Starting phenix.real_space_refine on Thu Jul 31 20:38:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ckz_16707/07_2025/8ckz_16707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ckz_16707/07_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_16707/07_2025/8ckz_16707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ckz_16707/07_2025/8ckz_16707.map" model { file = "/net/cci-nas-00/data/ceres_data/8ckz_16707/07_2025/8ckz_16707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ckz_16707/07_2025/8ckz_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-5711/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: 6.37, 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: 3.32 Conformation dependent library (CDL) restraints added in 1.7 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: 3.94 Time building geometry restraints manager: 3.95 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: 0.11 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } 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: 3.550 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.440 Find NCS groups from input model: 0.280 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.090 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.10908 ( 875) hydrogen bonds : angle 6.00765 ( 2550) covalent geometry : bond 0.00498 (14175) covalent geometry : angle 0.89635 (19235) *********************** 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 : 1.704 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: 0.2982 time to fit residues: 202.6561 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 : 1.589 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.162396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130018 restraints weight = 17040.031| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.98 r_work: 0.3121 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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= 0.153 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 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 875) hydrogen bonds : angle 4.32349 ( 2550) covalent geometry : bond 0.00363 (14175) covalent geometry : angle 0.59474 (19235) *********************** 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 : 1.634 Fit side-chains REVERT: A 185 MET cc_start: 0.8412 (mtm) cc_final: 0.7974 (mtm) REVERT: B 162 ARG cc_start: 0.8064 (ttp-110) cc_final: 0.6018 (ttt180) REVERT: B 169 TYR cc_start: 0.8731 (m-80) cc_final: 0.8502 (m-80) REVERT: B 183 ASN cc_start: 0.8516 (m-40) cc_final: 0.8243 (m-40) REVERT: B 192 GLN cc_start: 0.8177 (tp40) cc_final: 0.7420 (mm110) REVERT: B 199 LYS cc_start: 0.7586 (tttt) cc_final: 0.7193 (ttmt) REVERT: B 218 CYS cc_start: 0.8521 (m) cc_final: 0.8033 (m) REVERT: C 154 ARG cc_start: 0.8666 (ttm110) cc_final: 0.8348 (mtt-85) REVERT: D 192 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7975 (tm-30) REVERT: E 192 GLN cc_start: 0.8120 (tp40) cc_final: 0.7206 (mm110) REVERT: E 193 ASN cc_start: 0.8733 (m110) cc_final: 0.8268 (m110) REVERT: E 199 LYS cc_start: 0.7615 (tttt) cc_final: 0.7095 (ttpt) REVERT: F 154 ARG cc_start: 0.8765 (ttm110) cc_final: 0.8253 (mtt-85) REVERT: G 192 GLN cc_start: 0.8298 (tm-30) cc_final: 0.8033 (tm-30) REVERT: H 192 GLN cc_start: 0.8095 (tp40) cc_final: 0.7207 (mm110) REVERT: H 193 ASN cc_start: 0.8488 (m-40) cc_final: 0.8180 (m110) REVERT: H 199 LYS cc_start: 0.7538 (tttt) cc_final: 0.7042 (ttmt) REVERT: I 154 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8327 (mtt-85) REVERT: K 192 GLN cc_start: 0.8080 (tp40) cc_final: 0.7209 (mm110) REVERT: K 193 ASN cc_start: 0.8224 (m110) cc_final: 0.7832 (m110) REVERT: K 199 LYS cc_start: 0.7471 (tttt) cc_final: 0.7050 (ttmt) REVERT: K 218 CYS cc_start: 0.8543 (m) cc_final: 0.8158 (m) REVERT: L 154 ARG cc_start: 0.8772 (ttm110) cc_final: 0.8497 (mtt-85) REVERT: N 176 GLN cc_start: 0.7246 (pt0) cc_final: 0.6987 (pt0) REVERT: N 192 GLN cc_start: 0.8087 (tp40) cc_final: 0.7419 (mm110) REVERT: N 193 ASN cc_start: 0.8677 (m110) cc_final: 0.8242 (m110) REVERT: N 199 LYS cc_start: 0.7554 (tttt) cc_final: 0.7031 (ttmt) REVERT: O 154 ARG cc_start: 0.8632 (ttm110) cc_final: 0.8285 (mtt-85) outliers start: 16 outliers final: 10 residues processed: 406 average time/residue: 0.2845 time to fit residues: 163.7019 Evaluate side-chains 368 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 