Starting phenix.real_space_refine on Mon Dec 30 19:31:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ckz_16707/12_2024/8ckz_16707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ckz_16707/12_2024/8ckz_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_16707/12_2024/8ckz_16707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ckz_16707/12_2024/8ckz_16707.map" model { file = "/net/cci-nas-00/data/ceres_data/8ckz_16707/12_2024/8ckz_16707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ckz_16707/12_2024/8ckz_16707.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} 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: E, H, K, N, D, G, J, M, F, I, L, O Time building chain proxies: 6.42, per 1000 atoms: 0.46 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: 3.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.37 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: 3.84 Time building geometry restraints manager: 3.98 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: 0.00 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 'C' and (resid 148 through 157 or (resid 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 221)) selection = chain 'E' selection = (chain 'F' and (resid 148 through 157 or (resid 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 221)) selection = chain 'H' selection = (chain 'I' and (resid 148 through 157 or (resid 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 221)) selection = chain 'K' selection = (chain 'L' and (resid 148 through 157 or (resid 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 221)) selection = chain 'N' selection = (chain 'O' and (resid 148 through 157 or (resid 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 221)) } 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.480 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- 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= 0.325 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (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 TRP 0.020 0.005 TRP N 184 HIS 0.008 0.004 HIS D 62 PHE 0.019 0.003 PHE J 40 TYR 0.015 0.005 TYR G 130 ARG 0.012 0.002 ARG M 167 *********************** 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 : 1.615 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: 0.3023 time to fit residues: 204.0250 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 : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 179 GLN N 219 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14175 Z= 0.236 Angle : 0.595 8.214 19235 Z= 0.307 Chirality : 0.042 0.139 2200 Planarity : 0.005 0.043 2485 Dihedral : 4.589 18.530 1905 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.08 % Allowed : 7.68 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 1760 helix: 0.64 (0.14), residues: 1210 sheet: -1.90 (0.47), residues: 45 loop : 0.89 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 117 HIS 0.005 0.001 HIS A 120 PHE 0.006 0.001 PHE A 32 TYR 0.011 0.001 TYR I 169 ARG 0.006 0.001 ARG A 162 *********************** 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 416 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 400 time to evaluate : 1.626 Fit side-chains REVERT: A 185 MET cc_start: 0.8112 (mtm) cc_final: 0.7843 (mtm) REVERT: B 162 ARG cc_start: 0.8057 (ttp-110) cc_final: 0.6050 (ttt180) REVERT: B 169 TYR cc_start: 0.8548 (m-80) cc_final: 0.8317 (m-80) REVERT: B 183 ASN cc_start: 0.8631 (m-40) cc_final: 0.8407 (m-40) REVERT: B 192 GLN cc_start: 0.8001 (tp40) cc_final: 0.7571 (mm110) REVERT: B 199 LYS cc_start: 0.7756 (tttt) cc_final: 0.7510 (ttmt) REVERT: B 218 CYS cc_start: 0.7900 (m) cc_final: 0.7496 (m) REVERT: D 192 