Starting phenix.real_space_refine on Sat Aug 23 18:07:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ckz_16707/08_2025/8ckz_16707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ckz_16707/08_2025/8ckz_16707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ckz_16707/08_2025/8ckz_16707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ckz_16707/08_2025/8ckz_16707.map" model { file = "/net/cci-nas-00/data/ceres_data/8ckz_16707/08_2025/8ckz_16707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ckz_16707/08_2025/8ckz_16707.cif" } resolution = 3.07 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= 0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 45 atoms to isotropic. 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 110 5.16 5 C 8780 2.51 5 N 2400 2.21 5 O 2620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13910 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Restraints were copied for chains: D, G, J, M, E, H, K, N, F, I, L, O Time building chain proxies: 1.96, per 1000 atoms: 0.14 Number of scatterers: 13910 At special positions: 0 Unit cell: (151.59, 153.45, 93, 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 110 16.00 O 2620 8.00 N 2400 7.00 C 8780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 575.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 5 sheets defined 76.7% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 60 removed outlier: 4.139A pdb=" N THR A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 removed outlier: 3.516A pdb=" N MET A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.461A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.722A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.552A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 195 through 204 removed outlier: 3.657A pdb=" N ILE B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.885A pdb=" N THR C 200 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 60 removed outlier: 4.138A pdb=" N THR D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 84 removed outlier: 3.516A pdb=" N MET D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.462A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.722A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.552A pdb=" N ILE E 153 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 178 through 188 Processing helix chain 'E' and resid 188 through 193 Processing helix chain 'E' and resid 195 through 204 removed outlier: 3.657A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 178 through 188 Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.885A pdb=" N THR F 200 " --> pdb=" O PRO F 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'G' and resid 16 through 30 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 60 removed outlier: 4.139A pdb=" N THR G 58 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL G 59 " --> pdb=" O MET G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 84 removed outlier: 3.516A pdb=" N MET G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 175 Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.461A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.722A pdb=" N ILE G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'H' and resid 149 through 153 removed outlier: 3.552A pdb=" N ILE H 153 " --> pdb=" O ILE H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 176 Processing helix chain 'H' and resid 178 through 188 Processing helix chain 'H' and resid 188 through 193 Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.658A pdb=" N ILE H 201 " --> pdb=" O ASP H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 219 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 176 Processing helix chain 'I' and resid 178 through 188 Processing helix chain 'I' and resid 188 through 193 Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.885A pdb=" N THR I 200 " --> pdb=" O PRO I 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE I 201 " --> pdb=" O ASP I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 219 Processing helix chain 'J' and resid 16 through 30 Processing helix chain 'J' and resid 35 through 44 Processing helix chain 'J' and resid 48 through 60 removed outlier: 4.138A pdb=" N THR J 58 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL J 59 " --> pdb=" O MET J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 84 removed outlier: 3.516A pdb=" N MET J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 105 Processing helix chain 'J' and resid 110 through 120 Processing helix chain 'J' and resid 125 through 145 Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 160 through 175 Processing helix chain 'J' and resid 178 through 193 removed outlier: 4.462A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 205 removed outlier: 3.723A pdb=" N ILE J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 219 Processing helix chain 'K' and resid 149 through 153 removed outlier: 3.552A pdb=" N ILE K 153 " --> pdb=" O ILE K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 176 Processing helix chain 'K' and resid 178 through 188 Processing helix chain 'K' and resid 188 through 193 Processing helix chain 'K' and resid 195 through 204 removed outlier: 3.657A pdb=" N ILE K 201 " --> pdb=" O ASP K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 219 Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 160 through 176 Processing helix chain 'L' and resid 178 through 188 Processing helix chain 'L' and resid 188 through 193 Processing helix chain 'L' and resid 195 through 205 removed outlier: 3.885A pdb=" N THR L 200 " --> pdb=" O PRO L 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE L 201 " --> pdb=" O ASP L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 219 Processing helix chain 'M' and resid 16 through 30 Processing helix chain 'M' and resid 35 through 44 Processing helix chain 'M' and resid 48 through 60 removed outlier: 4.138A pdb=" N THR M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL M 59 " --> pdb=" O MET M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 84 removed outlier: 3.516A pdb=" N MET M 68 " --> pdb=" O ALA M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 105 Processing helix chain 'M' and resid 110 through 120 Processing helix chain 'M' and resid 125 through 145 Processing helix chain 'M' and resid 149 through 153 Processing helix chain 'M' and resid 160 through 175 Processing helix chain 'M' and resid 178 through 193 removed outlier: 4.461A pdb=" N LEU M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL M 191 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 205 removed outlier: 3.723A pdb=" N ILE M 201 " --> pdb=" O ASP M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 219 Processing helix chain 'N' and resid 149 through 153 removed outlier: 3.552A pdb=" N ILE N 153 " --> pdb=" O ILE N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 176 Processing helix chain 'N' and resid 178 through 188 Processing helix chain 'N' and resid 188 through 193 Processing helix chain 'N' and resid 195 through 204 removed outlier: 3.657A pdb=" N ILE N 201 " --> pdb=" O ASP N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 219 Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 160 through 176 Processing helix chain 'O' and resid 178 through 188 Processing helix chain 'O' and resid 188 through 193 Processing helix chain 'O' and resid 195 through 205 removed outlier: 3.886A pdb=" N THR O 200 " --> pdb=" O PRO O 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE O 201 " --> pdb=" O ASP O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 219 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'J' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'M' and resid 2 through 4 875 hydrogen bonds defined for protein. 2550 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: 2.06 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4590 1.34 - 1.46: 1439 1.46 - 1.57: 7956 1.57 - 1.69: 0 1.69 - 1.81: 190 Bond restraints: 14175 Sorted by residual: bond pdb=" N THR N 148 " pdb=" CA THR N 148 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.32e+00 bond pdb=" N THR I 148 " pdb=" CA THR I 148 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.29e+00 bond pdb=" N THR O 148 " pdb=" CA THR O 148 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" N THR C 148 " pdb=" CA THR C 148 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 bond pdb=" N THR E 148 " pdb=" CA THR E 148 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 ... (remaining 14170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 17114 1.31 - 2.63: 1724 2.63 - 3.94: 331 3.94 - 5.26: 51 5.26 - 6.57: 15 Bond angle restraints: 19235 Sorted by residual: angle pdb=" CA LYS G 131 " pdb=" CB LYS G 131 " pdb=" CG LYS G 131 " ideal model delta sigma weight residual 114.10 120.67 -6.57 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA LYS M 131 " pdb=" CB LYS M 131 " pdb=" CG LYS M 131 " ideal model delta sigma weight residual 114.10 120.67 -6.57 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA LYS A 131 " pdb=" CB LYS A 131 " pdb=" CG LYS A 131 " ideal model delta sigma weight residual 114.10 120.66 -6.56 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C GLU G 175 " pdb=" N GLN G 176 " pdb=" CA GLN G 176 " ideal model delta sigma weight residual 121.18 127.67 -6.49 1.98e+00 2.55e-01 1.08e+01 angle pdb=" C GLU J 175 " pdb=" N GLN J 176 " pdb=" CA GLN J 176 " ideal model delta sigma weight residual 121.18 127.67 -6.49 1.98e+00 2.55e-01 1.08e+01 ... (remaining 19230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8175 17.91 - 35.83: 400 35.83 - 53.74: 105 53.74 - 71.65: 15 71.65 - 89.57: 15 Dihedral angle restraints: 8710 sinusoidal: 3500 harmonic: 5210 Sorted by residual: dihedral pdb=" CA SER D 44 " pdb=" C SER D 44 " pdb=" N GLU D 45 " pdb=" CA GLU D 45 " ideal model delta harmonic sigma weight residual -180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER J 44 " pdb=" C SER J 44 " pdb=" N GLU J 45 " pdb=" CA GLU J 45 " ideal model delta harmonic sigma weight residual 180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER A 44 " pdb=" C SER A 44 " pdb=" N GLU A 45 " pdb=" CA GLU A 45 " ideal model delta harmonic sigma weight residual -180.00 -150.37 -29.63 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 8707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1223 0.037 - 0.074: 694 0.074 - 0.111: 197 0.111 - 0.149: 64 0.149 - 0.186: 22 Chirality restraints: 2200 Sorted by residual: chirality pdb=" CA GLN N 176 " pdb=" N GLN N 176 " pdb=" C GLN N 176 " pdb=" CB GLN N 176 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CA GLN E 176 " pdb=" N GLN E 176 " pdb=" C GLN E 176 " pdb=" CB GLN E 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA GLN B 176 " pdb=" N GLN B 176 " pdb=" C GLN B 176 " pdb=" CB GLN B 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 2197 not shown) Planarity restraints: 2485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU M 136 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C LEU M 136 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU M 136 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY M 137 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 136 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C LEU D 136 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU D 136 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY D 137 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 136 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C LEU A 136 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A 136 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 137 " -0.015 2.00e-02 2.50e+03 ... (remaining 2482 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 15 2.55 - 3.14: 11631 3.14 - 3.73: 21838 3.73 - 4.31: 30632 4.31 - 4.90: 50121 Nonbonded interactions: 114237 Sorted by model distance: nonbonded pdb=" CD1 LEU G 20 " pdb=" OE1 GLU J 45 " model vdw 1.966 3.460 nonbonded pdb=" CD1 LEU D 20 " pdb=" OE1 GLU G 45 " model vdw 1.966 3.460 nonbonded pdb=" OE1 GLU A 45 " pdb=" CD1 LEU M 20 " model vdw 1.966 3.460 nonbonded pdb=" CD1 LEU A 20 " pdb=" OE1 GLU D 45 " model vdw 1.966 3.460 nonbonded pdb=" CD1 LEU J 20 " pdb=" OE1 GLU M 45 " model vdw 1.966 3.460 ... (remaining 114232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.005 0.051 14175 Z= 0.249 Angle : 0.896 6.570 19235 Z= 0.530 Chirality : 0.051 0.186 2200 Planarity : 0.009 0.080 2485 Dihedral : 12.354 89.566 5320 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -1.16 (0.17), residues: 1760 helix: -1.05 (0.13), residues: 1170 sheet: -2.19 (0.46), residues: 45 loop : 0.57 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG M 167 TYR 0.015 0.005 TYR G 130 PHE 0.019 0.003 PHE J 40 TRP 0.020 0.005 TRP N 184 HIS 0.008 0.004 HIS D 62 Details of bonding type rmsd covalent geometry : bond 0.00498 (14175) covalent geometry : angle 0.89635 (19235) hydrogen bonds : bond 0.10908 ( 875) hydrogen bonds : angle 6.00765 ( 2550) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 0.444 Fit side-chains REVERT: A 83 LEU cc_start: 0.7573 (mp) cc_final: 0.7179 (mt) REVERT: A 96 MET cc_start: 0.6927 (ttp) cc_final: 0.6689 (ttt) REVERT: B 167 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7620 (mtm180) REVERT: B 199 LYS cc_start: 0.7598 (tttt) cc_final: 0.7355 (ttpt) REVERT: E 199 LYS cc_start: 0.7677 (tttt) cc_final: 0.7450 (ttmt) REVERT: G 83 LEU cc_start: 0.7583 (mp) cc_final: 0.7308 (mt) REVERT: H 192 GLN cc_start: 0.7918 (tp40) cc_final: 0.7599 (mm110) REVERT: H 193 ASN cc_start: 0.8251 (m-40) cc_final: 0.8035 (m110) REVERT: H 199 LYS cc_start: 0.7649 (tttt) cc_final: 0.7415 (ttmt) REVERT: K 199 LYS cc_start: 0.7596 (tttt) cc_final: 0.7393 (ttmt) REVERT: L 170 LYS cc_start: 0.8266 (tptt) cc_final: 0.8053 (tppt) REVERT: M 13 GLN cc_start: 0.7164 (tt0) cc_final: 0.6960 (tt0) REVERT: M 83 LEU cc_start: 0.7352 (mp) cc_final: 0.7148 (mt) REVERT: N 192 GLN cc_start: 0.7811 (tp40) cc_final: 0.7565 (mm110) REVERT: N 199 LYS cc_start: 0.7636 (tttt) cc_final: 0.7413 (ttpt) outliers start: 0 outliers final: 0 residues processed: 489 average time/residue: 0.1336 time to fit residues: 90.9462 Evaluate side-chains 386 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 120 HIS D 13 GLN E 219 GLN F 192 GLN G 13 GLN J 13 GLN J 120 HIS J 179 GLN N 219 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131101 restraints weight = 17179.148| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.10 r_work: 0.3139 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14175 Z= 0.138 Angle : 0.583 7.979 19235 Z= 0.302 Chirality : 0.041 0.138 2200 Planarity : 0.005 0.042 2485 Dihedral : 4.539 17.345 1905 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.94 % Allowed : 7.47 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.85 (0.18), residues: 1760 helix: 0.67 (0.14), residues: 1210 sheet: -1.91 (0.47), residues: 45 loop : 0.93 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 162 TYR 0.010 0.001 TYR I 169 PHE 0.007 0.001 PHE J 32 TRP 0.011 0.001 TRP M 184 HIS 0.003 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00317 (14175) covalent geometry : angle 0.58296 (19235) hydrogen bonds : bond 0.03997 ( 875) hydrogen bonds : angle 4.28880 ( 2550) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 401 time to evaluate : 0.538 Fit side-chains REVERT: A 185 MET cc_start: 0.8403 (mtm) cc_final: 0.7934 (mtm) REVERT: B 162 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.6041 (ttt180) REVERT: B 169 TYR cc_start: 0.8727 (m-80) cc_final: 0.8505 (m-80) REVERT: B 183 ASN cc_start: 0.8525 (m-40) cc_final: 0.8251 (m-40) REVERT: B 192 GLN cc_start: 0.8180 (tp40) cc_final: 0.7425 (mm110) REVERT: B 199 LYS cc_start: 0.7601 (tttt) cc_final: 0.7204 (ttmt) REVERT: B 218 CYS cc_start: 0.8517 (m) cc_final: 0.8018 (m) REVERT: C 154 ARG cc_start: 0.8615 (ttm110) cc_final: 0.8210 (mtt-85) REVERT: D 192 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7979 (tm-30) REVERT: E 192 GLN cc_start: 0.8119 (tp40) cc_final: 0.7307 (mm110) REVERT: E 193 ASN cc_start: 0.8732 (m110) cc_final: 0.8264 (m110) REVERT: E 199 LYS cc_start: 0.7624 (tttt) cc_final: 0.7150 (ttpt) REVERT: F 154 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8242 (mtt-85) REVERT: G 192 GLN cc_start: 0.8282 (tm-30) cc_final: 0.8006 (tm-30) REVERT: H 192 GLN cc_start: 0.8091 (tp40) cc_final: 0.7208 (mm110) REVERT: H 193 ASN cc_start: 0.8475 (m-40) cc_final: 0.8162 (m110) REVERT: H 199 LYS cc_start: 0.7477 (tttt) cc_final: 0.7004 (ttmt) REVERT: I 154 ARG cc_start: 0.8631 (mtm-85) cc_final: 0.8315 (mtt-85) REVERT: K 192 GLN cc_start: 0.8083 (tp40) cc_final: 0.7205 (mm110) REVERT: K 193 ASN cc_start: 0.8119 (m110) cc_final: 0.7727 (m110) REVERT: K 199 LYS cc_start: 0.7466 (tttt) cc_final: 0.7047 (ttmt) REVERT: K 218 CYS cc_start: 0.8549 (m) cc_final: 0.8158 (m) REVERT: L 154 ARG cc_start: 0.8758 (ttm110) cc_final: 0.8492 (mtt-85) REVERT: N 192 GLN cc_start: 0.8077 (tp40) cc_final: 0.7388 (mm110) REVERT: N 193 ASN cc_start: 0.8662 (m110) cc_final: 0.8227 (m110) REVERT: N 199 LYS cc_start: 0.7541 (tttt) cc_final: 0.7120 (ttpt) REVERT: O 154 ARG cc_start: 0.8624 (ttm110) cc_final: 0.8320 (mtt-85) outliers start: 14 outliers final: 8 residues processed: 407 average time/residue: 0.1260 time to fit residues: 72.4134 Evaluate side-chains 371 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 363 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 87 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 219 GLN D 13 GLN D 179 GLN E 193 ASN E 219 GLN G 13 GLN G 179 GLN H 219 GLN J 179 GLN K 219 GLN M 179 GLN N 193 ASN N 219 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.161144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123744 restraints weight = 17382.417| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.96 r_work: 0.3060 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14175 