358 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.165159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136835 restraints weight = 17290.272| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.55 r_work: 0.3088 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2794 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= 0.126 Angle : 0.528 6.748 19235 Z= 0.268 Chirality : 0.040 0.179 2200 Planarity : 0.004 0.046 2485 Dihedral : 4.094 16.871 1905 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.48 % Allowed : 10.10 % Favored : 88.42 % 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: 1.37 (0.19), residues: 1760 helix: 1.12 (0.14), residues: 1215 sheet: -1.72 (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 G 162 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 875) hydrogen bonds : angle 4.02405 ( 2550) covalent geometry : bond 0.00294 (14175) covalent geometry : angle 0.52824 (19235) *********************** 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 402 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 380 time to evaluate : 1.547 Fit side-chains REVERT: B 148 THR cc_start: 0.6964 (p) cc_final: 0.6690 (m) REVERT: B 192 GLN cc_start: 0.8170 (tp40) cc_final: 0.7494 (mm110) REVERT: B 193 ASN cc_start: 0.8302 (m110) cc_final: 0.8003 (m110) REVERT: B 199 LYS cc_start: 0.7752 (tttt) cc_final: 0.7362 (ttmt) REVERT: B 218 CYS cc_start: 0.8274 (m) cc_final: 0.7982 (m) REVERT: D 192 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8004 (tm-30) REVERT: E 192 GLN cc_start: 0.8104 (tp40) cc_final: 0.7388 (mm110) REVERT: E 193 ASN cc_start: 0.8828 (m-40) cc_final: 0.8312 (m110) REVERT: E 199 LYS cc_start: 0.7759 (tttt) cc_final: 0.7360 (ttmt) REVERT: F 154 ARG cc_start: 0.8749 (ttm110) cc_final: 0.8415 (mtt-85) REVERT: G 118 MET cc_start: 0.6612 (mtp) cc_final: 0.6352 (mtp) REVERT: G 192 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7965 (tm-30) REVERT: H 192 GLN cc_start: 0.8171 (tp40) cc_final: 0.7417 (mm110) REVERT: H 193 ASN cc_start: 0.8628 (m-40) cc_final: 0.8366 (m110) REVERT: H 199 LYS cc_start: 0.7655 (tttt) cc_final: 0.7281 (ttmt) REVERT: I 154 ARG cc_start: 0.8742 (mtm-85) cc_final: 0.8536 (mtt-85) REVERT: K 192 GLN cc_start: 0.8208 (tp40) cc_final: 0.7346 (mm110) REVERT: K 193 ASN cc_start: 0.8304 (m110) cc_final: 0.7941 (m110) REVERT: K 199 LYS cc_start: 0.7667 (tttt) cc_final: 0.7365 (ttmt) REVERT: K 218 CYS cc_start: 0.8189 (m) cc_final: 0.7929 (m) REVERT: L 154 ARG cc_start: 0.8783 (ttm110) cc_final: 0.8555 (mtt-85) REVERT: M 124 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.6895 (tp) REVERT: N 183 ASN cc_start: 0.8680 (m110) cc_final: 0.8450 (m-40) REVERT: N 191 VAL cc_start: 0.8849 (t) cc_final: 0.8633 (m) REVERT: N 192 GLN cc_start: 0.8183 (tp40) cc_final: 0.7544 (mm110) REVERT: N 199 LYS cc_start: 0.7708 (tttt) cc_final: 0.7313 (ttmt) REVERT: O 154 ARG cc_start: 0.8669 (ttm110) cc_final: 0.8461 (mtt-85) outliers start: 22 outliers final: 13 residues processed: 388 average time/residue: 0.2716 time to fit residues: 149.5176 Evaluate side-chains 368 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 354 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 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 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 161 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN D 13 GLN E 219 GLN G 13 GLN G 179 GLN J 13 GLN J 53 ASN J 179 GLN L 219 GLN M 13 GLN M 179 GLN N 176 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 = 0.3769 r_free = 0.3769 target = 0.160194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131184 restraints weight = 17098.960| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.64 r_work: 0.2988 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 14175 Z= 0.259 Angle : 0.642 7.354 19235 Z= 0.320 Chirality : 0.045 0.139 2200 Planarity : 0.005 0.054 2485 Dihedral : 4.398 20.872 1905 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.95 % Allowed : 10.30 % Favored : 87.74 % 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: 1.02 (0.18), residues: 1760 helix: 0.90 (0.14), residues: 1215 sheet: -1.48 (0.45), residues: 45 loop : 0.69 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 117 HIS 0.005 0.002 HIS J 120 PHE 0.009 0.002 PHE A 32 TYR 0.011 0.002 TYR O 169 ARG 0.005 0.001 ARG N 167 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 