Starting phenix.real_space_refine on Fri Aug 7 00:46:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubl_42094/08_2026/8ubl_42094.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubl_42094/08_2026/8ubl_42094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ubl_42094/08_2026/8ubl_42094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubl_42094/08_2026/8ubl_42094.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ubl_42094/08_2026/8ubl_42094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubl_42094/08_2026/8ubl_42094.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 324 5.49 5 S 35 5.16 5 C 10295 2.51 5 N 3315 2.21 5 O 4072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18041 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3311 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "J" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3331 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "O" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 506 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "P" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 642 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Q" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 313 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 8, 'ASN:plan1': 5, 'GLU:plan': 6, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "R" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 344 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 1, 'TRANS': 67} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 6, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 137 Time building chain proxies: 3.91, per 1000 atoms: 0.22 Number of scatterers: 18041 At special positions: 0 Unit cell: (139.392, 158.4, 177.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 324 15.00 O 4072 8.00 N 3315 7.00 C 10295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 42 " - pdb=" SG CYS M 107 " distance=2.04 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.04 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 559.4 milliseconds 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2794 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 22 sheets defined 55.3% alpha, 17.5% beta 162 base pairs and 292 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.710A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.606A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.781A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.339A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.558A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.320A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.639A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 236 through 240 Processing helix chain 'O' and resid 111 through 140 removed outlier: 3.503A pdb=" N GLU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS O 139 " --> pdb=" O THR O 135 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL O 140 " --> pdb=" O LEU O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 171 Processing helix chain 'P' and resid 535 through 578 removed outlier: 3.671A pdb=" N LYS P 540 " --> pdb=" O PRO P 536 " (cutoff:3.500A) Processing helix chain 'P' and resid 584 through 605 Processing helix chain 'Q' and resid 111 through 140 removed outlier: 3.754A pdb=" N HIS Q 139 " --> pdb=" O THR Q 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 171 Processing helix chain 'R' and resid 538 through 578 Processing helix chain 'R' and resid 584 through 605 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.902A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.518A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.250A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.630A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.632A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.997A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.760A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.328A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.328A pdb=" N MET M 30 " --> pdb=" O GLU M 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 removed outlier: 3.706A pdb=" N VAL M 167 " --> pdb=" O LEU M 232 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.265A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.265A pdb=" N GLU M 159 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 24 removed outlier: 3.781A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.725A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.536A pdb=" N THR N 116 " --> pdb=" O GLN N 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 removed outlier: 3.724A pdb=" N VAL N 167 " --> pdb=" O LEU N 232 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.644A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 4.041A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) 773 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 413 hydrogen bonds 826 hydrogen bond angles 0 basepair planarities 162 basepair parallelities 292 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2390 1.32 - 1.45: 6650 1.45 - 1.57: 9274 1.57 - 1.70: 647 1.70 - 1.82: 57 Bond restraints: 19018 Sorted by residual: bond pdb=" C1' DT I 85 " pdb=" N1 DT I 85 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.96e+01 bond pdb=" C1' DC I 106 " pdb=" N1 DC I 106 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.70e+01 bond pdb=" C1' DC J 107 " pdb=" N1 DC J 107 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.45e+01 bond pdb=" C1' DT I 14 " pdb=" N1 DT I 14 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" C1' DC I 83 " pdb=" N1 DC I 83 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.75e+01 ... (remaining 19013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 25456 1.81 - 3.62: 1443 3.62 - 5.43: 159 5.43 - 7.23: 38 7.23 - 9.04: 8 Bond angle restraints: 27104 Sorted by residual: angle pdb=" CA ASP A 81 " pdb=" CB ASP A 81 " pdb=" CG ASP A 81 " ideal model delta sigma weight residual 112.60 117.63 -5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" C3' DC J 94 " pdb=" O3' DC J 94 " pdb=" P DA J 95 " ideal model delta sigma weight residual 119.70 114.05 5.65 1.20e+00 6.94e-01 2.22e+01 angle pdb=" O4' DC I 30 " pdb=" C1' DC I 30 " pdb=" N1 DC I 30 " ideal model delta sigma weight residual 108.00 111.20 -3.20 7.00e-01 2.04e+00 2.08e+01 angle pdb=" C3' DC J 125 " pdb=" O3' DC J 125 " pdb=" P DA J 126 " ideal model delta sigma weight residual 119.70 125.12 -5.42 1.20e+00 6.94e-01 2.04e+01 angle pdb=" N3 DT J 58 " pdb=" C4 DT J 58 " pdb=" O4 DT J 58 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 27099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 9029 33.91 - 67.81: 1565 67.81 - 101.72: 49 101.72 - 