Starting phenix.real_space_refine on Thu Mar 5 02:50:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oxp_13103/03_2026/7oxp_13103.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oxp_13103/03_2026/7oxp_13103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oxp_13103/03_2026/7oxp_13103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oxp_13103/03_2026/7oxp_13103.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oxp_13103/03_2026/7oxp_13103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oxp_13103/03_2026/7oxp_13103.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 12130 2.51 5 N 3080 2.21 5 O 3430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18730 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1873 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 1.76, per 1000 atoms: 0.09 Number of scatterers: 18730 At special positions: 0 Unit cell: (152.07, 157.002, 83.844, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3430 8.00 N 3080 7.00 C 12130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 113 " - pdb=" SG CYS H 159 " distance=2.03 Simple disulfide: pdb=" SG CYS I 113 " - pdb=" SG CYS I 159 " distance=2.03 Simple disulfide: pdb=" SG CYS J 113 " - pdb=" SG CYS J 159 " distance=2.03 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: 1.33 Conformation dependent library (CDL) restraints added in 844.3 milliseconds 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 32.2% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.889A pdb=" N LEU B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 243 through 255 Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.891A pdb=" N LEU C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'D' and resid 235 through 243 Processing helix chain 'D' and resid 243 through 255 Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 177 through 186 Processing helix chain 'E' and resid 235 through 243 Processing helix chain 'E' and resid 243 through 255 Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE F 36 " --> pdb=" O LEU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 167 through 174 Processing helix chain 'F' and resid 177 through 186 Processing helix chain 'F' and resid 235 through 243 Processing helix chain 'F' and resid 243 through 255 Processing helix chain 'F' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE F 263 " --> pdb=" O ILE F 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.744A pdb=" N ILE G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'G' and resid 167 through 174 Processing helix chain 'G' and resid 177 through 186 Processing helix chain 'G' and resid 235 through 243 Processing helix chain 'G' and resid 243 through 255 Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU G 262 " --> pdb=" O ILE G 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE G 263 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE H 36 " --> pdb=" O LEU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 56 through 58 No H-bonds generated for 'chain 'H' and resid 56 through 58' Processing helix chain 'H' and resid 167 through 174 Processing helix chain 'H' and resid 177 through 186 Processing helix chain 'H' and resid 235 through 243 Processing helix chain 'H' and resid 243 through 255 Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU H 262 " --> pdb=" O ILE H 258 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE H 263 " --> pdb=" O ILE H 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE I 36 " --> pdb=" O LEU I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 48 No H-bonds generated for 'chain 'I' and resid 46 through 48' Processing helix chain 'I' and resid 56 through 58 No H-bonds generated for 'chain 'I' and resid 56 through 58' Processing helix chain 'I' and resid 167 through 174 Processing helix chain 'I' and resid 177 through 186 Processing helix chain 'I' and resid 235 through 243 Processing helix chain 'I' and resid 243 through 255 Processing helix chain 'I' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU I 262 " --> pdb=" O ILE I 258 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE I 263 " --> pdb=" O ILE I 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 45 removed outlier: 3.743A pdb=" N ILE J 36 " --> pdb=" O LEU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 48 No H-bonds generated for 'chain 'J' and resid 46 through 48' Processing helix chain 'J' and resid 56 through 58 No H-bonds generated for 'chain 'J' and resid 56 through 58' Processing helix chain 'J' and resid 167 through 174 Processing helix chain 'J' and resid 177 through 186 Processing helix chain 'J' and resid 235 through 243 Processing helix chain 'J' and resid 243 through 255 Processing helix chain 'J' and resid 255 through 265 removed outlier: 3.890A pdb=" N LEU J 262 " --> pdb=" O ILE J 258 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE J 263 " --> pdb=" O ILE J 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 50 through 54 current: chain 'A' and resid 68 through 77 removed outlier: 3.571A pdb=" N ILE A 77 " --> pdb=" O MET A 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 95 through 98 current: chain 'A' and resid 148 through 160 Processing sheet with id=AA2, first strand: chain 'B' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 50 through 54 current: chain 'B' and resid 68 through 77 removed outlier: 