875) hydrogen bonds : angle 4.24701 ( 2550) covalent geometry : bond 0.00651 (14175) covalent geometry : angle 0.64202 (19235) *********************** 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 388 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 359 time to evaluate : 1.466 Fit side-chains REVERT: A 185 MET cc_start: 0.8470 (mtm) cc_final: 0.8037 (mtm) REVERT: B 193 ASN cc_start: 0.8497 (m110) cc_final: 0.8126 (m110) REVERT: B 199 LYS cc_start: 0.7824 (tttt) cc_final: 0.7358 (ttmt) REVERT: B 218 CYS cc_start: 0.8387 (m) cc_final: 0.8119 (m) REVERT: C 205 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.6912 (tp) REVERT: D 179 GLN cc_start: 0.8323 (tp-100) cc_final: 0.8110 (tp40) REVERT: D 192 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8079 (tm-30) REVERT: E 152 ASP cc_start: 0.8052 (p0) cc_final: 0.7816 (p0) REVERT: E 192 GLN cc_start: 0.8156 (tp40) cc_final: 0.7334 (mm110) REVERT: E 193 ASN cc_start: 0.8871 (m-40) cc_final: 0.8500 (m110) REVERT: E 199 LYS cc_start: 0.7728 (tttt) cc_final: 0.7273 (ttmt) REVERT: F 154 ARG cc_start: 0.8848 (ttm110) cc_final: 0.8399 (mtt-85) REVERT: H 192 GLN cc_start: 0.8209 (tp40) cc_final: 0.7308 (mm110) REVERT: H 193 ASN cc_start: 0.8713 (m-40) cc_final: 0.8400 (m110) REVERT: H 199 LYS cc_start: 0.7645 (tttt) cc_final: 0.7268 (ttmt) REVERT: I 154 ARG cc_start: 0.8921 (mtm-85) cc_final: 0.8656 (mtt-85) REVERT: J 114 GLN cc_start: 0.7353 (mt0) cc_final: 0.7117 (mt0) REVERT: J 189 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8580 (tt) REVERT: K 192 GLN cc_start: 0.8235 (tp40) cc_final: 0.7306 (mm110) REVERT: K 193 ASN cc_start: 0.8547 (m110) cc_final: 0.8097 (m110) REVERT: K 199 LYS cc_start: 0.7758 (tttt) cc_final: 0.7404 (ttmt) REVERT: K 218 CYS cc_start: 0.8418 (m) cc_final: 0.8119 (m) REVERT: L 154 ARG cc_start: 0.8917 (ttm110) cc_final: 0.8672 (mtt-85) REVERT: L 205 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.6777 (tp) REVERT: M 124 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.6961 (tp) REVERT: N 192 GLN cc_start: 0.8182 (tp40) cc_final: 0.7493 (mm110) REVERT: N 193 ASN cc_start: 0.8865 (m-40) cc_final: 0.8531 (m110) REVERT: N 199 LYS cc_start: 0.7710 (tttt) cc_final: 0.7293 (ttmt) REVERT: O 154 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8472 (mtt-85) outliers start: 29 outliers final: 20 residues processed: 370 average time/residue: 0.2550 time to fit residues: 136.1518 Evaluate side-chains 372 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 348 time to evaluate : 1.541 ------------------------------------------------------------------------------- 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 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 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 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 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 124 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 35 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN D 63 GLN E 179 GLN E 183 ASN 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 = 0.3805 r_free = 0.3805 target = 0.163681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.134333 restraints weight = 17155.227| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.68 r_work: 0.3072 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14175 Z= 0.136 Angle : 0.525 5.583 19235 Z= 0.265 Chirality : 0.040 0.133 2200 Planarity : 0.004 0.049 2485 Dihedral : 4.059 20.296 1905 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.35 % Allowed : 11.45 % Favored : 87.21 % 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: 1.35 (0.19), residues: 1760 helix: 1.14 (0.14), residues: 1220 sheet: -1.45 (0.47), residues: 45 loop : 0.81 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 117 HIS 0.003 0.001 HIS D 120 PHE 0.005 0.001 PHE J 32 TYR 0.010 0.001 TYR F 169 ARG 0.004 0.000 ARG H 167 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 875) hydrogen bonds : angle 4.03943 ( 2550) covalent geometry : bond 0.00327 (14175) covalent geometry : angle 0.52504 (19235) *********************** 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 388 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 368 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8398 (mtm) cc_final: 0.8080 (mtm) REVERT: B 192 GLN cc_start: 0.8231 (tp40) cc_final: 0.7418 (mm110) REVERT: B 193 