Z= 0.221 Angle : 0.622 7.837 19235 Z= 0.312 Chirality : 0.044 0.153 2200 Planarity : 0.005 0.050 2485 Dihedral : 4.437 20.556 1905 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.89 % Allowed : 9.97 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.96 (0.18), residues: 1760 helix: 0.81 (0.14), residues: 1210 sheet: -1.67 (0.44), residues: 45 loop : 0.79 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 162 TYR 0.012 0.002 TYR O 169 PHE 0.006 0.002 PHE J 32 TRP 0.013 0.002 TRP G 117 HIS 0.006 0.002 HIS G 120 Details of bonding type rmsd covalent geometry : bond 0.00553 (14175) covalent geometry : angle 0.62161 (19235) hydrogen bonds : bond 0.04126 ( 875) hydrogen bonds : angle 4.24484 ( 2550) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 378 time to evaluate : 0.464 Fit side-chains REVERT: A 185 MET cc_start: 0.8516 (mtm) cc_final: 0.8224 (mtm) REVERT: B 193 ASN cc_start: 0.8450 (m110) cc_final: 0.8094 (m110) REVERT: B 199 LYS cc_start: 0.7771 (tttt) cc_final: 0.7358 (ttmt) REVERT: B 218 CYS cc_start: 0.8479 (m) cc_final: 0.8212 (m) REVERT: C 154 ARG cc_start: 0.8841 (ttm110) cc_final: 0.8593 (mtt-85) REVERT: D 192 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8056 (tm-30) REVERT: E 192 GLN cc_start: 0.8200 (tp40) cc_final: 0.7367 (mm110) REVERT: E 193 ASN cc_start: 0.8905 (m-40) cc_final: 0.8536 (m110) REVERT: E 199 LYS cc_start: 0.7714 (tttt) cc_final: 0.7248 (ttmt) REVERT: F 154 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8421 (mtt-85) REVERT: G 124 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.6925 (tp) REVERT: H 192 GLN cc_start: 0.8248 (tp40) cc_final: 0.7355 (mm110) REVERT: H 193 ASN cc_start: 0.8678 (m-40) cc_final: 0.8413 (m110) REVERT: H 199 LYS cc_start: 0.7586 (tttt) cc_final: 0.7170 (ttmt) REVERT: I 154 ARG cc_start: 0.8904 (mtm-85) cc_final: 0.8639 (mtt-85) REVERT: J 124 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.6996 (tp) REVERT: J 189 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8537 (tt) REVERT: J 192 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8248 (tm-30) REVERT: K 192 GLN cc_start: 0.8276 (tp40) cc_final: 0.7341 (mm110) REVERT: K 193 ASN cc_start: 0.8442 (m110) cc_final: 0.8005 (m110) REVERT: K 199 LYS cc_start: 0.7680 (tttt) cc_final: 0.7311 (ttmt) REVERT: K 218 CYS cc_start: 0.8419 (m) cc_final: 0.8167 (m) REVERT: L 154 ARG cc_start: 0.8922 (ttm110) cc_final: 0.8647 (mtt-85) REVERT: M 124 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.6810 (tp) REVERT: N 192 GLN cc_start: 0.8199 (tp40) cc_final: 0.7428 (mm110) REVERT: N 193 ASN cc_start: 0.8802 (m-40) cc_final: 0.8436 (m110) REVERT: N 199 LYS cc_start: 0.7630 (tttt) cc_final: 0.7116 (ttmt) REVERT: O 154 ARG cc_start: 0.8815 (ttm110) cc_final: 0.8459 (mtt-85) outliers start: 28 outliers final: 16 residues processed: 387 average time/residue: 0.1095 time to fit residues: 60.5679 Evaluate side-chains 382 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 362 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN G 13 GLN G 63 GLN J 13 GLN J 179 GLN M 13 GLN M 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.164589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134903 restraints weight = 17226.100| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.69 r_work: 0.3067 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14175 Z= 0.122 Angle : 0.515 5.960 19235 Z= 0.261 Chirality : 0.040 0.133 2200 Planarity : 0.004 0.049 2485 Dihedral : 4.037 18.802 1905 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.55 % Allowed : 10.44 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.34 (0.19), residues: 1760 helix: 1.14 (0.14), residues: 1215 sheet: -1.62 (0.45), residues: 45 loop : 0.83 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 167 TYR 0.012 0.001 TYR M 145 PHE 0.005 0.001 PHE N 161 TRP 0.011 0.002 TRP G 117 HIS 0.003 0.001 HIS G 120 Details of bonding type rmsd covalent geometry : bond 0.00284 (14175) covalent geometry : angle 0.51549 (19235) hydrogen bonds : bond 0.03468 ( 875) hydrogen bonds : angle 4.00755 ( 2550) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 376 time to evaluate : 0.530 Fit side-chains REVERT: B 192 GLN cc_start: 0.8175 (tp40) cc_final: 0.7363 (mm110) REVERT: B 193 ASN cc_start: 0.8360 (m110) cc_final: 0.8040 (m110) REVERT: B 199 LYS cc_start: 0.7740 (tttt) cc_final: 0.7274 (ttmt) REVERT: B 218 CYS cc_start: 0.8299 (m) cc_final: 0.7971 (m) REVERT: C 154 ARG cc_start: 0.8761 (ttm110) cc_final: 0.8516 (mtt-85) REVERT: C 205 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.6929 (tp) REVERT: D 192 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7970 (tm-30) REVERT: E 183 ASN cc_start: 0.8516 (m-40) cc_final: 0.8304 (m110) REVERT: E 192 GLN cc_start: 0.8156 (tp40) cc_final: 0.7360 (mm110) REVERT: E 193 ASN cc_start: 0.8824 (m-40) cc_final: 0.8594 (m110) REVERT: E 199 LYS cc_start: 0.7760 (tttt) cc_final: 0.7305 (ttmt) REVERT: F 154 ARG cc_start: 0.8827 (ttm110) cc_final: 0.8475 (mtt-85) REVERT: G 192 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8001 (tm-30) REVERT: H 192 GLN cc_start: 0.8203 (tp40) cc_final: 0.7335 (mm110) REVERT: H 193 ASN cc_start: 0.8664 (m-40) cc_final: 0.8367 (m110) REVERT: H 199 LYS cc_start: 0.7673 (tttt) cc_final: 0.7287 (ttmt) REVERT: J 192 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8089 (tm-30) REVERT: K 183 ASN cc_start: 0.8537 (m110) cc_final: 0.8159 (m110) REVERT: K 192 GLN cc_start: 0.8211 (tp40) cc_final: 0.7321 (mm110) REVERT: K 193 ASN cc_start: 0.8418 (m110) cc_final: 0.7965 (m110) REVERT: K 199 LYS cc_start: 0.7657 (tttt) cc_final: 0.7329 (ttmt) REVERT: K 214 MET cc_start: 0.8053 (mtp) cc_final: 0.7744 (mtp) REVERT: K 218 CYS cc_start: 0.8361 (m) cc_final: 0.8087 (m) REVERT: L 154 ARG cc_start: 0.8883 (ttm110) cc_final: 0.8552 (mtt-85) REVERT: L 205 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.6783 (tp) REVERT: N 183 ASN cc_start: 0.8607 (m110) cc_final: 0.8340 (m-40) REVERT: N 