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7872 (tm-30) REVERT: E 192 GLN cc_start: 0.7959 (tp40) cc_final: 0.7382 (mm110) REVERT: E 193 ASN cc_start: 0.8679 (m110) cc_final: 0.8332 (m110) REVERT: E 199 LYS cc_start: 0.7748 (tttt) cc_final: 0.7411 (ttpt) REVERT: F 154 ARG cc_start: 0.8445 (ttm110) cc_final: 0.8182 (mtt-85) REVERT: G 192 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7913 (tm-30) REVERT: H 192 GLN cc_start: 0.7949 (tp40) cc_final: 0.7480 (mm110) REVERT: H 199 LYS cc_start: 0.7776 (tttt) cc_final: 0.7440 (ttmt) REVERT: I 154 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.8104 (mtt-85) REVERT: K 192 GLN cc_start: 0.7926 (tp40) cc_final: 0.7314 (mm110) REVERT: K 193 ASN cc_start: 0.8199 (m110) cc_final: 0.7870 (m110) REVERT: K 199 LYS cc_start: 0.7670 (tttt) cc_final: 0.7391 (ttmt) REVERT: K 218 CYS cc_start: 0.7979 (m) cc_final: 0.7690 (m) REVERT: M 13 GLN cc_start: 0.7102 (tt0) cc_final: 0.6878 (tt0) REVERT: N 192 GLN cc_start: 0.7940 (tp40) cc_final: 0.7590 (mm110) REVERT: N 193 ASN cc_start: 0.8680 (m110) cc_final: 0.8367 (m110) REVERT: N 199 LYS cc_start: 0.7726 (tttt) cc_final: 0.7379 (ttmt) outliers start: 16 outliers final: 10 residues processed: 406 average time/residue: 0.2881 time to fit residues: 164.8804 Evaluate side-chains 367 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 357 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 L residue 210 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain N residue 197 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 108 optimal weight: 0.0870 chunk 43 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 127 optimal weight: 0.2980 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 E 193 ASN E 219 GLN G 13 GLN H 219 GLN K 219 GLN N 193 ASN N 219 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14175 Z= 0.193 Angle : 0.532 6.698 19235 Z= 0.270 Chirality : 0.040 0.173 2200 Planarity : 0.004 0.047 2485 Dihedral : 4.099 16.914 1905 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.55 % Allowed : 10.17 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 1760 helix: 1.11 (0.14), residues: 1215 sheet: -1.73 (0.45), residues: 45 loop : 0.99 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 117 HIS 0.004 0.001 HIS G 120 PHE 0.005 0.001 PHE J 32 TYR 0.010 0.001 TYR G 145 ARG 0.004 0.000 ARG O 154 *********************** 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 400 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 377 time to evaluate : 1.851 Fit side-chains REVERT: B 148 THR cc_start: 0.6946 (p) cc_final: 0.6695 (m) REVERT: B 192 GLN cc_start: 0.7945 (tp40) cc_final: 0.7452 (mm110) REVERT: B 193 ASN cc_start: 0.8227 (m110) cc_final: 0.7956 (m110) REVERT: B 199 LYS cc_start: 0.7800 (tttt) cc_final: 0.7519 (ttmt) REVERT: B 218 CYS cc_start: 0.7798 (m) cc_final: 0.7512 (m) REVERT: D 192 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7754 (tm-30) REVERT: E 192 GLN cc_start: 0.7887 (tp40) cc_final: 0.7329 (mm110) REVERT: E 193 ASN cc_start: 0.8706 (m-40) cc_final: 0.8234 (m110) REVERT: E 199 LYS cc_start: 0.7807 (tttt) cc_final: 0.7516 (ttmt) REVERT: G 192 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7748 (tm-30) REVERT: H 192 GLN cc_start: 0.7965 (tp40) cc_final: 0.7342 (mm110) REVERT: H 193 ASN cc_start: 0.8206 (m110) cc_final: 0.7915 (m110) REVERT: H 199 LYS cc_start: 0.7749 (tttt) cc_final: 0.7463 (ttmt) REVERT: J 189 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8486 (tt) REVERT: K 192 GLN cc_start: 0.7937 (tp40) cc_final: 0.7324 (mm110) REVERT: K 193 ASN cc_start: 0.8210 (m110) cc_final: 0.7878 (m110) REVERT: K 218 CYS cc_start: 0.7900 (m) cc_final: 0.7637 (m) REVERT: M 13 GLN cc_start: 0.7110 (tt0) cc_final: 