3.570A pdb=" N ILE B 77 " --> pdb=" O MET B 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 95 through 98 current: chain 'B' and resid 148 through 160 Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 50 through 54 current: chain 'C' and resid 68 through 77 removed outlier: 3.571A pdb=" N ILE C 77 " --> pdb=" O MET C 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 95 through 98 current: chain 'C' and resid 148 through 160 Processing sheet with id=AA4, first strand: chain 'D' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 50 through 54 current: chain 'D' and resid 68 through 77 removed outlier: 3.570A pdb=" N ILE D 77 " --> pdb=" O MET D 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 95 through 98 current: chain 'D' and resid 148 through 160 Processing sheet with id=AA5, first strand: chain 'E' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 50 through 54 current: chain 'E' and resid 68 through 77 removed outlier: 3.571A pdb=" N ILE E 77 " --> pdb=" O MET E 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 95 through 98 current: chain 'E' and resid 148 through 160 Processing sheet with id=AA6, first strand: chain 'F' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 50 through 54 current: chain 'F' and resid 68 through 77 removed outlier: 3.570A pdb=" N ILE F 77 " --> pdb=" O MET F 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 95 through 98 current: chain 'F' and resid 148 through 160 Processing sheet with id=AA7, first strand: chain 'G' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 50 through 54 current: chain 'G' and resid 68 through 77 removed outlier: 3.571A pdb=" N ILE G 77 " --> pdb=" O MET G 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 95 through 98 current: chain 'G' and resid 148 through 160 Processing sheet with id=AA8, first strand: chain 'H' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 50 through 54 current: chain 'H' and resid 68 through 77 removed outlier: 3.571A pdb=" N ILE H 77 " --> pdb=" O MET H 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 95 through 98 current: chain 'H' and resid 148 through 160 Processing sheet with id=AA9, first strand: chain 'I' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 50 through 54 current: chain 'I' and resid 68 through 77 removed outlier: 3.570A pdb=" N ILE I 77 " --> pdb=" O MET I 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 95 through 98 current: chain 'I' and resid 148 through 160 Processing sheet with id=AB1, first strand: chain 'J' and resid 50 through 54 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 50 through 54 current: chain 'J' and resid 68 through 77 removed outlier: 3.570A pdb=" N ILE J 77 " --> pdb=" O MET J 97 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 95 through 98 current: chain 'J' and resid 148 through 160 440 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6000 1.34 - 1.46: 3958 1.46 - 1.58: 8992 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 19090 Sorted by residual: bond pdb=" N HIS F 119 " pdb=" CA HIS F 119 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.86e-01 bond pdb=" N HIS G 119 " pdb=" CA HIS G 119 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.51e-01 bond pdb=" N HIS B 119 " pdb=" CA HIS B 119 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.51e-01 bond pdb=" N HIS A 119 " pdb=" CA HIS A 119 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.46e-01 bond pdb=" N HIS D 119 " pdb=" CA HIS D 119 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.40e-01 ... (remaining 19085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 25316 1.60 - 3.20: 411 3.20 - 4.79: 73 4.79 - 6.39: 30 6.39 - 7.99: 10 Bond angle restraints: 25840 Sorted by residual: angle pdb=" CA LEU G 30 " pdb=" CB LEU G 30 " pdb=" CG LEU G 30 " ideal model delta sigma weight residual 116.30 124.29 -7.99 3.50e+00 8.16e-02 5.21e+00 angle pdb=" CA LEU D 30 " pdb=" CB LEU D 30 " pdb=" CG LEU D 30 " ideal model delta sigma weight residual 116.30 124.28 -7.98 3.50e+00 8.16e-02 5.20e+00 angle pdb=" CA LEU F 30 " pdb=" CB LEU F 30 " pdb=" CG LEU F 30 " ideal model delta sigma weight residual 116.30 124.28 -7.98 3.50e+00 8.16e-02 5.20e+00 angle pdb=" CA LEU A 30 " pdb=" CB LEU A 30 " pdb=" CG LEU A 30 " ideal model delta sigma weight residual 116.30 124.27 -7.97 3.50e+00 8.16e-02 5.19e+00 angle pdb=" CA LEU I 30 " pdb=" CB LEU I 30 " pdb=" CG LEU I 30 " ideal model delta sigma weight residual 116.30 124.26 -7.96 3.50e+00 8.16e-02 5.18e+00 ... (remaining 25835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 10540 16.59 - 33.18: 870 33.18 - 49.77: 190 49.77 - 66.36: 30 66.36 - 82.95: 30 Dihedral angle restraints: 11660 sinusoidal: 4880 harmonic: 6780 Sorted by residual: dihedral pdb=" CB GLU I 185 " pdb=" CG GLU I 185 " pdb=" CD GLU I 185 " pdb=" OE1 GLU I 185 " ideal model delta sinusoidal sigma weight residual 0.00 -82.95 82.95 1 3.00e+01 1.11e-03 9.36e+00 dihedral pdb=" CB GLU J 185 " pdb=" CG GLU J 185 " pdb=" CD GLU J 185 " pdb=" OE1 GLU J 185 " ideal model delta sinusoidal sigma weight residual 0.00 -82.92 82.92 1 3.00e+01 1.11e-03 9.35e+00 dihedral pdb=" CB GLU A 185 " pdb=" CG GLU A 185 " pdb=" CD GLU A 185 " pdb=" OE1 GLU A 185 " ideal model delta sinusoidal sigma weight residual 0.00 -82.89 82.89 1 3.00e+01 1.11e-03 9.35e+00 ... (remaining 11657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1683 