ASN cc_start: 0.8467 (m110) cc_final: 0.8138 (m110) REVERT: B 199 LYS cc_start: 0.7785 (tttt) cc_final: 0.7327 (ttmt) REVERT: B 218 CYS cc_start: 0.8281 (m) cc_final: 0.7931 (m) REVERT: C 154 ARG cc_start: 0.8942 (mtt-85) cc_final: 0.8653 (mtt-85) REVERT: C 205 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.6820 (tp) REVERT: D 189 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8682 (tt) REVERT: D 192 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8057 (tm-30) REVERT: E 183 ASN cc_start: 0.8500 (m-40) cc_final: 0.8217 (m110) REVERT: E 192 GLN cc_start: 0.8144 (tp40) cc_final: 0.7387 (mm110) REVERT: E 193 ASN cc_start: 0.8832 (m-40) cc_final: 0.8471 (m110) REVERT: E 199 LYS cc_start: 0.7776 (tttt) cc_final: 0.7334 (ttmt) REVERT: F 154 ARG cc_start: 0.8848 (ttm110) cc_final: 0.8489 (mtt-85) REVERT: H 192 GLN cc_start: 0.8234 (tp40) cc_final: 0.7317 (mm110) REVERT: H 193 ASN cc_start: 0.8702 (m-40) cc_final: 0.8407 (m110) REVERT: H 199 LYS cc_start: 0.7729 (tttt) cc_final: 0.7329 (ttmt) REVERT: J 189 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8632 (tt) REVERT: K 183 ASN cc_start: 0.8565 (m110) cc_final: 0.8230 (m110) REVERT: K 192 GLN cc_start: 0.8257 (tp40) cc_final: 0.7404 (mm110) REVERT: K 193 ASN cc_start: 0.8500 (m110) cc_final: 0.8034 (m110) REVERT: K 199 LYS cc_start: 0.7704 (tttt) cc_final: 0.7375 (ttmt) REVERT: K 218 CYS cc_start: 0.8324 (m) cc_final: 0.8054 (m) REVERT: L 205 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.6728 (tp) REVERT: N 183 ASN cc_start: 0.8608 (m110) cc_final: 0.8398 (m-40) REVERT: N 192 GLN cc_start: 0.8142 (tp40) cc_final: 0.7465 (mm110) REVERT: N 193 ASN cc_start: 0.8881 (m-40) cc_final: 0.8498 (m110) REVERT: N 199 LYS cc_start: 0.7707 (tttt) cc_final: 0.7317 (ttmt) REVERT: O 154 ARG cc_start: 0.8774 (ttm110) cc_final: 0.8501 (mtt-85) outliers start: 20 outliers final: 14 residues processed: 373 average time/residue: 0.2516 time to fit residues: 135.6044 Evaluate side-chains 373 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 355 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 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 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 K residue 201 ILE Chi-restraints excluded: chain L residue 205 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 149 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 179 GLN J 13 GLN M 13 GLN M 63 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.165189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136679 restraints weight = 17326.279| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.55 r_work: 0.3217 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3286 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= 0.118 Angle : 0.502 5.379 19235 Z= 0.253 Chirality : 0.039 0.134 2200 Planarity : 0.004 0.048 2485 Dihedral : 3.870 19.338 1905 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.89 % Allowed : 11.85 % Favored : 86.26 % 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: 1.57 (0.19), residues: 1760 helix: 1.32 (0.15), residues: 1220 sheet: -1.49 (0.51), residues: 45 loop : 0.87 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 117 HIS 0.002 0.001 HIS D 120 PHE 0.006 0.001 PHE A 32 TYR 0.009 0.001 TYR C 169 ARG 0.008 0.000 ARG B 167 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 875) hydrogen bonds : angle 3.92268 ( 2550) covalent geometry : bond 0.00276 (14175) covalent geometry : angle 0.50161 (19235) *********************** 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 403 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 375 time to evaluate : 1.566 Fit side-chains REVERT: A 114 GLN cc_start: 0.7678 (mt0) cc_final: 0.7376 (mt0) REVERT: A 185 MET cc_start: 0.8313 (mtm) cc_final: 0.8055 (mtm) REVERT: B 192 GLN cc_start: 0.8231 (tp40) cc_final: 0.7406 (mm110) REVERT: B 193 ASN cc_start: 0.8478 (m110) cc_final: 0.8179 (m110) REVERT: B 199 LYS cc_start: 0.7777 (tttt) cc_final: 0.7338 (ttmt) REVERT: B 218 CYS cc_start: 0.8251 (m) cc_final: 0.7887 (m) REVERT: D 152 ASP cc_start: 0.8540 (t0) cc_final: 0.8303 (t0) REVERT: E 183 ASN cc_start: 0.8580 (m-40) cc_final: 0.8346 (m110) REVERT: E 192 GLN cc_start: 0.8160 (tp40) cc_final: 0.7401 (mm110) REVERT: E 193 ASN cc_start: 0.8871 (m-40) cc_final: 0.8592 (m110) REVERT: E 199 LYS cc_start: 0.7872 (tttt) cc_final: 0.7507 (ttpt) REVERT: F 154 ARG