0.6875 (tt0) REVERT: M 124 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7067 (tp) REVERT: N 183 ASN cc_start: 0.8551 (m110) cc_final: 0.8341 (m-40) REVERT: N 192 GLN cc_start: 0.7929 (tp40) cc_final: 0.7492 (mm110) REVERT: N 199 LYS cc_start: 0.7772 (tttt) cc_final: 0.7500 (ttmt) outliers start: 23 outliers final: 14 residues processed: 387 average time/residue: 0.2765 time to fit residues: 152.4383 Evaluate side-chains 369 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 353 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 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 J residue 2 ILE Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 151 LEU 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 178 SER 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 157 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 0.0030 chunk 83 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN E 219 GLN G 13 GLN G 179 GLN J 13 GLN J 53 ASN L 219 GLN M 179 GLN N 193 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3080 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= 0.152 Angle : 0.495 5.340 19235 Z= 0.250 Chirality : 0.039 0.133 2200 Planarity : 0.004 0.047 2485 Dihedral : 3.826 15.400 1905 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.08 % Allowed : 10.98 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 1760 helix: 1.42 (0.15), residues: 1215 sheet: -1.60 (0.47), residues: 45 loop : 0.92 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 117 HIS 0.003 0.001 HIS G 120 PHE 0.005 0.001 PHE J 168 TYR 0.008 0.001 TYR C 169 ARG 0.006 0.001 ARG N 167 *********************** 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 385 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 369 time to evaluate : 1.501 Fit side-chains REVERT: A 117 TRP cc_start: 0.6995 (m-10) cc_final: 0.6769 (m-10) REVERT: A 185 MET cc_start: 0.8153 (mtm) cc_final: 0.7814 (mtm) REVERT: B 192 GLN cc_start: 0.7943 (tp40) cc_final: 0.7419 (mm110) REVERT: B 193 ASN cc_start: 0.8258 (m110) cc_final: 0.8002 (m110) REVERT: B 199 LYS cc_start: 0.7737 (tttt) cc_final: 0.7468 (ttmt) REVERT: B 218 CYS cc_start: 0.7782 (m) cc_final: 0.7499 (m) REVERT: C 205 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.6827 (tp) REVERT: D 192 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7888 (tm-30) REVERT: E 192 GLN cc_start: 0.7910 (tp40) cc_final: 0.7363 (mm110) REVERT: E 193 ASN cc_start: 0.8704 (m-40) cc_final: 0.8263 (m110) REVERT: E 199 LYS cc_start: 0.7765 (tttt) cc_final: 0.7461 (ttmt) REVERT: G 192 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7722 (tm-30) REVERT: H 192 GLN cc_start: 0.7929 (tp40) cc_final: 0.7332 (mm110) REVERT: H 193 ASN cc_start: 0.8256 (m110) cc_final: 0.7927 (m110) REVERT: H 199 LYS cc_start: 0.7797 (tttt) cc_final: 0.7531 (ttmt) REVERT: H 212 GLU cc_start: 0.6841 (mp0) cc_final: 0.6620 (mp0) REVERT: K 183 ASN cc_start: 0.8455 (m-40) cc_final: 0.8116 (m110) REVERT: K 192 GLN cc_start: 0.7943 (tp40) cc_final: 0.7456 (mm110) REVERT: K 193 ASN cc_start: 0.8290 (m110) cc_final: 0.7942 (m110) REVERT: K 218 CYS cc_start: 0.7939 (m) cc_final: 0.7661 (m) REVERT: M 13 GLN cc_start: 0.7058 (tt0) cc_final: 0.6795 (tt0) REVERT: N 192 GLN cc_start: 0.7967 (tp40) cc_final: 0.7455 (mm110) REVERT: N 193 ASN cc_start: 0.8761 (m-40) cc_final: 0.8410 (m110) REVERT: N 199 LYS cc_start: 0.7773 (tttt) cc_final: 0.7469 (ttmt) outliers start: 16 outliers final: 13 residues processed: 374 average time/residue: 0.2621 time to fit residues: 141.6237 Evaluate side-chains 364 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 350 time to evaluate : 1.762 ------------------------------------------------------------------------------- 