0.025 - 0.050: 770 0.050 - 0.076: 321 0.076 - 0.101: 140 0.101 - 0.126: 116 Chirality restraints: 3030 Sorted by residual: chirality pdb=" CA ILE I 95 " pdb=" N ILE I 95 " pdb=" C ILE I 95 " pdb=" CB ILE I 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA ILE B 95 " pdb=" N ILE B 95 " pdb=" C ILE B 95 " pdb=" CB ILE B 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE J 95 " pdb=" N ILE J 95 " pdb=" C ILE J 95 " pdb=" CB ILE J 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 3027 not shown) Planarity restraints: 3260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 95 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO B 96 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 95 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO E 96 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 95 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO H 96 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 96 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 96 " -0.017 5.00e-02 4.00e+02 ... (remaining 3257 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 312 2.68 - 3.23: 17062 3.23 - 3.79: 28768 3.79 - 4.34: 40978 4.34 - 4.90: 66546 Nonbonded interactions: 153666 Sorted by model distance: nonbonded pdb=" OE2 GLU H 102 " pdb=" OG SER H 197 " model vdw 2.120 3.040 nonbonded pdb=" OE2 GLU C 102 " pdb=" OG SER C 197 " model vdw 2.121 3.040 nonbonded pdb=" OE2 GLU F 102 " pdb=" OG SER F 197 " model vdw 2.121 3.040 nonbonded pdb=" OE2 GLU G 102 " pdb=" OG SER G 197 " model vdw 2.121 3.040 nonbonded pdb=" OE2 GLU B 102 " pdb=" OG SER B 197 " model vdw 2.121 3.040 ... (remaining 153661 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 5.420 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 13.760 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.003 0.023 19100 Z= 0.124 Angle : 0.585 7.989 25860 Z= 0.306 Chirality : 0.042 0.126 3030 Planarity : 0.004 0.030 3260 Dihedral : 13.631 82.946 7210 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.18), residues: 2260 helix: 0.23 (0.21), residues: 620 sheet: 0.38 (0.17), residues: 890 loop : -0.28 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 191 TYR 0.018 0.002 TYR J 248 PHE 0.008 0.001 PHE I 58 TRP 0.003 0.001 TRP B 186 HIS 0.003 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00260 (19090) covalent geometry : angle 0.58526 (25840) SS BOND : bond 0.00131 ( 10) SS BOND : angle 0.38051 ( 20) hydrogen bonds : bond 0.23475 ( 440) hydrogen bonds : angle 6.35313 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.734 Fit side-chains REVERT: A 42 LEU cc_start: 0.8395 (mm) cc_final: 0.8098 (mm) REVERT: B 169 GLN cc_start: 0.7771 (mp10) cc_final: 0.7548 (mp10) REVERT: C 42 LEU cc_start: 0.8327 (mm) cc_final: 0.8058 (mm) REVERT: D 42 LEU cc_start: 0.8508 (mm) cc_final: 0.8234 (mm) REVERT: D 240 MET cc_start: 0.8483 (mtm) cc_final: 0.8270 (mtm) REVERT: G 42 LEU cc_start: 0.8447 (mm) cc_final: 0.8148 (mm) REVERT: H 42 LEU cc_start: 0.8351 (mm) cc_final: 0.8078 (mm) REVERT: I 42 LEU cc_start: 0.8422 (mm) cc_final: 0.8137 (mm) REVERT: I 110 GLN cc_start: 0.8536 (mt0) cc_final: 0.8332 (mt0) REVERT: I 215 GLN cc_start: 0.7650 (mm110) cc_final: 0.7279 (mp-120) REVERT: J 42 LEU cc_start: 0.8542 (mm) cc_final: 0.8263 (mm) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.9149 time to fit residues: 426.8019 Evaluate side-chains 364 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 85 GLN A 173 GLN B 85 GLN B 173 GLN C 85 GLN C 173 GLN D 72 GLN D 85 GLN D 173 GLN E 85 GLN F 72 GLN F 85 GLN F 173 GLN G 85 GLN G 173 GLN H 85 GLN H 173 GLN I 72 GLN I 85 GLN I 173 GLN J 72 GLN J 85 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.167997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.106673 restraints weight = 19563.523| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.22 r_work: 0.2936 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19100 Z= 0.223 Angle : 0.615 8.453 25860 Z= 0.303 Chirality : 0.044 0.138 3030 Planarity : 0.004 0.034 3260 Dihedral : 4.629 14.807 2470 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.19 % Allowed : 10.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.17), residues: 2260 helix: -0.12 (0.19), residues: 640 sheet: 0.49 (0.17), residues: 910 loop : -0.30 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 191 TYR 0.011 0.002 TYR E 37 PHE 0.017 0.002 PHE G 70 TRP 0.004 0.001 TRP E 186 HIS 0.004 0.002 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00520 (19090) covalent geometry : angle 0.61492 (25840) SS BOND : bond 0.00287 ( 10) SS BOND : angle 0.25661 ( 20) hydrogen bonds : bond 0.04582 ( 440) hydrogen bonds : angle 5.08120 ( 1290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 336 time to evaluate : 0.764 Fit side-chains REVERT: C 42 LEU cc_start: 0.8273 (mm) cc_final: 0.8008 (mm) REVERT: C 227 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8843 (ttpp) REVERT: C 244 ARG cc_start: 0.7615 (tpp80) cc_final: 0.6642 (ttp-170) REVERT: D 42 LEU cc_start: 0.8252 (mm) cc_final: 0.7986 (mm) REVERT: D 169 GLN cc_start: 0.8278 (mp-120) cc_final: 0.8039 (mp-120) REVERT: D 184 GLU cc_start: 0.8563 (tp30) cc_final: 0.8301 (tp30) REVERT: E 42 LEU cc_start: 0.8272 (mm) cc_final: 0.8047 (mm) REVERT: E 166 MET cc_start: 0.8505 (ttm) cc_final: 0.8246 (ttm) REVERT: H 42 LEU cc_start: 0.8238 (mm) cc_final: 0.7958 (mm) REVERT: I 42 LEU cc_start: 0.8107 (mm) cc_final: 0.7846 (mm) REVERT: I 110 GLN cc_start: 0.9155 (mt0) cc_final: 0.8904 (mt0) REVERT: I 169 GLN cc_start: 0.8284 (mp-120) cc_final: 0.8038 (mp-120) REVERT: I 215 GLN cc_start: 0.8176 (mm110) cc_final: 0.7943 (mp10) REVERT: J 166 MET cc_start: 0.8487 (ttm) cc_final: 0.8226 (ttm) REVERT: J 227 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8912 (ttpp) outliers start: 26 outliers final: 10 residues processed: 347 average time/residue: 0.8816 time to fit residues: 331.0214 Evaluate side-chains 292 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 280 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 227 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 0.0000 chunk 155 optimal weight: 0.9980 chunk 101 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 213 optimal weight: 0.0060 chunk 212 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 85 GLN A 173 GLN B 56 ASN B 85 GLN B 173 GLN C 56 ASN C 85 GLN C 173 GLN D 56 ASN D 85 GLN D 173 GLN E 85 GLN F 56 ASN F 85 GLN G 85 GLN G 173 GLN H 56 ASN H 85 GLN H 173 GLN I 56 ASN I 85 GLN I 173 GLN J 85 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110778 restraints weight = 19756.941| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.23 r_work: 0.3000 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19100 Z= 0.097 Angle : 0.511 8.234 25860 Z= 0.251 Chirality : 0.041 0.131 3030 Planarity : 0.003 0.031 3260 Dihedral : 4.059 11.943 2470 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.79 % Allowed : 13.21 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2260 helix: 0.16 (0.19), residues: 640 sheet: 0.53 (0.17), residues: 910 loop : -0.19 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 237 TYR 0.009 0.001 TYR A 103 PHE 0.008 0.001 PHE C 245 TRP 0.003 0.001 TRP I 186 HIS 0.002 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00210 (19090) covalent geometry : angle 0.51063 (25840) SS BOND : bond 0.00123 ( 10) SS BOND : angle 0.44446 ( 20) hydrogen bonds : bond 0.03768 ( 440) hydrogen bonds : angle 4.82645 ( 1290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 354 time to evaluate : 0.724 Fit side-chains REVERT: A 121 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.8000 (t0) REVERT: B 42 LEU cc_start: 0.8274 (mm) cc_final: 0.8014 (mm) REVERT: B 88 ASP cc_start: 0.8597 (t0) cc_final: 0.8395 (t70) REVERT: B 179 LEU cc_start: 0.9141 (tp) cc_final: 0.8908 (tp) REVERT: B 184 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7882 (mp0) REVERT: C 42 LEU cc_start: 0.8138 (mm) cc_final: 0.7892 (mm) REVERT: C 184 GLU cc_start: 0.8619 (tp30) cc_final: 0.8388 (tp30) REVERT: C 244 ARG cc_start: 0.7560 (tpp80) cc_final: 0.6612 (ttp-170) REVERT: D 42 LEU cc_start: 0.8172 (mm) cc_final: 0.7925 (mm) REVERT: D 166 MET cc_start: 0.8543 (ttm) cc_final: 0.8304 (ttm) REVERT: D 215 GLN cc_start: 0.8143 (mm110) cc_final: 0.7350 (mp-120) REVERT: E 42 LEU cc_start: 0.8269 (mm) cc_final: 0.7984 (mm) REVERT: E 166 MET cc_start: 0.8437 (ttm) cc_final: 0.8187 (ttm) REVERT: F 121 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.8019 (t0) REVERT: G 42 LEU cc_start: 0.8278 (mm) cc_final: 0.8067 (mm) REVERT: G 88 ASP cc_start: 0.8700 (t0) cc_final: 0.8483 (t70) REVERT: G 179 LEU cc_start: 0.9144 (tp) cc_final: 0.8900 (tp) REVERT: H 42 LEU cc_start: 0.8122 (mm) cc_final: 0.7882 (mm) REVERT: H 121 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7880 (t0) REVERT: I 166 MET cc_start: 0.8554 (ttm) cc_final: 0.8287 (ttm) REVERT: I 215 GLN cc_start: 0.8157 (mm110) cc_final: 0.7921 (mp-120) REVERT: I 244 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6707 (ttp80) REVERT: J 42 LEU cc_start: 0.8247 (mm) cc_final: 0.7959 (mm) REVERT: J 166 MET cc_start: 0.8396 (ttm) cc_final: 0.8143 (ttm) outliers start: 39 outliers final: 10 residues processed: 373 average time/residue: 0.8196 time to fit residues: 333.5201 Evaluate side-chains 334 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 320 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 244 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 204 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 183 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 206 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 196 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 85 GLN B 173 GLN C 85 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 173 GLN G 56 ASN G 85 GLN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN J 173 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.106766 restraints weight = 19726.136| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.40 r_work: 0.2918 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19100 Z= 0.182 Angle : 0.557 8.125 25860 Z= 0.275 Chirality : 0.043 0.139 3030 Planarity : 0.003 0.035 3260 Dihedral : 4.418 12.721 2470 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.88 % Allowed : 16.70 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 2260 helix: 0.28 (0.20), residues: 640 sheet: 0.49 (0.17), residues: 910 loop : -0.22 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 191 TYR 0.010 0.002 TYR B 103 PHE 0.009 0.001 PHE I 70 TRP 0.003 0.001 TRP B 186 HIS 0.004 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00422 (19090) covalent geometry : angle 0.55662 (25840) SS BOND : bond 0.00273 ( 10) SS