191 VAL cc_start: 0.8813 (t) cc_final: 0.8594 (m) REVERT: N 192 GLN cc_start: 0.8173 (tp40) cc_final: 0.7432 (mm110) REVERT: N 199 LYS cc_start: 0.7655 (tttt) cc_final: 0.7273 (ttmt) REVERT: O 154 ARG cc_start: 0.8752 (ttm110) cc_final: 0.8457 (mtt-85) outliers start: 23 outliers final: 18 residues processed: 388 average time/residue: 0.1199 time to fit residues: 67.0243 Evaluate side-chains 378 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 358 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 178 SER Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain O residue 165 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 179 GLN D 13 GLN D 63 GLN G 13 GLN G 179 GLN J 13 GLN J 179 GLN K 219 GLN M 13 GLN M 63 GLN M 179 GLN N 193 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.163243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129077 restraints weight = 17330.929| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.84 r_work: 0.3135 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14175 Z= 0.157 Angle : 0.538 6.035 19235 Z= 0.270 Chirality : 0.041 0.133 2200 Planarity : 0.004 0.049 2485 Dihedral : 4.051 19.514 1905 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.42 % Allowed : 10.10 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.38 (0.19), residues: 1760 helix: 1.17 (0.14), residues: 1220 sheet: -1.54 (0.47), residues: 45 loop : 0.84 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 167 TYR 0.011 0.001 TYR F 169 PHE 0.007 0.001 PHE A 32 TRP 0.013 0.002 TRP M 117 HIS 0.004 0.001 HIS D 120 Details of bonding type rmsd covalent geometry : bond 0.00386 (14175) covalent geometry : angle 0.53818 (19235) hydrogen bonds : bond 0.03591 ( 875) hydrogen bonds : angle 4.01908 ( 2550) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 371 time to evaluate : 0.557 Fit side-chains REVERT: A 185 MET cc_start: 0.8454 (mtm) cc_final: 0.8048 (mtm) REVERT: B 192 GLN cc_start: 0.8237 (tp40) cc_final: 0.7373 (mm110) REVERT: B 193 ASN cc_start: 0.8481 (m110) cc_final: 0.8161 (m110) REVERT: B 199 LYS cc_start: 0.7708 (tttt) cc_final: 0.7216 (ttmt) REVERT: B 218 CYS cc_start: 0.8419 (m) cc_final: 0.8087 (m) REVERT: C 154 ARG cc_start: 0.8892 (ttm110) cc_final: 0.8629 (mtt-85) REVERT: C 205 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.6882 (tp) REVERT: D 152 ASP cc_start: 0.8677 (t0) cc_final: 0.8428 (t0) REVERT: D 189 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8622 (tt) REVERT: D 192 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8065 (tm-30) REVERT: E 183 ASN cc_start: 0.8534 (m-40) cc_final: 0.8318 (m110) REVERT: E 192 GLN cc_start: 0.8183 (tp40) cc_final: 0.7352 (mm110) REVERT: E 193 ASN cc_start: 0.8907 (m-40) cc_final: 0.8529 (m110) REVERT: E 199 LYS cc_start: 0.7804 (tttt) cc_final: 0.7371 (ttpt) REVERT: F 154 ARG cc_start: 0.8917 (ttm110) cc_final: 0.8422 (mtt-85) REVERT: G 192 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8026 (tm-30) REVERT: H 192 GLN cc_start: 0.8239 (tp40) cc_final: 0.7323 (mm110) REVERT: H 193 ASN cc_start: 0.8719 (m-40) cc_final: 0.8410 (m110) REVERT: H 199 LYS cc_start: 0.7689 (tttt) cc_final: 0.7274 (ttmt) REVERT: I 205 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.6999 (tp) REVERT: J 189 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8577 (tt) REVERT: J 192 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8159 (tm-30) REVERT: K 183 ASN cc_start: 0.8540 (m110) cc_final: 0.8160 (m110) REVERT: K 192 GLN cc_start: 0.8249 (tp40) cc_final: 0.7340 (mm110) REVERT: K 193 ASN cc_start: 0.8505 (m110) cc_final: 0.8049 (m110) REVERT: K 199 LYS cc_start: 0.7656 (tttt) cc_final: 0.7294 (ttmt) REVERT: K 218 CYS cc_start: 0.8488 (m) cc_final: 0.8214 (m) REVERT: L 154 ARG cc_start: 0.8956 (ttm110) cc_final: 0.8592 (mtt-85) REVERT: L 205 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.6782 (tp) REVERT: N 192 GLN cc_start: 0.8173 (tp40) cc_final: 0.7422 (mm110) REVERT: N 199 LYS cc_start: 0.7684 (tttt) cc_final: 0.7267 (ttmt) REVERT: O 154 ARG cc_start: 0.8828 (ttm110) cc_final: 0.8503 (mtt-85) outliers start: 36 outliers final: 22 residues processed: 384 average time/residue: 0.1185 time to fit residues: 66.0212 Evaluate side-chains 389 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 362 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 178 SER Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 141 optimal weight: 0.0570 chunk 146 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 63 GLN D 13 GLN D 63 GLN G 13 GLN G 63 GLN G 179 GLN J 13 GLN M 13 GLN M 63 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.165614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137117 restraints weight = 17146.465| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.60 r_work: 0.3170 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14175 Z= 0.115 Angle : 0.495 5.485 19235 Z= 0.250 Chirality : 0.039 0.138 2200 Planarity : 0.004 0.047 2485 Dihedral : 3.845 17.755 1905 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.09 % Allowed : 11.58 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.60 (0.19), residues: 1760 helix: 1.34 (0.15), residues: 1220 sheet: -1.49 (0.50), residues: 45 loop : 0.89 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 167 TYR 0.009 0.001 TYR C 169 PHE 0.005 0.001 PHE A 32 TRP 0.019 0.002 TRP A 117 HIS 0.002 0.001 HIS D 120 Details of bonding type rmsd covalent geometry : bond 0.00268 (14175) covalent geometry : angle 0.49533 (19235) hydrogen bonds : bond 0.03261 ( 875) hydrogen bonds : angle 3.93032 ( 2550) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 368 time to evaluate : 0.669 Fit side-chains REVERT: A 67 GLN cc_start: 0.8188 (tp40) cc_final: 0.7983 (mt0) REVERT: A 114 GLN cc_start: 0.7601 (mt0) cc_final: 0.7309 (mt0) REVERT: A 185 MET cc_start: 0.8324 (mtm) cc_final: 0.7985 (mtm) REVERT: B 192 GLN cc_start: 0.8195 (tp40) cc_final: 0.7348 (mm110) REVERT: B 193 ASN cc_start: 0.8466 (m110) cc_final: 0.8191 (m110) REVERT: B 199 LYS cc_start: 0.7740 (tttt) cc_final: 0.7283 (ttmt) REVERT: B 218 CYS cc_start: 0.8281 (m) cc_final: 0.7927 (m) REVERT: C 154 ARG cc_start: 0.8801 (ttm110) cc_final: 0.8552 (mtt-85) REVERT: D 152 ASP cc_start: 0.8581 (t0) cc_final: 0.8322 (t0) REVERT: D 192 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8172 (tm-30) REVERT: E 183 ASN cc_start: 0.8478 (m-40) cc_final: 0.8254 (m110) REVERT: E 192 GLN cc_start: 0.8170 (tp40) cc_final: 0.7378 (mm110) REVERT: E 193 ASN cc_start: 0.8904 (m-40) cc_final: 0.8538 (m110) REVERT: E 199 LYS cc_start: 0.7852 (tttt) cc_final: 0.7467 (ttpt) REVERT: F 154 ARG cc_start: 0.8848 (ttm110) cc_final: 0.8445 (mtt-85) REVERT: G 192 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8010 (tm-30) REVERT: H 192 GLN cc_start: 0.8225 (tp40) cc_final: 0.7348 (mm110) REVERT: H 193 ASN cc_start: 0.8682 (m-40) cc_final: 0.8383 (m110) REVERT: H 199 LYS cc_start: 0.7720 (tttt) cc_final: 0.7335 (ttmt) REVERT: I 205 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.6963 (tp) REVERT: J 192 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8139 (tm-30) REVERT: K 183 ASN cc_start: 0.8406 (m110) cc_final: 0.8063 (m110) REVERT: K 192 GLN cc_start: 0.8228 (tp40) cc_final: 0.7356 (mm110) REVERT: K 193 ASN cc_start: 0.8498 (m110) cc_final: 0.8016 (m110) REVERT: K 199 LYS cc_start: 0.7707 (tttt) cc_final: 0.7372 (ttmt) REVERT: K 218 CYS cc_start: 0.8325 (m) cc_final: 0.8020 (m) REVERT: L 154 ARG cc_start: 0.8881 (ttm110) cc_final: 0.8612 (mtt-85) REVERT: L 166 ASP cc_start: 0.8402 (m-30) cc_final: 0.8163 (m-30) REVERT: L 172 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8637 (tp) REVERT: N 192 GLN cc_start: 0.8152 (tp40) cc_final: 0.7377 (mm110) REVERT: N 199 LYS cc_start: 0.7685 (tttt) cc_final: 0.7234 (ttpt) REVERT: O 154 ARG cc_start: 0.8824 (ttm110) cc_final: 0.8528 (mtt-85) outliers start: 31 outliers final: 22 residues processed: 380 average time/residue: 0.1215 time to fit residues: 66.8380 Evaluate side-chains 376 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 352 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain O residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 6 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 143 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 63 GLN D 13 GLN D 63 GLN D 67 GLN G 13 GLN G 63 GLN G 179 GLN J 13 GLN J 53 ASN J 179 GLN M 13 GLN M 63 GLN M 179 GLN N 193 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.163649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126611 restraints weight = 17183.192| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.94 r_work: 0.3214 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14175 Z= 0.158 Angle : 0.551 8.238 19235 Z= 0.273 Chirality : 0.041 0.213 2200 Planarity : 0.004 0.052 2485 Dihedral : 3.968 19.476 1905 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.42 % Allowed : 11.72 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.50 (0.19), residues: 1760 helix: 1.27 (0.14), residues: 1220 sheet: -1.49 (0.51), residues: 45 loop : 0.85 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 167 TYR 0.011 0.001 TYR F 169 PHE 0.007 0.001 PHE A 32 TRP 0.015 0.002 TRP M 117 HIS 0.003 0.001 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00389 (14175) covalent geometry : angle 0.55118 (19235) hydrogen bonds : bond 0.03499 ( 875) hydrogen bonds : angle 4.01336 ( 2550) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 364 time to evaluate : 0.598 Fit side-chains REVERT: A 67 GLN cc_start: 0.8393 (tp40) cc_final: 0.8076 (mt0) REVERT: A 114 GLN cc_start: 0.7635 (mt0) cc_final: 0.7308 (mt0) REVERT: A 185 MET cc_start: 0.8433 (mtm) cc_final: 0.8100 (mtm) REVERT: B 192 GLN cc_start: 0.8282 (tp40) cc_final: 0.7401 (mm110) REVERT: B 193 ASN cc_start: 0.8516 (m110) cc_final: 0.8275 (m-40) REVERT: B 199 LYS cc_start: 0.7743 (tttt) cc_final: 0.7246 (ttmt) REVERT: B 218 CYS cc_start: 0.8444 (m) cc_final: 0.8110 (m) REVERT: C 154 ARG cc_start: 0.8911 (ttm110) cc_final: 0.8592 (mtt-85) REVERT: D 152 ASP cc_start: 0.8712 (t0) cc_final: 0.8463 (t0) REVERT: D 189 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8625 (tt) REVERT: D 192 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8114 (tm-30) REVERT: E 183 ASN cc_start: 0.8538 (m-40) cc_final: 0.8332 (m110) REVERT: E 192 GLN cc_start: 0.8214 (tp40) cc_final: 0.7388 (mm110) REVERT: E 193 ASN cc_start: 0.8934 (m-40) cc_final: 0.8583 (m110) REVERT: E 199 LYS cc_start: 0.7821 (tttt) cc_final: 0.7430 (ttpt) REVERT: F 154 ARG cc_start: 0.8929 (ttm110) cc_final: 0.8483 (mtt-85) REVERT: H 192 GLN cc_start: 0.8263 (tp40) cc_final: 0.7313 (mm110) REVERT: H 193 ASN cc_start: 0.8749 (m-40) cc_final: 0.8440 (m110) REVERT: H 199 LYS cc_start: 0.7705 (tttt) cc_final: 0.7280 (ttmt) REVERT: I 205 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.6987 (tp) REVERT: J 189 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8600 (tt) REVERT: J 192 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8204 (tm-30) REVERT: K 183 ASN cc_start: 0.8479 (m110) cc_final: 0.8142 (m110) REVERT: K 192 GLN cc_start: 0.8269 (tp40) cc_final: 0.7364 (mm110) REVERT: K 193 ASN cc_start: 0.8546 (m110) cc_final: 0.8098 (m110) REVERT: K 199 LYS cc_start: 0.7697 (tttt) cc_final: 0.7333 (ttmt) REVERT: K 218 CYS cc_start: 0.8450 (m) cc_final: 0.8180 (m) REVERT: L 154 ARG cc_start: 0.8972 (ttm110) cc_final: 0.8688 (mtt-85) REVERT: M 124 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.6967 (tp) REVERT: M 152 ASP cc_start: 0.8695 (t0) cc_final: 0.8390 (t0) REVERT: N 192 GLN cc_start: 0.8117 (tp40) cc_final: 0.7356 (mm110) REVERT: N 199 LYS cc_start: 0.7696 (tttt) cc_final: 0.7201 (ttpt) REVERT: O 154 ARG cc_start: 0.8913 (ttm110) cc_final: 0.8588 (mtt-85) outliers start: 36 outliers final: 25 residues processed: 378 average time/residue: 0.1210 time to fit residues: 66.6389 Evaluate side-chains 385 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 356 