLN D 79 GLN F 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.176000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.150563 restraints weight = 2301.065| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.01 r_work: 0.4002 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2220 Z= 0.235 Angle : 0.501 2.994 3006 Z= 0.291 Chirality : 0.051 0.131 402 Planarity : 0.002 0.006 378 Dihedral : 4.669 13.294 324 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.95 % Allowed : 3.60 % Favored : 91.44 % 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: -2.19 (0.44), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.003 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.209 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 11 residues processed: 28 average time/residue: 0.1240 time to fit residues: 4.3067 Evaluate side-chains 37 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 0.0050 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.1400 ------------------------------------------------------------------------------- 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 = 0.4364 r_free = 0.4364 target = 0.173744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.148436 restraints weight = 2343.000| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.04 r_work: 0.3968 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2220 Z= 0.351 Angle : 0.577 3.221 3006 Z= 0.336 Chirality : 0.052 0.132 402 Planarity : 0.002 0.007 378 Dihedral : 5.141 13.565 324 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.31 % Allowed : 4.95 % Favored : 88.74 % 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: -1.92 (0.45), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS B 50 PHE 0.003 0.001 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: F 60 LYS cc_start: 0.8018 (tttt) cc_final: 0.7661 (tttm) outliers start: 14 outliers final: 13 residues processed: 30 average time/residue: 0.2903 time to fit residues: 9.6243 Evaluate side-chains 41 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4442 r_free = 0.4442 target = 0.179617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.154732 restraints weight = 2335.879| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.01 r_work: 0.4066 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2220 Z= 0.121 Angle : 0.403 2.657 3006 Z= 0.236 Chirality : 0.051 0.129 402 Planarity : 0.001 0.007 378 Dihedral : 4.087 10.528 324 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.86 % Allowed : 5.41 % Favored : 88.74 % 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: -1.70 (0.47), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 50 PHE 0.004 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.244 Fit side-chains REVERT: E 60 LYS cc_start: 0.7786 (tttt) cc_final: 0.7539 (tttm) outliers start: 13 outliers final: 13 residues processed: 28 average time/residue: 0.2830 time to fit residues: 8.7887 Evaluate side-chains 34 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 0.0010 chunk 19 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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 = 0.4393 r_free = 0.4393 target = 0.175831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.150461 restraints weight = 2341.269| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.05 r_work: 0.4000 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2220 Z= 0.249 Angle : 0.483 2.961 3006 Z= 0.283 Chirality : 0.050 0.131 402 Planarity : 0.002 0.007 378 Dihedral : 4.632 12.424 324 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.31 % Allowed : 5.41 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.46), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.004 0.001 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 27 time to evaluate : 0.217 Fit side-chains REVERT: E 60 LYS cc_start: 0.7851 (tttt) cc_final: 0.7578 (tttm) REVERT: F 60 LYS cc_start: 0.8040 (tttt) cc_final: 0.7692 (tttm) outliers start: 14 outliers final: 13 residues processed: 30 average time/residue: 0.3641 time to fit residues: 11.8364 Evaluate side-chains 40 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 29 optimal weight: 0.0370 chunk 22 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.4660 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.177131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.151727 restraints weight = 2301.912| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.04 r_work: 0.4019 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2220 Z= 0.174 Angle : 0.431 2.774 3006 Z= 0.253 Chirality : 0.050 0.131 402 Planarity : 0.001 0.007 378 Dihedral : 4.328 11.684 324 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.86 % Allowed : 5.86 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.46), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.004 0.001 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 22 time to evaluate : 0.222 Fit side-chains REVERT: E 60 LYS cc_start: 0.7861 (tttt) cc_final: 0.7596 (tttp) REVERT: F 60 LYS cc_start: 0.8050 (tttt) cc_final: 0.7714 (tttm) outliers start: 13 outliers final: 13 residues processed: 28 average time/residue: 0.2885 time to fit residues: 8.9572 Evaluate side-chains 35 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 22 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.172328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.147122 restraints weight = 2357.445| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.06 r_work: 0.3957 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 2220 Z= 0.475 Angle : 0.653 3.361 3006 Z= 0.382 Chirality : 0.054 0.134 402 Planarity : 0.003 0.009 378 Dihedral : 5.401 14.179 324 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.31 % Allowed : 5.41 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.45), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS A 50 PHE 0.005 0.002 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.243 Fit side-chains REVERT: F 60 LYS cc_start: 0.8084 (tttt) cc_final: 0.7712 (tttm) outliers start: 14 outliers final: 13 residues processed: 33 average time/residue: 0.4944 time to fit residues: 17.2760 Evaluate side-chains 45 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.176571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.151324 restraints weight = 2409.305| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.06 r_work: 0.4007 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2220 Z= 0.185 Angle : 0.452 2.859 3006 Z= 0.265 Chirality : 0.051 0.132 402 Planarity : 0.002 0.008 378 Dihedral : 4.529 12.191 324 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.31 % Allowed : 5.86 % Favored : 87.84 % 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 (0.46), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.004 0.001 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.243 Fit side-chains REVERT: E 60 LYS cc_start: 0.7827 (tttt) cc_final: 0.7570 (tttp) REVERT: F 60 LYS cc_start: 0.8051 (tttt) cc_final: 0.7716 (tttm) outliers start: 14 outliers final: 14 residues processed: 31 average time/residue: 0.3802 time to fit residues: 12.7439 Evaluate side-chains 40 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 0.0470 chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.176426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.151247 restraints weight = 2316.049| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.03 r_work: 0.4010 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2220 Z= 0.209 Angle : 0.457 2.871 3006 Z= 0.268 Chirality : 0.051 0.131 402 Planarity : 0.002 0.008 378 Dihedral : 4.533 12.371 324 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.31 % Allowed : 5.86 % Favored : 87.84 % 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 (0.46), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.004 0.001 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.227 Fit side-chains REVERT: E 60 LYS cc_start: 0.7830 (tttt) cc_final: 0.7569 (tttm) REVERT: F 60 LYS cc_start: 0.8052 (tttt) cc_final: 0.7711 (tttm) outliers start: 14 outliers final: 14 residues processed: 31 average time/residue: 0.3700 time to fit residues: 12.4098 Evaluate side-chains 42 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.178615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.153353 restraints weight = 2313.696| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.03 r_work: 0.4054 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2220 Z= 0.130 Angle : 0.398 2.625 3006 Z= 0.234 Chirality : 0.050 0.130 402 Planarity : 0.001 0.007 378 Dihedral : 4.108 10.978 324 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.31 % Allowed : 5.86 % Favored : 87.84 % 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: -1.69 (0.46), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.004 0.001 PHE B 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 22 time to evaluate : 0.220 Fit side-chains REVERT: E 60 LYS cc_start: 0.7794 (tttt) cc_final: 0.7555 (tttp) REVERT: F 60 LYS cc_start: 0.8058 (tttt) cc_final: 0.7700 (tttm) outliers start: 14 outliers final: 14 residues processed: 30 average time/residue: 0.3737 time to fit residues: 12.1072 Evaluate side-chains 36 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 22 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.174619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.149271 restraints weight = 2350.045| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.04 r_work: 0.3988 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3872 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2220 Z= 0.301 Angle : 0.520 3.085 3006 Z= 0.305 Chirality : 0.051 0.131 402 Planarity : 0.002 0.007 378 Dihedral : 4.805 13.076 324 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.31 % Allowed : 6.76 % Favored : 86.94 % 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: -1.77 (0.46), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS A 50 PHE 0.004 0.002 PHE F 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1697.72 seconds wall clock time: 30 minutes 48.05 seconds (1848.05 seconds total)