BOND : angle 0.36925 ( 20) hydrogen bonds : bond 0.03790 ( 440) hydrogen bonds : angle 4.71007 ( 1290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 307 time to evaluate : 0.729 Fit side-chains REVERT: A 184 GLU cc_start: 0.8700 (tp30) cc_final: 0.8438 (tp30) REVERT: B 184 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7953 (mp0) REVERT: C 42 LEU cc_start: 0.8062 (mm) cc_final: 0.7790 (mm) REVERT: C 244 ARG cc_start: 0.7542 (tpp80) cc_final: 0.6558 (ttp-170) REVERT: D 42 LEU cc_start: 0.8074 (mm) cc_final: 0.7828 (mm) REVERT: D 103 TYR cc_start: 0.9411 (m-80) cc_final: 0.9200 (m-80) REVERT: D 166 MET cc_start: 0.8520 (ttm) cc_final: 0.8296 (ttm) REVERT: E 42 LEU cc_start: 0.8112 (mm) cc_final: 0.7834 (mm) REVERT: E 166 MET cc_start: 0.8445 (ttm) cc_final: 0.8204 (ttm) REVERT: E 184 GLU cc_start: 0.8513 (tp30) cc_final: 0.8027 (mp0) REVERT: G 42 LEU cc_start: 0.8303 (mm) cc_final: 0.8076 (mm) REVERT: H 42 LEU cc_start: 0.8088 (mm) cc_final: 0.7825 (mm) REVERT: I 215 GLN cc_start: 0.8195 (mm110) cc_final: 0.7962 (mp-120) REVERT: J 42 LEU cc_start: 0.8126 (mm) cc_final: 0.7867 (mm) REVERT: J 166 MET cc_start: 0.8419 (ttm) cc_final: 0.8179 (ttm) REVERT: J 227 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8930 (ttpp) outliers start: 41 outliers final: 16 residues processed: 326 average time/residue: 0.8605 time to fit residues: 304.5790 Evaluate side-chains 288 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 271 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 227 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 193 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 30 optimal weight: 0.0570 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 173 GLN B 85 GLN B 173 GLN C 72 GLN C 85 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN F 121 ASN G 56 ASN G 85 GLN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.170172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110133 restraints weight = 19575.157| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.19 r_work: 0.2995 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19100 Z= 0.092 Angle : 0.501 8.448 25860 Z= 0.246 Chirality : 0.041 0.128 3030 Planarity : 0.003 0.033 3260 Dihedral : 3.970 11.704 2470 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.20 % Allowed : 18.35 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2260 helix: 0.49 (0.20), residues: 640 sheet: 0.47 (0.17), residues: 910 loop : -0.11 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 191 TYR 0.009 0.001 TYR E 103 PHE 0.006 0.001 PHE A 245 TRP 0.002 0.001 TRP I 186 HIS 0.002 0.000 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00199 (19090) covalent geometry : angle 0.50126 (25840) SS BOND : bond 0.00102 ( 10) SS BOND : angle 0.44084 ( 20) hydrogen bonds : bond 0.03306 ( 440) hydrogen bonds : angle 4.59671 ( 1290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 321 time to evaluate : 0.762 Fit side-chains REVERT: B 42 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7801 (mm) REVERT: B 179 LEU cc_start: 0.9133 (tp) cc_final: 0.8906 (tp) REVERT: B 184 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7830 (mp0) REVERT: C 244 ARG cc_start: 0.7516 (tpp80) cc_final: 0.6557 (ttp-170) REVERT: D 42 LEU cc_start: 0.7979 (mm) cc_final: 0.7740 (mm) REVERT: E 42 LEU cc_start: 0.7990 (mm) cc_final: 0.7700 (mm) REVERT: E 184 GLU cc_start: 0.8447 (tp30) cc_final: 0.7946 (mp0) REVERT: G 42 LEU cc_start: 0.8172 (mm) cc_final: 0.7927 (mm) REVERT: G 179 LEU cc_start: 0.9126 (tp) cc_final: 0.8879 (tp) REVERT: I 215 GLN cc_start: 0.8106 (mm110) cc_final: 0.7884 (mp10) REVERT: I 244 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6658 (ttp80) outliers start: 48 outliers final: 14 residues processed: 350 average time/residue: 0.7172 time to fit residues: 276.4062 Evaluate side-chains 308 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 292 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 244 ARG Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 240 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 83 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 155 optimal weight: 0.4980 chunk 46 optimal weight: 20.0000 chunk 202 optimal weight: 0.3980 chunk 87 optimal weight: 0.3980 chunk 172 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 85 GLN B 173 GLN C 85 GLN C 173 GLN D 85 GLN D 121 ASN D 173 GLN E 85 GLN E 173 GLN G 85 GLN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 121 ASN I 173 GLN J 173 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.168721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108218 restraints weight = 19451.377| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.18 r_work: 0.2964 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19100 Z= 0.129 Angle : 0.517 8.331 25860 Z= 0.254 Chirality : 0.042 0.128 3030 Planarity : 0.003 0.039 3260 Dihedral : 4.089 12.081 2470 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.80 % Allowed : 19.04 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 2260 helix: 0.63 (0.20), residues: 640 sheet: 0.52 (0.17), residues: 910 loop : -0.15 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 191 TYR 0.011 0.001 TYR J 103 PHE 0.006 0.001 PHE I 71 TRP 0.001 0.001 TRP C 186 HIS 0.002 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00293 (19090) covalent geometry : angle 0.51678 (25840) SS BOND : bond 0.00162 ( 10) SS BOND : angle 0.36626 ( 20) hydrogen bonds : bond 0.03379 ( 440) hydrogen bonds : angle 4.57624 ( 1290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 324 time to evaluate : 0.790 Fit side-chains REVERT: A 42 LEU cc_start: 0.7930 (mm) cc_final: 0.7689 (mm) REVERT: A 184 GLU cc_start: 0.8628 (tp30) cc_final: 0.8357 (tp30) REVERT: B 184 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7875 (mp0) REVERT: C 184 GLU cc_start: 0.8642 (tp30) cc_final: 0.8416 (tp30) REVERT: C 203 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7660 (pm20) REVERT: C 244 ARG cc_start: 0.7519 (tpp80) cc_final: 0.6547 (ttp-170) REVERT: D 42 LEU cc_start: 0.7986 (mm) cc_final: 0.7724 (mm) REVERT: E 42 LEU cc_start: 0.8018 (mm) cc_final: 0.7715 (mm) REVERT: E 184 GLU cc_start: 0.8530 (tp30) cc_final: 0.8004 (mp0) REVERT: G 179 LEU cc_start: 0.9124 (tp) cc_final: 0.8876 (tp) REVERT: H 42 LEU cc_start: 0.7954 (mm) cc_final: 0.7695 (mm) REVERT: I 215 GLN cc_start: 0.8116 (mm110) cc_final: 0.7889 (mp-120) REVERT: J 227 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8881 (ttpp) outliers start: 61 outliers final: 19 residues processed: 369 average time/residue: 0.7514 time to fit residues: 303.5582 Evaluate side-chains 311 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 291 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 227 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 58 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 85 GLN B 173 GLN C 85 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 173 GLN G 85 GLN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN J 173 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.106870 restraints weight = 19406.642| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.18 r_work: 0.2935 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19100 Z= 0.167 Angle : 0.559 8.277 25860 Z= 0.277 Chirality : 0.043 0.127 3030 Planarity : 0.004 0.044 3260 Dihedral : 4.257 12.766 2470 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.20 % Allowed : 19.77 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2260 helix: 0.69 (0.20), residues: 640 sheet: 0.54 (0.17), residues: 910 loop : -0.24 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 191 TYR 0.011 0.001 TYR J 103 PHE 0.006 0.001 PHE I 71 TRP 0.003 0.001 TRP B 186 HIS 0.003 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00387 (19090) covalent geometry : angle 0.55936 (25840) SS BOND : bond 0.00219 ( 10) SS BOND : angle 0.34893 ( 20) hydrogen bonds : bond 0.03484 ( 440) hydrogen bonds : angle 4.54352 ( 1290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 320 time to evaluate : 0.734 Fit side-chains REVERT: A 42 LEU cc_start: 0.7913 (mm) cc_final: 0.7654 (mm) REVERT: B 42 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7849 (mm) REVERT: B 102 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8210 (tp30) REVERT: B 184 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7891 (mp0) REVERT: C 42 LEU cc_start: 0.7912 (mm) cc_final: 0.7636 (mm) REVERT: C 244 ARG cc_start: 0.7511 (tpp80) cc_final: 0.6495 (ttp-170) REVERT: D 42 LEU cc_start: 0.7959 (mm) cc_final: 0.7688 (mm) REVERT: D 166 MET cc_start: 0.8219 (ttm) cc_final: 0.7907 (ttm) REVERT: E 42 LEU cc_start: 0.7953 (mm) cc_final: 0.7677 (mm) REVERT: E 184 GLU cc_start: 0.8563 (tp30) cc_final: 0.8063 (mp0) REVERT: G 184 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7846 (mp0) REVERT: H 169 GLN cc_start: 0.8257 (mp-120) cc_final: 0.7875 (mp-120) REVERT: H 203 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7629 (pm20) REVERT: I 101 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8163 (tpp) REVERT: I 166 MET cc_start: 0.8197 (ttm) cc_final: 0.7876 (ttm) REVERT: I 215 GLN cc_start: 0.8096 (mm110) cc_final: 0.7880 (mp-120) REVERT: J 227 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8909 (ttpp) outliers start: 48 outliers final: 20 residues processed: 352 average time/residue: 0.8424 time to fit residues: 323.4281 Evaluate side-chains 329 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 306 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 195 LYS Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain J residue 240 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 10 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 0.0570 chunk 179 optimal weight: 0.0030 chunk 87 optimal weight: 0.0050 chunk 193 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 overall best weight: 0.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN B 85 GLN B 173 GLN C 85 GLN C 173 GLN D 85 GLN D 173 GLN E 72 GLN E 85 GLN E 173 GLN G 72 GLN G 85 GLN G 173 GLN H 72 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN J 173 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.112185 restraints weight = 19660.704| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.24 r_work: 0.3018 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19100 Z= 0.083 Angle : 0.507 8.590 25860 Z= 0.250 Chirality : 0.041 0.131 3030 Planarity : 0.003 0.035 3260 Dihedral : 3.738 11.759 2470 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.56 % Allowed : 20.83 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2260 helix: 0.88 (0.20), residues: 640 sheet: 0.50 (0.17), residues: 910 loop : -0.10 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 191 TYR 