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain O residue 165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 58 optimal weight: 0.0670 chunk 78 optimal weight: 9.9990 chunk 45 optimal weight: 0.0970 chunk 69 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 63 GLN D 13 GLN D 63 GLN G 13 GLN G 63 GLN G 179 GLN J 13 GLN J 179 GLN M 13 GLN M 63 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.166781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.137191 restraints weight = 17180.128| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.68 r_work: 0.3120 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14175 Z= 0.103 Angle : 0.498 8.731 19235 Z= 0.250 Chirality : 0.039 0.232 2200 Planarity : 0.004 0.048 2485 Dihedral : 3.726 17.207 1905 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.82 % Allowed : 12.46 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.71 (0.19), residues: 1760 helix: 1.44 (0.15), residues: 1220 sheet: -1.49 (0.51), residues: 45 loop : 0.91 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 167 TYR 0.008 0.001 TYR F 169 PHE 0.005 0.001 PHE H 161 TRP 0.018 0.001 TRP M 117 HIS 0.002 0.001 HIS D 120 Details of bonding type rmsd covalent geometry : bond 0.00230 (14175) covalent geometry : angle 0.49761 (19235) hydrogen bonds : bond 0.03101 ( 875) hydrogen bonds : angle 3.93839 ( 2550) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 369 time to evaluate : 0.589 Fit side-chains REVERT: A 67 GLN cc_start: 0.8170 (tp40) cc_final: 0.7886 (mt0) REVERT: A 114 GLN cc_start: 0.7579 (mt0) cc_final: 0.7351 (mt0) REVERT: A 185 MET cc_start: 0.8370 (mtm) cc_final: 0.8017 (mtm) REVERT: B 192 GLN cc_start: 0.8160 (tp40) cc_final: 0.7276 (mm110) REVERT: B 193 ASN cc_start: 0.8446 (m110) cc_final: 0.8195 (m-40) REVERT: B 199 LYS cc_start: 0.7682 (tttt) cc_final: 0.7219 (ttmt) REVERT: C 154 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8586 (mtt-85) REVERT: D 152 ASP cc_start: 0.8591 (t0) cc_final: 0.8303 (t0) REVERT: D 192 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8123 (tm-30) REVERT: E 183 ASN cc_start: 0.8333 (m-40) cc_final: 0.8103 (m110) REVERT: E 192 GLN cc_start: 0.8088 (tp40) cc_final: 0.7275 (mm110) REVERT: E 193 ASN cc_start: 0.8865 (m-40) cc_final: 0.8519 (m110) REVERT: E 199 LYS cc_start: 0.7818 (tttt) cc_final: 0.7428 (ttpt) REVERT: F 154 ARG cc_start: 0.8910 (ttm110) cc_final: 0.8548 (mtt-85) REVERT: H 183 ASN cc_start: 0.8229 (m-40) cc_final: 0.7838 (m110) REVERT: H 192 GLN cc_start: 0.8181 (tp40) cc_final: 0.7280 (mm110) REVERT: H 193 ASN cc_start: 0.8704 (m-40) cc_final: 0.8387 (m110) REVERT: H 199 LYS cc_start: 0.7702 (tttt) cc_final: 0.7305 (ttmt) REVERT: I 205 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.6851 (tp) REVERT: J 192 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8065 (tm-30) REVERT: K 183 ASN cc_start: 0.8265 (m110) cc_final: 0.7943 (m110) REVERT: K 192 GLN cc_start: 0.8155 (tp40) cc_final: 0.7217 (mm110) REVERT: K 193 ASN cc_start: 0.8432 (m110) cc_final: 0.7974 (m110) REVERT: K 199 LYS cc_start: 0.7668 (tttt) cc_final: 0.7250 (ttmt) REVERT: L 154 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8636 (mtt-85) REVERT: L 166 ASP cc_start: 0.8310 (m-30) cc_final: 0.8086 (m-30) REVERT: L 172 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8613 (tp) REVERT: M 152 ASP cc_start: 0.8579 (t0) cc_final: 0.8268 (t0) REVERT: N 176 GLN cc_start: 0.7246 (pt0) cc_final: 0.6738 (pm20) REVERT: N 192 GLN cc_start: 0.7957 (tp40) cc_final: 0.7256 (mm110) REVERT: N 199 LYS cc_start: 0.7686 (tttt) cc_final: 0.7167 (ttpt) REVERT: O 154 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8561 (mtt-85) outliers start: 27 outliers final: 20 residues processed: 380 average time/residue: 0.1238 time to fit residues: 68.1775 Evaluate side-chains 373 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 351 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain O residue 148 THR Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 78 optimal weight: 10.0000 chunk 74 optimal weight: 0.2980 chunk 170 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 63 GLN D 13 GLN D 63 GLN G 13 GLN G 63 GLN G 179 GLN J 13 GLN J 53 ASN M 13 GLN M 63 GLN N 179 GLN N 183 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.163232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.125184 restraints weight = 17318.160| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.01 r_work: 0.3102 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14175 Z= 0.179 Angle : 0.577 8.571 19235 Z= 0.287 Chirality : 0.043 0.258 2200 Planarity : 0.004 0.050 2485 Dihedral : 3.974 17.883 1905 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.02 % Allowed : 13.06 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.52 (0.19), residues: 1760 helix: 1.29 (0.14), residues: 1220 sheet: -1.50 (0.52), residues: 45 loop : 0.84 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 167 TYR 0.011 0.001 TYR F 169 PHE 0.008 0.001 PHE A 32 TRP 0.015 0.002 TRP M 117 HIS 0.004 0.002 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00448 (14175) covalent geometry : angle 0.57711 (19235) hydrogen bonds : bond 0.03562 ( 875) hydrogen bonds : angle 4.08285 ( 2550) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 354 time to evaluate : 0.580 Fit side-chains REVERT: A 67 GLN cc_start: 0.8402 (tp40) cc_final: 0.7937 (mt0) REVERT: A 185 MET cc_start: 0.8498 (mtm) cc_final: 0.8139 (mtm) REVERT: B 193 ASN cc_start: 0.8471 (m110) cc_final: 0.8168 (m110) REVERT: B 199 LYS cc_start: 0.7688 (tttt) cc_final: 0.7181 (ttmt) REVERT: C 154 ARG cc_start: 0.8973 (ttm110) cc_final: 0.8597 (mtt-85) REVERT: D 152 ASP cc_start: 0.8741 (t0) cc_final: 0.8436 (t0) REVERT: D 192 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7957 (tm-30) REVERT: D 197 ASP cc_start: 0.7597 (m-30) cc_final: 0.7339 (t0) REVERT: E 183 ASN cc_start: 0.8323 (m-40) cc_final: 0.8103 (m110) REVERT: E 192 GLN cc_start: 0.8142 (tp40) cc_final: 0.7256 (mm110) REVERT: E 193 ASN