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 205 LEU 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 G residue 83 LEU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 151 LEU 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 O residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN D 13 GLN D 63 GLN E 179 GLN E 183 ASN G 13 GLN G 53 ASN J 13 GLN J 53 ASN J 179 GLN L 219 GLN M 63 GLN M 179 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14175 Z= 0.309 Angle : 0.567 6.205 19235 Z= 0.283 Chirality : 0.042 0.135 2200 Planarity : 0.004 0.050 2485 Dihedral : 4.093 19.795 1905 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.09 % Allowed : 10.51 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.19), residues: 1760 helix: 1.23 (0.15), residues: 1220 sheet: -1.54 (0.47), residues: 45 loop : 0.91 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 117 HIS 0.004 0.002 HIS D 120 PHE 0.008 0.001 PHE A 32 TYR 0.011 0.001 TYR O 169 ARG 0.007 0.001 ARG B 167 *********************** 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 391 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 360 time to evaluate : 1.560 Fit side-chains REVERT: A 185 MET cc_start: 0.8173 (mtm) cc_final: 0.7887 (mtm) REVERT: B 192 GLN cc_start: 0.8000 (tp40) cc_final: 0.7348 (mm110) REVERT: B 193 ASN cc_start: 0.8452 (m110) cc_final: 0.8156 (m110) REVERT: B 199 LYS cc_start: 0.7843 (tttt) cc_final: 0.7547 (ttmt) REVERT: B 218 CYS cc_start: 0.7899 (m) cc_final: 0.7593 (m) REVERT: C 205 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.6828 (tp) REVERT: D 189 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8498 (tt) REVERT: D 192 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7842 (tm-30) REVERT: E 183 ASN cc_start: 0.8342 (m-40) cc_final: 0.8106 (m110) REVERT: E 192 GLN cc_start: 0.7970 (tp40) cc_final: 0.7402 (mm110) REVERT: E 193 ASN cc_start: 0.8782 (m-40) cc_final: 0.8452 (m110) REVERT: E 199 LYS cc_start: 0.7825 (tttt) cc_final: 0.7481 (ttmt) REVERT: H 192 GLN cc_start: 0.7994 (tp40) cc_final: 0.7261 (mm110) REVERT: H 193 ASN cc_start: 0.8355 (m110) cc_final: 0.7999 (m110) REVERT: H 199 LYS cc_start: 0.7794 (tttt) cc_final: 0.7510 (ttmt) REVERT: J 189 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8515 (tt) REVERT: K 183 ASN cc_start: 0.8406 (m-40) cc_final: 0.8099 (m110) REVERT: K 192 GLN cc_start: 0.7956 (tp40) cc_final: 0.7487 (mm110) REVERT: K 193 ASN cc_start: 0.8340 (m110) cc_final: 0.7966 (m110) REVERT: K 218 CYS cc_start: 0.8012 (m) cc_final: 0.7739 (m) REVERT: M 13 GLN cc_start: 0.7202 (tt0) cc_final: 0.6944 (tt0) REVERT: N 192 GLN cc_start: 0.7978 (tp40) cc_final: 0.7488 (mm110) REVERT: N 199 LYS cc_start: 0.7809 (tttt) cc_final: 0.7517 (ttmt) outliers start: 31 outliers final: 23 residues processed: 371 average time/residue: 0.2767 time to fit residues: 149.2993 Evaluate side-chains 375 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 349 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 148 THR 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 180 GLU 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 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 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 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 56 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 163 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN D 13 GLN G 13 GLN G 53 ASN G 63 GLN J 13 GLN J 53 ASN L 219 GLN M 63 GLN N 193 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14175 Z= 0.165 Angle : 0.493 5.334 19235 Z= 0.250 Chirality : 0.039 0.136 2200 Planarity : 0.004 0.047 2485 Dihedral : 3.794 17.820 1905 