0.007 0.001 TYR F 103 PHE 0.006 0.001 PHE A 232 TRP 0.004 0.001 TRP F 186 HIS 0.003 0.000 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00176 (19090) covalent geometry : angle 0.50705 (25840) SS BOND : bond 0.00053 ( 10) SS BOND : angle 0.38206 ( 20) hydrogen bonds : bond 0.02989 ( 440) hydrogen bonds : angle 4.50491 ( 1290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 333 time to evaluate : 0.802 Fit side-chains REVERT: A 42 LEU cc_start: 0.7906 (mm) cc_final: 0.7654 (mm) REVERT: A 184 GLU cc_start: 0.8621 (tp30) cc_final: 0.8352 (tp30) REVERT: A 203 GLU cc_start: 0.7409 (pm20) cc_final: 0.7001 (pp20) REVERT: B 42 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7766 (mm) REVERT: C 42 LEU cc_start: 0.7854 (mm) cc_final: 0.7596 (mm) REVERT: C 169 GLN cc_start: 0.8221 (mp-120) cc_final: 0.7732 (tt0) REVERT: C 231 ASN cc_start: 0.8670 (t0) cc_final: 0.8457 (t0) REVERT: C 244 ARG cc_start: 0.7472 (tpp80) cc_final: 0.6495 (ttp-170) REVERT: D 42 LEU cc_start: 0.7930 (mm) cc_final: 0.7676 (mm) REVERT: D 166 MET cc_start: 0.8111 (ttm) cc_final: 0.7733 (ttm) REVERT: D 215 GLN cc_start: 0.8114 (mm110) cc_final: 0.7907 (mp-120) REVERT: E 42 LEU cc_start: 0.7970 (mm) cc_final: 0.7672 (mm) REVERT: E 169 GLN cc_start: 0.8204 (mp-120) cc_final: 0.7560 (tt0) REVERT: E 184 GLU cc_start: 0.8516 (tp30) cc_final: 0.8018 (mp0) REVERT: G 102 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8089 (tp30) REVERT: G 184 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7861 (mp0) REVERT: H 42 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7539 (mm) REVERT: H 169 GLN cc_start: 0.8296 (mp-120) cc_final: 0.7737 (tt0) REVERT: H 203 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7596 (pm20) REVERT: I 166 MET cc_start: 0.8071 (ttm) cc_final: 0.7677 (ttm) REVERT: I 215 GLN cc_start: 0.8066 (mm110) cc_final: 0.7848 (mp-120) REVERT: J 103 TYR cc_start: 0.8554 (m-80) cc_final: 0.8326 (m-80) REVERT: J 169 GLN cc_start: 0.8191 (mp-120) cc_final: 0.7559 (tt0) outliers start: 34 outliers final: 15 residues processed: 353 average time/residue: 0.7588 time to fit residues: 295.4493 Evaluate side-chains 328 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 311 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 107 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 206 optimal weight: 0.0870 chunk 79 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 144 optimal weight: 0.0050 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN B 173 GLN C 85 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 173 GLN G 72 GLN G 85 GLN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.169043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109804 restraints weight = 19533.826| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.13 r_work: 0.2986 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19100 Z= 0.120 Angle : 0.533 8.506 25860 Z= 0.262 Chirality : 0.042 0.125 3030 Planarity : 0.004 0.053 3260 Dihedral : 3.964 12.460 2470 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.87 % Allowed : 22.20 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2260 helix: 0.94 (0.20), residues: 640 sheet: 0.60 (0.17), residues: 910 loop : -0.15 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 191 TYR 0.009 0.001 TYR B 103 PHE 0.006 0.001 PHE I 71 TRP 0.001 0.000 TRP H 186 HIS 0.004 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00275 (19090) covalent geometry : angle 0.53305 (25840) SS BOND : bond 0.00120 ( 10) SS BOND : angle 0.39937 ( 20) hydrogen bonds : bond 0.03163 ( 440) hydrogen bonds : angle 4.50978 ( 1290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 345 time to evaluate : 0.553 Fit side-chains REVERT: A 42 LEU cc_start: 0.7918 (mm) cc_final: 0.7656 (mm) REVERT: A 184 GLU cc_start: 0.8578 (tp30) cc_final: 0.8313 (tp30) REVERT: A 203 GLU cc_start: 0.7396 (pm20) cc_final: 0.6946 (pp20) REVERT: B 42 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7723 (mm) REVERT: B 179 LEU cc_start: 0.9110 (tp) cc_final: 0.8869 (tp) REVERT: B 184 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7886 (mp0) REVERT: C 42 LEU cc_start: 0.7874 (mm) cc_final: 0.7613 (mm) REVERT: C 169 GLN cc_start: 0.8256 (mp-120) cc_final: 0.7702 (tt0) REVERT: C 244 ARG cc_start: 0.7424 (tpp80) cc_final: 0.6414 (ttp-170) REVERT: D 102 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8303 (tp30) REVERT: D 215 GLN cc_start: 0.8092 (mm110) cc_final: 0.7319 (mp-120) REVERT: E 42 LEU cc_start: 0.7987 (mm) cc_final: 0.7673 (mm) REVERT: E 169 GLN cc_start: 0.8294 (mp-120) cc_final: 0.7619 (tt0) REVERT: E 184 GLU cc_start: 0.8538 (tp30) cc_final: 0.8006 (mp0) REVERT: E 227 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8759 (tttm) REVERT: F 102 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8201 (tp30) REVERT: G 42 LEU cc_start: 0.8221 (mm) cc_final: 0.8004 (mm) REVERT: G 179 LEU cc_start: 0.9107 (tp) cc_final: 0.8848 (tp) REVERT: G 184 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7883 (mp0) REVERT: H 42 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7559 (mm) REVERT: H 148 GLU cc_start: 0.8176 (pt0) cc_final: 0.7899 (pt0) REVERT: H 169 GLN cc_start: 0.8199 (mp-120) cc_final: 0.7621 (tt0) REVERT: H 184 GLU cc_start: 0.8626 (tp30) cc_final: 0.8395 (tp30) REVERT: I 215 GLN cc_start: 0.8045 (mm110) cc_final: 0.7839 (mp-120) REVERT: J 169 GLN cc_start: 