cc_start: 0.8828 (ttm110) cc_final: 0.8452 (mtt-85) REVERT: H 192 GLN cc_start: 0.8233 (tp40) cc_final: 0.7322 (mm110) REVERT: H 193 ASN cc_start: 0.8730 (m-40) cc_final: 0.8434 (m110) REVERT: H 199 LYS cc_start: 0.7752 (tttt) cc_final: 0.7365 (ttmt) REVERT: K 183 ASN cc_start: 0.8566 (m110) cc_final: 0.8268 (m110) REVERT: K 192 GLN cc_start: 0.8258 (tp40) cc_final: 0.7425 (mm110) REVERT: K 193 ASN cc_start: 0.8500 (m110) cc_final: 0.8064 (m110) REVERT: K 199 LYS cc_start: 0.7736 (tttt) cc_final: 0.7411 (ttmt) REVERT: K 218 CYS cc_start: 0.8308 (m) cc_final: 0.8018 (m) REVERT: N 183 ASN cc_start: 0.8644 (m110) cc_final: 0.8419 (m-40) REVERT: N 192 GLN cc_start: 0.8151 (tp40) cc_final: 0.7470 (mm110) REVERT: N 199 LYS cc_start: 0.7731 (tttt) cc_final: 0.7283 (ttpt) REVERT: O 154 ARG cc_start: 0.8780 (ttm110) cc_final: 0.8520 (mtt-85) outliers start: 28 outliers final: 21 residues processed: 385 average time/residue: 0.3120 time to fit residues: 172.1522 Evaluate side-chains 381 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 360 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 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 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 O residue 148 THR 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 51 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 179 GLN J 13 GLN J 179 GLN M 13 GLN M 63 GLN N 176 GLN N 193 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.163644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134538 restraints weight = 17278.024| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.62 r_work: 0.3190 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 0.041 14175 Z= 0.156 Angle : 0.551 8.140 19235 Z= 0.275 Chirality : 0.041 0.219 2200 Planarity : 0.004 0.052 2485 Dihedral : 3.956 18.258 1905 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.02 % Allowed : 12.26 % 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: 1.43 (0.19), residues: 1760 helix: 1.22 (0.14), residues: 1220 sheet: -1.49 (0.52), residues: 45 loop : 0.81 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 F 169 ARG 0.009 0.001 ARG L 154 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 875) hydrogen bonds : angle 4.01201 ( 2550) covalent geometry : bond 0.00386 (14175) covalent geometry : angle 0.55090 (19235) *********************** 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 394 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 364 time to evaluate : 2.154 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8348 (mtm) cc_final: 0.8110 (mtm) REVERT: B 192 GLN cc_start: 0.8284 (tp40) cc_final: 0.7437 (mm110) REVERT: B 193 ASN cc_start: 0.8497 (m110) cc_final: 0.8270 (m-40) REVERT: B 199 LYS cc_start: 0.7797 (tttt) cc_final: 0.7352 (ttmt) REVERT: B 218 CYS cc_start: 0.8348 (m) cc_final: 0.7975 (m) REVERT: D 152 ASP cc_start: 0.8559 (t0) cc_final: 0.8340 (t0) REVERT: D 185 MET cc_start: 0.8305 (mtm) cc_final: 0.7941 (mtm) REVERT: D 189 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8717 (tt) REVERT: D 192 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8124 (tm-30) REVERT: E 183 ASN cc_start: 0.8599 (m-40) cc_final: 0.8315 (m110) REVERT: E 192 GLN cc_start: 0.8214 (tp40) cc_final: 0.7451 (mm110) REVERT: E 193 ASN cc_start: 0.8968 (m-40) cc_final: 0.8616 (m110) REVERT: E 199 LYS cc_start: 0.7882 (tttt) cc_final: 0.7510 (ttpt) REVERT: F 154 ARG cc_start: 0.8846 (ttm110) cc_final: 0.8375 (mtt-85) REVERT: H 192 GLN cc_start: 0.8230 (tp40) cc_final: 0.7326 (mm110) REVERT: H 193 ASN cc_start: 0.8746 (m-40) cc_final: 0.8545 (m110) REVERT: H 199 LYS cc_start: 0.7741 (tttt) cc_final: 0.7356 (ttmt) REVERT: J 189 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8639 (tt) REVERT: K 183 ASN cc_start: 0.8480 (m110) cc_final: 0.8167 (m110) REVERT: K 192 GLN cc_start: 0.8266 (tp40) cc_final: 0.7428 (mm110) REVERT: K 193 ASN cc_start: 0.8533 (m110) cc_final: 0.8060 (m110) REVERT: K 199 LYS cc_start: 0.7754 (tttt) cc_final: 0.7428 (ttmt) REVERT: K 218 CYS cc_start: 0.8339 (m) cc_final: 0.8070 (m) REVERT: M 124 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7121 (tp) REVERT: N 192 GLN cc_start: 0.8162 (tp40) cc_final: 0.7459 (mm110) REVERT: N 193 ASN cc_start: 0.8851 (m-40) cc_final: 0.8542 (m110) REVERT: N 199 LYS cc_start: 0.7764 (tttt) cc_final: 0.7301 (ttpt) REVERT: O 154 ARG cc_start: 0.8845 (ttm110) cc_final: 