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.55 % Allowed : 12.53 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 1760 helix: 1.41 (0.15), residues: 1220 sheet: -1.48 (0.49), residues: 45 loop : 0.91 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 117 HIS 0.002 0.001 HIS D 120 PHE 0.004 0.001 PHE H 161 TYR 0.009 0.001 TYR F 169 ARG 0.008 0.001 ARG L 154 *********************** 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 387 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 364 time to evaluate : 1.640 Fit side-chains REVERT: A 185 MET cc_start: 0.8129 (mtm) cc_final: 0.7899 (mtm) REVERT: B 192 GLN cc_start: 0.7954 (tp40) cc_final: 0.7282 (mm110) REVERT: B 193 ASN cc_start: 0.8397 (m110) cc_final: 0.8153 (m110) REVERT: B 199 LYS cc_start: 0.7805 (tttt) cc_final: 0.7525 (ttmt) REVERT: B 218 CYS cc_start: 0.7782 (m) cc_final: 0.7444 (m) REVERT: D 192 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7954 (tm-30) REVERT: E 192 GLN cc_start: 0.7942 (tp40) cc_final: 0.7383 (mm110) REVERT: E 193 ASN cc_start: 0.8731 (m-40) cc_final: 0.8379 (m110) REVERT: E 199 LYS cc_start: 0.7875 (tttt) cc_final: 0.7589 (ttpt) REVERT: G 192 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7813 (tm-30) REVERT: H 183 ASN cc_start: 0.8177 (m110) cc_final: 0.7851 (m110) REVERT: H 192 GLN cc_start: 0.7976 (tp40) cc_final: 0.7332 (mm110) REVERT: H 193 ASN cc_start: 0.8373 (m110) cc_final: 0.8019 (m110) REVERT: H 199 LYS cc_start: 0.7806 (tttt) cc_final: 0.7520 (ttmt) REVERT: K 162 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.5951 (ttt-90) REVERT: K 183 ASN cc_start: 0.8321 (m-40) cc_final: 0.8023 (m110) REVERT: K 192 GLN cc_start: 0.7961 (tp40) cc_final: 0.7366 (mm110) REVERT: K 193 ASN cc_start: 0.8261 (m110) cc_final: 0.7880 (m110) REVERT: K 218 CYS cc_start: 0.8007 (m) cc_final: 0.7706 (m) REVERT: L 166 ASP cc_start: 0.7885 (m-30) cc_final: 0.7669 (m-30) REVERT: L 172 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8492 (tp) REVERT: M 13 GLN cc_start: 0.7114 (tt0) cc_final: 0.6865 (tt0) REVERT: N 192 GLN cc_start: 0.7989 (tp40) cc_final: 0.7497 (mm110) REVERT: N 199 LYS cc_start: 0.7824 (tttt) cc_final: 0.7531 (ttmt) outliers start: 23 outliers final: 15 residues processed: 372 average time/residue: 0.2753 time to fit residues: 145.8794 Evaluate side-chains 362 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 346 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 168 optimal weight: 0.0870 chunk 105 optimal weight: 7.9990 chunk 102 optimal weight: 0.0570 chunk 77 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN D 13 GLN D 63 GLN D 67 GLN E 183 ASN G 13 GLN G 53 ASN G 179 GLN J 13 GLN J 53 ASN L 219 GLN M 63 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14175 Z= 0.139 Angle : 0.485 8.580 19235 Z= 0.245 Chirality : 0.038 0.161 2200 Planarity : 0.004 0.046 2485 Dihedral : 3.631 18.242 1905 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.55 % Allowed : 12.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 1760 helix: 1.54 (0.15), residues: 1220 sheet: -1.48 (0.50), residues: 45 loop : 0.93 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 117 HIS 0.002 0.001 HIS D 120 PHE 0.006 0.001 PHE J 168 TYR 0.007 0.001 TYR C 169 ARG 0.008 0.001 ARG L 154 *********************** 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 384 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 361 time to evaluate : 1.680 Fit side-chains REVERT: A 185 MET cc_start: 0.8136 (mtm) cc_final: 0.7868 (mtm) REVERT: B 192 GLN cc_start: 0.7955 (tp40) cc_final: 0.7273 (mm110) REVERT: B 193 ASN cc_start: 0.8339 (m110) cc_final: 0.8128 (m110) REVERT: B 199 LYS cc_start: 0.7801 (tttt) cc_final: 0.7525 (ttmt) REVERT: B 218 CYS cc_start: 0.7831 (m) cc_final: 0.7460 (m) REVERT: D 114 GLN cc_start: 0.6923 (mt0) cc_final: 0.6716 (mt0) REVERT: D 192 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7909 (tm-30) REVERT: E 192 GLN cc_start: 0.7956 (tp40) cc_final: 0.7414 (mm110) REVERT: E 193 ASN cc_start: 0.8801 (m-40) cc_final: 0.8497 (m110) REVERT: E 199 LYS cc_start: 0.7926 (tttt) cc_final: 0.7644 (ttpt) REVERT: G 192 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7839 (tm-30) REVERT: H 183 ASN cc_start: 0.8184 (m110) cc_final: 0.7796 (m110) REVERT: H 192 GLN cc_start: 0.8010 (tp40) cc_final: 0.7350 (mm110) REVERT: H 193 ASN cc_start: 0.8369 (m110) cc_final: 0.8026 (m110) REVERT: H 199 LYS cc_start: 0.7831 (tttt) cc_final: 0.7551 (ttmt) REVERT: K 162 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.5996 (ttt-90) REVERT: K 183 ASN cc_start: 0.8203 (m-40) cc_final: 0.7958 (m110) REVERT: K 192 GLN cc_start: 0.7977 (tp40) cc_final: 0.7355 (mm110) REVERT: K 193 ASN cc_start: 0.8259 (m110) cc_final: 0.7872 (m110) REVERT: N 192 GLN cc_start: 0.7830 (tp40) cc_final: 0.7412 (mm110) REVERT: N 193 ASN cc_start: 0.8784 (m110) cc_final: 0.8518 (m110) REVERT: N 199 LYS cc_start: 0.7850 (tttt) cc_final: 0.7628 (ttpt) outliers start: 23 outliers final: 21 residues processed: 372 average time/residue: 0.2590 time to fit residues: 139.6357 Evaluate side-chains 371 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 350 time to evaluate : 1.875 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain I residue 165 VAL 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 L residue 210 THR 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 O residue 148 THR Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 132 optimal weight: 0.1980 chunk 153 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 63 GLN D 13 GLN D 63 GLN D 67 GLN G 13 GLN G 53 ASN G 179 GLN H 176 GLN J 13 GLN L 219 GLN M 63 GLN N 179 GLN N 183 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14175 Z= 0.179 Angle : 0.510 8.630 19235 Z= 0.256 Chirality : 0.040 0.233 2200 Planarity : 0.004 0.047 2485 Dihedral : 3.654 15.899 1905 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.15 % Allowed : 12.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.19), residues: 1760 helix: 1.50 (0.15), residues: 1220 sheet: -1.42 (0.50), residues: 45 loop : 0.91 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 117 HIS 0.002 0.001 HIS G 12 PHE 0.006 0.001 PHE A 32 TYR 0.009 0.001 TYR C 169 ARG 0.009 0.001 ARG C 154 *********************** 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 394 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 362 time to evaluate : 1.643 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8140 (mtm) cc_final: 0.7878 (mtm) REVERT: B 192 GLN cc_start: 0.7977 (tp40) cc_final: 0.7290 (mm110) REVERT: B 199 LYS cc_start: 0.7812 (tttt) cc_final: 0.7541 (ttmt) REVERT: B 218 CYS cc_start: 0.7784 (m) cc_final: 0.7420 (m) REVERT: D 192 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7963 (tm-30) REVERT: E 192 GLN cc_start: 0.8007 (tp40) cc_final: 0.7444 (mm110) REVERT: E 193 ASN cc_start: 0.8820 (m-40) cc_final: 0.8520 (m110) REVERT: E 199 LYS cc_start: 0.7936 (tttt) cc_final: 0.7656 (ttpt) REVERT: G 192 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7807 (tm-30) REVERT: H 183 ASN cc_start: 0.8192 (m110) cc_final: 0.7800 (m110) REVERT: H 192 GLN cc_start: 0.7946 (tp40) cc_final: 0.7235 (mm110) REVERT: H 193 ASN cc_start: 0.8411 (m110) cc_final: 0.8032 (m110) REVERT: H 199 LYS cc_start: 0.7843 (tttt) cc_final: 0.7568 (ttmt) REVERT: K 183 ASN cc_start: 0.8222 (m-40) cc_final: 0.7968 (m110) REVERT: K 192 GLN cc_start: 0.7982 (tp40) cc_final: 