cc_start: 0.8853 (m-40) cc_final: 0.8450 (m110) REVERT: E 199 LYS cc_start: 0.7737 (tttt) cc_final: 0.7348 (ttpt) REVERT: F 154 ARG cc_start: 0.8977 (ttm110) cc_final: 0.8384 (mtt-85) REVERT: H 183 ASN cc_start: 0.8270 (m-40) cc_final: 0.7824 (m110) REVERT: H 192 GLN cc_start: 0.8203 (tp40) cc_final: 0.7183 (mm110) REVERT: H 193 ASN cc_start: 0.8723 (m-40) cc_final: 0.8373 (m110) REVERT: H 199 LYS cc_start: 0.7609 (tttt) cc_final: 0.7282 (ttmt) REVERT: I 205 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.6908 (tp) REVERT: J 192 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8116 (tm-30) REVERT: K 183 ASN cc_start: 0.8306 (m110) cc_final: 0.7957 (m110) REVERT: K 192 GLN cc_start: 0.8137 (tp40) cc_final: 0.7141 (mm110) REVERT: K 193 ASN cc_start: 0.8485 (m110) cc_final: 0.7966 (m110) REVERT: K 199 LYS cc_start: 0.7608 (tttt) cc_final: 0.7154 (ttmt) REVERT: L 154 ARG cc_start: 0.8994 (ttm110) cc_final: 0.8686 (mtt-85) REVERT: M 124 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.6891 (tp) REVERT: N 199 LYS cc_start: 0.7587 (tttt) cc_final: 0.7024 (ttpt) REVERT: O 154 ARG cc_start: 0.8942 (ttm110) cc_final: 0.8544 (mtt-85) outliers start: 30 outliers final: 23 residues processed: 367 average time/residue: 0.1125 time to fit residues: 60.5142 Evaluate side-chains 374 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 349 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 1 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 63 GLN D 13 GLN D 63 GLN E 219 GLN G 13 GLN G 63 GLN G 179 GLN J 13 GLN J 179 GLN M 13 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.163155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125168 restraints weight = 17299.177| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.02 r_work: 0.3108 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14175 Z= 0.173 Angle : 0.580 9.778 19235 Z= 0.289 Chirality : 0.042 0.255 2200 Planarity : 0.004 0.049 2485 Dihedral : 4.034 17.762 1905 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.68 % Allowed : 13.80 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.39 (0.19), residues: 1760 helix: 1.21 (0.14), residues: 1215 sheet: -1.64 (0.52), residues: 45 loop : 0.74 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 167 TYR 0.011 0.001 TYR F 169 PHE 0.007 0.001 PHE A 32 TRP 0.017 0.002 TRP M 117 HIS 0.004 0.001 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00430 (14175) covalent geometry : angle 0.58047 (19235) hydrogen bonds : bond 0.03597 ( 875) hydrogen bonds : angle 4.15144 ( 2550) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 352 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8368 (tp40) cc_final: 0.7914 (mt0) REVERT: A 185 MET cc_start: 0.8468 (mtm) cc_final: 0.8095 (mtm) REVERT: B 193 ASN cc_start: 0.8474 (m110) cc_final: 0.8165 (m110) REVERT: B 199 LYS cc_start: 0.7771 (tttt) cc_final: 0.7255 (ttmt) REVERT: C 154 ARG cc_start: 0.8975 (ttm110) cc_final: 0.8596 (mtt-85) REVERT: D 152 ASP cc_start: 0.8754 (t0) cc_final: 0.8437 (t0) REVERT: D 192 GLN cc_start: 0.8439 (tm-30) cc_final: 0.7983 (tm-30) REVERT: D 197 ASP cc_start: 0.7629 (m-30) cc_final: 0.7361 (t0) REVERT: E 183 ASN cc_start: 0.8322 (m-40) cc_final: 0.8098 (m110) REVERT: E 192 GLN cc_start: 0.8144 (tp40) cc_final: 0.7245 (mm110) REVERT: E 193 ASN cc_start: 0.8838 (m-40) cc_final: 0.8441 (m110) REVERT: E 199 LYS cc_start: 0.7743 (tttt) cc_final: 0.7349 (ttpt) REVERT: F 154 ARG cc_start: 0.8958 (ttm110) cc_final: 0.8338 (mtt-85) REVERT: H 192 GLN cc_start: 0.8205 (tp40) cc_final: 0.7232 (mm110) REVERT: H 199 LYS cc_start: 0.7583 (tttt) cc_final: 0.7283 (ttmt) REVERT: I 205 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.6902 (tp) REVERT: J 67 GLN cc_start: 0.8432 (tp40) cc_final: 0.8102 (mt0) REVERT: J 192 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8060 (tm-30) REVERT: K 183 ASN cc_start: 0.8322 (m110) cc_final: 0.7990 (m110) REVERT: K 192 GLN cc_start: 0.8160 (tp40) cc_final: 0.7125 (mm110) REVERT: K 193 ASN cc_start: 0.8483 (m110) cc_final: 0.7948 (m110) REVERT: K 199 LYS cc_start: 0.7611 (tttt) cc_final: 0.7162 (ttmt) REVERT: L 154 ARG cc_start: 0.9007 (ttm110) cc_final: 0.8673 (mtt-85) REVERT: M 124 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6712 (tp) REVERT: M 152 ASP cc_start: 0.8676 (t0) cc_final: 0.8265 (t0) REVERT: N 199 LYS cc_start: 0.7537 (tttt) cc_final: 0.7125 (ttpt) REVERT: O 154 ARG cc_start: 0.8973 (ttm110) cc_final: 0.8523 (mtt-85) outliers start: 25 outliers final: 22 residues processed: 361 average time/residue: 0.1159 time to fit residues: 61.1804 Evaluate side-chains 374 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 350 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 146 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 63 GLN D 13 GLN D 63 GLN G 13 GLN G 63 GLN G 179 GLN H 193 ASN J 13 GLN J 53 ASN M 13 GLN M 63 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.165327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127619 restraints weight = 17266.654| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.02 r_work: 0.3236 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14175 Z= 0.126 Angle : 0.542 10.704 19235 Z= 0.272 Chirality : 0.041 0.243 2200 Planarity : 0.004 0.047 2485 Dihedral : 3.847 17.029 1905 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.62 % Allowed : 13.20 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.55 (0.19), residues: 1760 helix: 1.32 (0.14), residues: 1220 sheet: -1.61 (0.52), residues: 45 loop : 0.83 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 167 TYR 0.009 0.001 TYR C 169 PHE 0.005 0.001 PHE A 32 TRP 0.016 0.002 TRP M 117 HIS 0.003 0.001 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00302 (14175) covalent geometry : angle 0.54249 (19235) hydrogen bonds : bond 0.03299 ( 875) hydrogen bonds : angle 4.08826 ( 2550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4147.82 seconds wall clock time: 71 minutes 33.56 seconds (4293.56 seconds total)