0.8577 (mtt-85) outliers start: 30 outliers final: 20 residues processed: 376 average time/residue: 0.3792 time to fit residues: 209.3422 Evaluate side-chains 381 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 358 time to evaluate : 2.937 ------------------------------------------------------------------------------- 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 210 THR 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 I residue 165 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 57 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 75 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 N 179 GLN N 183 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.165107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135418 restraints weight = 17188.110| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.70 r_work: 0.3166 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3449 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= 0.119 Angle : 0.513 8.499 19235 Z= 0.258 Chirality : 0.040 0.248 2200 Planarity : 0.004 0.049 2485 Dihedral : 3.815 16.690 1905 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.02 % Allowed : 12.79 % 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 (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: 1.57 (0.19), residues: 1760 helix: 1.32 (0.14), residues: 1220 sheet: -1.50 (0.51), residues: 45 loop : 0.87 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 117 HIS 0.002 0.001 HIS G 12 PHE 0.005 0.001 PHE A 32 TYR 0.009 0.001 TYR C 169 ARG 0.009 0.001 ARG L 154 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 875) hydrogen bonds : angle 3.95381 ( 2550) covalent geometry : bond 0.00280 (14175) covalent geometry : angle 0.51334 (19235) *********************** 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 398 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 368 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8386 (mtm) cc_final: 0.8113 (mtm) REVERT: B 192 GLN cc_start: 0.8169 (tp40) cc_final: 0.7291 (mm110) REVERT: B 193 ASN cc_start: 0.8447 (m110) cc_final: 0.8163 (m110) REVERT: B 199 LYS cc_start: 0.7724 (tttt) cc_final: 0.7222 (ttmt) REVERT: D 152 ASP cc_start: 0.8615 (t0) cc_final: 0.8359 (t0) REVERT: D 192 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8043 (tm-30) REVERT: E 183 ASN cc_start: 0.8454 (m-40) cc_final: 0.8150 (m110) REVERT: E 192 GLN cc_start: 0.8113 (tp40) cc_final: 0.7287 (mm110) REVERT: E 193 ASN cc_start: 0.8896 (m-40) cc_final: 0.8519 (m110) REVERT: E 199 LYS cc_start: 0.7816 (tttt) cc_final: 0.7426 (ttpt) REVERT: F 154 ARG cc_start: 0.8910 (ttm110) cc_final: 0.8431 (mtt-85) REVERT: H 183 ASN cc_start: 0.8259 (m-40) cc_final: 0.7837 (m110) REVERT: H 192 GLN cc_start: 0.8210 (tp40) cc_final: 0.7303 (mm110) REVERT: H 199 LYS cc_start: 0.7705 (tttt) cc_final: 0.7295 (ttmt) REVERT: J 67 GLN cc_start: 0.8252 (tp40) cc_final: 0.8031 (mt0) REVERT: K 183 ASN cc_start: 0.8349 (m110) cc_final: 0.8060 (m110) REVERT: K 192 GLN cc_start: 0.8194 (tp40) cc_final: 0.7287 (mm110) REVERT: K 193 ASN cc_start: 0.8503 (m110) cc_final: 0.7990 (m110) REVERT: K 199 LYS cc_start: 0.7685 (tttt) cc_final: 0.7324 (ttmt) REVERT: M 124 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7003 (tp) REVERT: M 152 ASP cc_start: 0.8570 (t0) cc_final: 0.8272 (t0) REVERT: N 192 GLN cc_start: 0.8098 (tp40) cc_final: 0.7282 (mm110) REVERT: N 193 ASN cc_start: 0.8814 (m-40) cc_final: 0.8400 (m110) REVERT: N 199 LYS cc_start: 0.7679 (tttt) cc_final: 0.7196 (ttpt) REVERT: O 154 ARG cc_start: 0.8879 (ttm110) cc_final: 0.8564 (mtt-85) outliers start: 30 outliers final: 24 residues processed: 381 average time/residue: 0.3375 time to fit residues: 187.9434 Evaluate side-chains 384 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 359 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 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 165 VAL 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 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 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 32 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 53 ASN G 63 GLN G 179 GLN H 176 GLN M 13 GLN N 176 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.163728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125995 restraints weight = 17201.406| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.99 r_work: 