0.7348 (mm110) REVERT: K 193 ASN cc_start: 0.8290 (m110) cc_final: 0.7908 (m110) REVERT: L 172 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8279 (mp) REVERT: M 152 ASP cc_start: 0.7914 (t0) cc_final: 0.7690 (t0) REVERT: N 192 GLN cc_start: 0.7811 (tp40) cc_final: 0.7336 (mm110) REVERT: N 193 ASN cc_start: 0.8794 (m110) cc_final: 0.8507 (m110) REVERT: N 199 LYS cc_start: 0.7860 (tttt) cc_final: 0.7633 (ttpt) outliers start: 32 outliers final: 26 residues processed: 375 average time/residue: 0.2513 time to fit residues: 137.5487 Evaluate side-chains 383 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 356 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain I residue 165 VAL 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 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 83 LEU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 215 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 63 GLN B 193 ASN D 13 GLN D 63 GLN G 13 GLN G 53 ASN G 179 GLN J 13 GLN L 219 GLN M 63 GLN N 193 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14175 Z= 0.215 Angle : 0.533 8.576 19235 Z= 0.269 Chirality : 0.041 0.242 2200 Planarity : 0.004 0.052 2485 Dihedral : 3.755 15.540 1905 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.02 % Allowed : 12.66 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 1760 helix: 1.40 (0.14), residues: 1220 sheet: -1.36 (0.51), residues: 45 loop : 0.91 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 117 HIS 0.003 0.001 HIS G 12 PHE 0.007 0.001 PHE A 32 TYR 0.010 0.001 TYR O 169 ARG 0.008 0.001 ARG B 167 *********************** 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 383 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 353 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8142 (mtm) cc_final: 0.7875 (mtm) REVERT: B 199 LYS cc_start: 0.7833 (tttt) cc_final: 0.7542 (ttmt) REVERT: B 218 CYS cc_start: 0.7823 (m) cc_final: 0.7464 (m) REVERT: E 192 GLN cc_start: 0.8014 (tp40) cc_final: 0.7447 (mm110) REVERT: E 193 ASN cc_start: 0.8837 (m-40) cc_final: 0.8499 (m110) REVERT: E 199 LYS cc_start: 0.7907 (tttt) cc_final: 0.7628 (ttpt) REVERT: G 192 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7803 (tm-30) REVERT: H 192 GLN cc_start: 0.7964 (tp40) cc_final: 0.7229 (mm110) REVERT: H 193 ASN cc_start: 0.8378 (m110) cc_final: 0.8010 (m110) REVERT: H 199 LYS cc_start: 0.7863 (tttt) cc_final: 0.7569 (ttmt) REVERT: K 183 ASN cc_start: 0.8202 (m-40) cc_final: 0.7954 (m110) REVERT: K 192 GLN cc_start: 0.7951 (tp40) cc_final: 0.7335 (mm110) REVERT: K 193 ASN cc_start: 0.8299 (m110) cc_final: 0.7895 (m110) REVERT: L 172 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8316 (mp) REVERT: N 192 GLN cc_start: 0.7818 (tp40) cc_final: 0.7358 (mm110) REVERT: N 193 ASN cc_start: 0.8888 (m-40) cc_final: 0.8592 (m110) REVERT: N 199 LYS cc_start: 0.7875 (tttt) cc_final: 0.7642 (ttpt) outliers start: 30 outliers final: 25 residues processed: 366 average time/residue: 0.2524 time to fit residues: 134.4944 Evaluate side-chains 372 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 346 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 148 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain I residue 165 VAL 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 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 83 LEU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 215 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 63 GLN D 13 GLN D 63 GLN E 219 GLN G 13 GLN G 53 ASN G 63 GLN G 179 GLN N 183 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14175 Z= 0.234 Angle : 0.547 8.699 19235 Z= 0.276 Chirality : 0.041 0.245 2200 Planarity : 0.004 0.052 2485 