0.8254 (mp-120) cc_final: 0.7587 (tt0) outliers start: 19 outliers final: 15 residues processed: 356 average time/residue: 0.8322 time to fit residues: 322.5885 Evaluate side-chains 339 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 322 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 195 LYS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 80 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 201 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 173 GLN B 85 GLN B 173 GLN C 85 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 173 GLN G 85 GLN G 173 GLN H 85 GLN H 173 GLN I 85 GLN I 173 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.168043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.108775 restraints weight = 19619.181| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.10 r_work: 0.2973 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19100 Z= 0.152 Angle : 0.557 8.440 25860 Z= 0.275 Chirality : 0.042 0.126 3030 Planarity : 0.004 0.061 3260 Dihedral : 4.182 13.321 2470 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.10 % Allowed : 22.11 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2260 helix: 0.93 (0.20), residues: 640 sheet: 0.61 (0.17), residues: 910 loop : -0.23 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 191 TYR 0.010 0.001 TYR G 202 PHE 0.006 0.001 PHE I 71 TRP 0.003 0.001 TRP B 186 HIS 0.003 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00354 (19090) covalent geometry : angle 0.55749 (25840) SS BOND : bond 0.00180 ( 10) SS BOND : angle 0.35643 ( 20) hydrogen bonds : bond 0.03303 ( 440) hydrogen bonds : angle 4.50052 ( 1290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4520 Ramachandran restraints generated. 2260 Oldfield, 0 Emsley, 2260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 321 time to evaluate : 0.810 Fit side-chains REVERT: A 42 LEU cc_start: 0.7906 (mm) cc_final: 0.7633 (mm) REVERT: A 102 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8046 (tp30) REVERT: A 184 GLU cc_start: 0.8587 (tp30) cc_final: 0.8334 (tp30) REVERT: A 203 GLU cc_start: 0.7395 (pm20) cc_final: 0.6980 (pp20) REVERT: B 42 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7793 (mm) REVERT: B 184 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7934 (mp0) REVERT: C 42 LEU cc_start: 0.7926 (mm) cc_final: 0.7645 (mm) REVERT: C 169 GLN cc_start: 0.8210 (mp-120) cc_final: 0.7623 (tt0) REVERT: C 244 ARG cc_start: 0.7417 (tpp80) cc_final: 0.6420 (ttp-170) REVERT: D 166 MET cc_start: 0.8117 (ttm) cc_final: 0.7733 (ttm) REVERT: D 203 GLU cc_start: 0.7294 (pm20) cc_final: 0.6941 (pp20) REVERT: D 215 GLN cc_start: 0.8099 (mm110) cc_final: 0.7877 (mp-120) REVERT: E 42 LEU cc_start: 0.7974 (mm) cc_final: 0.7690 (mm) REVERT: E 169 GLN cc_start: 0.8267 (mp-120) cc_final: 0.7625 (tt0) REVERT: E 227 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8756 (tttm) REVERT: G 122 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8778 (mp) REVERT: H 42 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7583 (mm) REVERT: H 102 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8156 (tp30) REVERT: H 169 GLN cc_start: 0.8203 (mp-120) cc_final: 0.7626 (tt0) REVERT: H 184 GLU cc_start: 0.8642 (tp30) cc_final: 0.8406 (tp30) REVERT: I 215 GLN cc_start: 0.8055 (mm110) cc_final: 0.7844 (mp-120) REVERT: J 169 GLN cc_start: 0.8251 (mp-120) cc_final: 0.7605 (tt0) outliers start: 24 outliers final: 17 residues processed: 338 average time/residue: 0.8802 time to fit residues: 323.3389 Evaluate side-chains 333 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 313 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 195 LYS Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 75 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 160 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 152 optimal weight: 0.1980 chunk 147 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 chunk 156 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 162 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 173 GLN B 85 GLN B 173 GLN C 85 GLN C 173 GLN D 85 GLN D 173 GLN E 85 GLN E 173 GLN F 169 GLN F 173 GLN G 85 GLN G 173 GLN H 173 GLN I 85 GLN I 173 GLN J 173 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.168739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108992 restraints weight = 19749.394| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.18 r_work: 0.2976 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19100 Z= 0.120 Angle : 0.539 8.540 25860 Z= 0.265 Chirality : 0.042 0.125 3030 Planarity : 0.004 0.055 3260 Dihedral : 4.068 13.697 2470 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.06 % Allowed : 21.83 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 2260 helix: 0.94 (0.20), residues: 640 sheet: 0.56 (0.17), residues: 910 loop : -0.22 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 191 TYR 0.010 0.001 TYR E 103 PHE 0.006 0.001 PHE I 71 TRP 0.002 0.001 TRP G 186 HIS 0.002 0.001 HIS I 152 Details of bonding type rmsd covalent geometry : bond 0.00275 (19090) covalent geometry : angle 0.53949 (25840) SS BOND : bond 0.00124 ( 10) SS BOND : angle 0.35212 ( 20) hydrogen bonds : bond 0.03175 ( 440) hydrogen bonds : angle 4.50353 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9364.32 seconds wall clock time: 159 minutes 33.65 seconds (9573.65 seconds total)