0.3119 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3448 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= 0.155 Angle : 0.551 8.705 19235 Z= 0.276 Chirality : 0.041 0.248 2200 Planarity : 0.004 0.049 2485 Dihedral : 3.914 16.856 1905 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.09 % Allowed : 12.66 % Favored : 85.25 % 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: 1.49 (0.19), residues: 1760 helix: 1.27 (0.14), residues: 1215 sheet: -1.51 (0.52), residues: 45 loop : 0.81 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 117 HIS 0.004 0.001 HIS G 12 PHE 0.007 0.001 PHE A 32 TYR 0.011 0.001 TYR F 169 ARG 0.009 0.001 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 875) hydrogen bonds : angle 4.02978 ( 2550) covalent geometry : bond 0.00381 (14175) covalent geometry : angle 0.55125 (19235) *********************** 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 392 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 361 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8511 (mtm) cc_final: 0.8186 (mtm) REVERT: B 192 GLN cc_start: 0.8160 (tp40) cc_final: 0.7266 (mm110) REVERT: B 193 ASN cc_start: 0.8472 (m110) cc_final: 0.8191 (m110) REVERT: B 199 LYS cc_start: 0.7693 (tttt) cc_final: 0.7154 (ttmt) REVERT: B 212 GLU cc_start: 0.7071 (mp0) cc_final: 0.6867 (mp0) REVERT: D 152 ASP cc_start: 0.8757 (t0) cc_final: 0.8490 (t0) REVERT: D 189 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8557 (tt) REVERT: D 192 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7999 (tm-30) REVERT: D 197 ASP cc_start: 0.7632 (m-30) cc_final: 0.7375 (t0) REVERT: E 183 ASN cc_start: 0.8441 (m-40) cc_final: 0.8079 (m110) REVERT: E 192 GLN cc_start: 0.8156 (tp40) cc_final: 0.7243 (mm110) REVERT: E 193 ASN cc_start: 0.8896 (m-40) cc_final: 0.8518 (m110) REVERT: E 199 LYS cc_start: 0.7756 (tttt) cc_final: 0.7358 (ttpt) REVERT: F 154 ARG cc_start: 0.8963 (ttm110) cc_final: 0.8373 (mtt-85) REVERT: H 192 GLN cc_start: 0.8231 (tp40) cc_final: 0.7391 (mm110) REVERT: H 199 LYS cc_start: 0.7628 (tttt) cc_final: 0.7299 (ttmt) REVERT: J 67 GLN cc_start: 0.8362 (tp40) cc_final: 0.8008 (mt0) REVERT: J 189 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8514 (tt) REVERT: K 183 ASN cc_start: 0.8351 (m110) cc_final: 0.8019 (m110) REVERT: K 192 GLN cc_start: 0.8171 (tp40) cc_final: 0.7201 (mm110) REVERT: K 193 ASN cc_start: 0.8476 (m110) cc_final: 0.7955 (m110) REVERT: K 199 LYS cc_start: 0.7631 (tttt) cc_final: 0.7251 (ttmt) REVERT: M 124 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.6917 (tp) REVERT: N 192 GLN cc_start: 0.8110 (tp40) cc_final: 0.7275 (mm110) REVERT: N 193 ASN cc_start: 0.8826 (m-40) cc_final: 0.8377 (m110) REVERT: N 199 LYS cc_start: 0.7587 (tttt) cc_final: 0.7088 (ttpt) REVERT: O 154 ARG cc_start: 0.8946 (ttm110) cc_final: 0.8549 (mtt-85) outliers start: 31 outliers final: 24 residues processed: 375 average time/residue: 0.3920 time to fit residues: 217.9731 Evaluate side-chains 380 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 353 time to evaluate : 2.236 ------------------------------------------------------------------------------- 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 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 E residue 151 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 G residue 144 MET 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 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 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 160 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 143 optimal weight: 0.0670 chunk 83 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 53 ASN G 63 GLN G 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 = 0.3832 r_free = 0.3832 target = 0.165721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136140 restraints weight = 17169.721| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.69 r_work: 0.3077 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 0.038 14175 Z= 0.117 Angle : 0.520 8.865 19235 Z= 0.262 Chirality : 0.040 0.248 2200 Planarity : 0.004 0.047 2485 Dihedral : 3.778 16.010 1905 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.95 % Allowed : 12.86 % 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 (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: 1.58 (0.19), residues: 1760 helix: 1.32 (0.14), residues: 1220 sheet: -1.46 (0.51), residues: 45 loop : 0.90 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 117 HIS 0.002 0.001 HIS M 12 PHE 0.005 0.001 PHE A 32 TYR 0.009 0.001 TYR C 169 ARG 0.009 0.001 ARG L 154 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 875) hydrogen bonds : angle 3.97907 ( 2550) covalent geometry : bond 0.00275 (14175) covalent geometry : angle 0.51983 (19235) ********************** 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 394 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 365 time to evaluate : 1.636 Fit side-chains revert: symmetry clash REVERT: A 185 MET cc_start: 0.8454 (mtm) cc_final: 0.8166 (mtm) REVERT: B 192 GLN cc_start: 0.8186 (tp40) cc_final: 0.7302 (mm110) REVERT: B 193 ASN cc_start: 0.8511 (m110) cc_final: 0.8245 (m110) REVERT: B 199 LYS cc_start: 0.7766 (tttt) cc_final: 0.7293 (ttmt) REVERT: B 212 GLU cc_start: 0.7109 (mp0) cc_final: 0.6906 (mp0) REVERT: D 152 ASP cc_start: 0.8624 (t0) cc_final: 0.8334 (t0) REVERT: E 183 ASN cc_start: 0.8445 (m-40) cc_final: 0.8143 (m110) REVERT: E 192 GLN cc_start: 0.8152 (tp40) cc_final: 0.7335 (mm110) REVERT: E 193 ASN cc_start: 0.8948 (m-40) cc_final: 0.8575 (m110) REVERT: E 199 LYS cc_start: 0.7786 (tttt) cc_final: 0.7407 (ttpt) REVERT: F 154 ARG cc_start: 0.8918 (ttm110) cc_final: 0.8443 (mtt-85) REVERT: H 183 ASN cc_start: 0.8282 (m-40) cc_final: 0.7884 (m110) REVERT: H 192 GLN cc_start: 0.8279 (tp40) cc_final: 0.7514 (mm110) REVERT: H 193 ASN cc_start: 0.8767 (m110) cc_final: 0.8218 (m-40) REVERT: H 199 LYS cc_start: 0.7659 (tttt) cc_final: 0.7366 (ttmt) REVERT: J 67 GLN cc_start: 0.8283 (tp40) cc_final: 0.7992 (mt0) REVERT: K 183 ASN cc_start: 0.8348 (m110) cc_final: 0.8049 (m110) REVERT: K 192 GLN cc_start: 0.8203 (tp40) cc_final: 0.7279 (mm110) REVERT: K 193 ASN cc_start: 0.8520 (m110) cc_final: 0.8052 (m110) REVERT: K 199 LYS cc_start: 0.7695 (tttt) cc_final: 0.7288 (ttmt) REVERT: M 124 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7084 (tp) REVERT: N 176 GLN cc_start: 0.7454 (pt0) cc_final: 0.7052 (pm20) REVERT: N 192 GLN cc_start: 0.8156 (tp40) cc_final: 0.7368 (mm110) REVERT: N 193 ASN cc_start: 0.8854 (m-40) cc_final: 0.8431 (m110) REVERT: N 199 LYS cc_start: 0.7670 (tttt) cc_final: 0.7180 (ttpt) REVERT: O 154 ARG cc_start: 0.8879 (ttm110) cc_final: 0.8559 (mtt-85) outliers start: 29 outliers final: 26 residues processed: 376 average time/residue: 0.2528 time to fit residues: 137.9988 Evaluate side-chains 381 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 354 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain B residue 201 ILE 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 144 MET 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 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 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 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 43 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 143 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 154 optimal weight: 0.0870 chunk 150 optimal weight: 0.7980 overall best weight: 0.4916 ------------------------------------------------------------------------------- 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 53 ASN G 63 GLN G 179 GLN M 13 GLN N 183 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.167661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.138479 restraints weight = 17239.609| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.42 r_work: 0.3154 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14175 Z= 0.105 Angle : 0.511 8.948 19235 Z= 0.258 Chirality : 0.039 0.235 2200 Planarity : 0.004 0.046 2485 Dihedral : 3.669 15.613 1905 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.48 % Allowed : 13.54 % Favored : 84.98 % 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: 1.66 (0.19), residues: 1760 helix: 1.39 (0.14), residues: 1220 sheet: -1.38 (0.50), residues: 45 loop : 0.92 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 117 HIS 0.002 0.001 HIS G 12 PHE 0.005 0.001 PHE K 161 TYR 0.007 0.001 TYR F 169 ARG 0.010 0.001 ARG L 154 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 875) hydrogen bonds : angle 3.96755 ( 2550) covalent geometry : bond 0.00238 (14175) covalent geometry : angle 0.51131 (19235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8377.60 seconds wall clock time: 151 minutes 4.58 seconds (9064.58 seconds total)