Dihedral : 3.809 15.524 1905 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.89 % Allowed : 12.79 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 1760 helix: 1.33 (0.14), residues: 1220 sheet: -1.43 (0.52), residues: 45 loop : 0.90 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 117 HIS 0.003 0.001 HIS M 12 PHE 0.007 0.001 PHE A 32 TYR 0.010 0.001 TYR F 169 ARG 0.010 0.001 ARG L 154 ********************** 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 378 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 350 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8154 (mtm) cc_final: 0.7901 (mtm) REVERT: B 193 ASN cc_start: 0.8363 (m110) cc_final: 0.8017 (m110) REVERT: B 218 CYS cc_start: 0.7877 (m) cc_final: 0.7505 (m) REVERT: D 152 ASP cc_start: 0.7920 (t0) cc_final: 0.7711 (t0) REVERT: D 192 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7915 (tm-30) REVERT: E 192 GLN cc_start: 0.8018 (tp40) cc_final: 0.7453 (mm110) REVERT: E 193 ASN cc_start: 0.8836 (m-40) cc_final: 0.8519 (m110) REVERT: E 199 LYS cc_start: 0.7933 (tttt) cc_final: 0.7658 (ttpt) REVERT: G 114 GLN cc_start: 0.7338 (mt0) cc_final: 0.7126 (mt0) REVERT: H 183 ASN cc_start: 0.8131 (m-40) cc_final: 0.7799 (m110) REVERT: H 192 GLN cc_start: 0.7979 (tp40) cc_final: 0.7252 (mm110) REVERT: H 193 ASN cc_start: 0.8372 (m110) cc_final: 0.8006 (m110) REVERT: H 199 LYS cc_start: 0.7833 (tttt) cc_final: 0.7543 (ttmt) REVERT: K 183 ASN cc_start: 0.8215 (m-40) cc_final: 0.7930 (m110) REVERT: K 192 GLN cc_start: 0.7946 (tp40) cc_final: 0.7340 (mm110) REVERT: K 193 ASN cc_start: 0.8248 (m110) cc_final: 0.8027 (m110) REVERT: L 172 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8315 (mp) REVERT: N 192 GLN cc_start: 0.7804 (tp40) cc_final: 0.7356 (mm110) REVERT: N 193 ASN cc_start: 0.8888 (m-40) cc_final: 0.8573 (m110) REVERT: N 199 LYS cc_start: 0.7856 (tttt) cc_final: 0.7644 (ttpt) outliers start: 28 outliers final: 22 residues processed: 363 average time/residue: 0.2643 time to fit residues: 138.8092 Evaluate side-chains 369 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 346 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 148 THR 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 180 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain I residue 165 VAL 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 83 LEU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain O residue 165 VAL 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 147 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 0.0970 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 0.0270 chunk 142 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 63 GLN D 13 GLN D 63 GLN G 13 GLN G 53 ASN G 63 GLN G 179 GLN J 179 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 = 0.3849 r_free = 0.3849 target = 0.167287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137911 restraints weight = 17154.818| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.51 r_work: 0.3155 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14175 Z= 0.164 Angle : 0.511 8.544 19235 Z= 0.261 Chirality : 0.040 0.238 2200 Planarity : 0.004 0.050 2485 Dihedral : 3.661 14.713 1905 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.89 % Allowed : 12.79 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 1760 helix: 1.40 (0.14), residues: 1220 sheet: -1.44 (0.51), residues: 45 loop : 0.95 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 117 HIS 0.002 0.001 HIS M 12 PHE 0.005 0.001 PHE L 168 TYR 0.008 0.001 TYR C 169 ARG 0.007 0.001 ARG L 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3544.90 seconds wall clock time: 65 minutes 17.03 seconds (3917.03 seconds total)