135.62: 0 135.62 - 169.53: 3 Dihedral angle restraints: 10646 sinusoidal: 6314 harmonic: 4332 Sorted by residual: dihedral pdb=" CB CYS M 42 " pdb=" SG CYS M 42 " pdb=" SG CYS M 107 " pdb=" CB CYS M 107 " ideal model delta sinusoidal sigma weight residual 93.00 54.60 38.40 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C4' DT J 143 " pdb=" C3' DT J 143 " pdb=" O3' DT J 143 " pdb=" P DG J 144 " ideal model delta sinusoidal sigma weight residual 220.00 50.47 169.53 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 10643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2733 0.103 - 0.206: 346 0.206 - 0.309: 0 0.309 - 0.412: 0 0.412 - 0.515: 2 Chirality restraints: 3081 Sorted by residual: chirality pdb=" P DC J 94 " pdb=" OP1 DC J 94 " pdb=" OP2 DC J 94 " pdb=" O5' DC J 94 " both_signs ideal model delta sigma weight residual True 2.34 -2.85 -0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" P DA J 95 " pdb=" OP1 DA J 95 " pdb=" OP2 DA J 95 " pdb=" O5' DA J 95 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" CA TRP N 60 " pdb=" N TRP N 60 " pdb=" C TRP N 60 " pdb=" CB TRP N 60 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.32e-01 ... (remaining 3078 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 30 " 0.007 2.00e-02 2.50e+03 1.94e-02 8.51e+00 pdb=" N1 DC I 30 " -0.014 2.00e-02 2.50e+03 pdb=" C2 DC I 30 " 0.045 2.00e-02 2.50e+03 pdb=" O2 DC I 30 " -0.026 2.00e-02 2.50e+03 pdb=" N3 DC I 30 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DC I 30 " 0.015 2.00e-02 2.50e+03 pdb=" N4 DC I 30 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 30 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 30 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 37 " -0.224 9.50e-02 1.11e+02 1.01e-01 6.97e+00 pdb=" NE ARG N 37 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG N 37 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG N 37 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG N 37 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 81 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" C ASP A 81 " -0.041 2.00e-02 2.50e+03 pdb=" O ASP A 81 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 82 " 0.013 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 86 2.59 - 3.17: 14179 3.17 - 3.75: 31494 3.75 - 4.32: 43079 4.32 - 4.90: 64721 Nonbonded interactions: 153559 Sorted by model distance: nonbonded pdb=" OH TYR H 42 " pdb=" OP2 DC I 36 " model vdw 2.017 3.040 nonbonded pdb=" O LYS O 151 " pdb=" OG1 THR O 154 " model vdw 2.127 3.040 nonbonded pdb=" OD2 ASP N 222 " pdb=" OG SER N 225 " model vdw 2.179 3.040 nonbonded pdb=" NH2 ARG O 137 " pdb=" O GLY O 143 " model vdw 2.192 3.120 nonbonded pdb=" O ASN G 73 " pdb=" ND2 ASN G 73 " model vdw 2.210 3.120 ... (remaining 153554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 40 through 133) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'O' and ((resid 109 through 131 and (name N or name CA or name C or name \ O or name CB )) or resid 132 or (resid 133 through 142 and (name N or name CA or \ name C or name O or name CB )) or (resid 143 through 171 and (name N or name CA \ or name C or name O or name CB )))) selection = chain 'Q' } ncs_group { reference = (chain 'P' and ((resid 537 through 569 and (name N or name CA or name C or name \ O or name CB )) or resid 570 or (resid 571 through 605 and (name N or name CA or \ name C or name O or name CB )))) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.300 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.007 0.076 19022 Z= 0.524 Angle : 0.906 9.042 27112 Z= 0.684 Chirality : 0.058 0.515 3081 Planarity : 0.006 0.101 2327 Dihedral : 25.430 169.529 7840 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.87 % Allowed : 15.22 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.22), residues: 1457 helix: 2.60 (0.18), residues: 764 sheet: 0.66 (0.33), residues: 240 loop : -0.16 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 37 TYR 0.015 0.002 TYR B 98 PHE 0.026 0.001 PHE P 566 TRP 0.017 0.002 TRP N 185 HIS 0.021 0.002 HIS P 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.52 (19018) covalent geometry : angle 0.90527 / 0.68 (27104) SS BOND : bond 0.00904 / 0.46 ( 4) SS BOND : angle 2.04289 / 1.14 ( 8) hydrogen bonds : bond 0.11326 / 7.82 ( 1166) hydrogen bonds : angle 4.67708 / 3.46 ( 3004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 285 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.9142 (m-40) cc_final: 0.8923 (m-40) REVERT: B 68 ASP cc_start: 0.9171 (m-30) cc_final: 0.8919 (m-30) REVERT: C 15 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7635 (pttp) REVERT: C 56 GLU cc_start: 0.9119 (tt0) cc_final: 0.8800 (tt0) REVERT: C 64 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8823 (tt0) REVERT: C 76 THR cc_start: 0.8798 (m) cc_final: 0.8389 (p) REVERT: C 92 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8666 (mt-10) REVERT: D 71 GLU cc_start: 0.8347 (mp0) cc_final: 0.8090 (mp0) REVERT: D 113 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8463 (mm-30) REVERT: E 50 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8748 (mt-10) REVERT: E 56 LYS cc_start: 0.8850 (ttpp) cc_final: 0.8543 (ttpt) REVERT: G 61 GLU cc_start: 0.8896 (tp30) cc_final: 0.8604 (tp30) REVERT: H 68 ASP cc_start: 0.9009 (t0) cc_final: 0.8728 (t0) REVERT: H 113 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8648 (mm-30) REVERT: M 222 ASP cc_start: 0.8570 (t70) cc_final: 0.7995 (t0) REVERT: N 96 ASN cc_start: 0.8592 (m-40) cc_final: 0.8364 (m-40) REVERT: N 191 ARG cc_start: 0.8353 (ptm160) cc_final: 0.7905 (tmm-80) REVERT: O 119 ASN cc_start: 0.9037 (m110) cc_final: 0.8742 (m110) REVERT: O 149 MET cc_start: 0.6952 (tmm) cc_final: 0.6449 (tmt) outliers start: 10 outliers final: 4 residues processed: 293 average time/residue: 0.8751 time to fit residues: 279.5001 Evaluate side-chains 253 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 248 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain N residue 263 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 50.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN D 63 ASN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN M 56 GLN M 95 ASN M 152 GLN M 210 ASN N 192 GLN O 124 ASN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.121586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075413 restraints weight = 32773.210| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.75 r_work: 0.2848 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19022 Z= 0.214 Angle : 0.682 11.535 27112 Z= 0.391 Chirality : 0.045 0.265 3081 Planarity : 0.005 0.057 2327 Dihedral : 28.348 178.413 5193 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.03 % Allowed : 15.57 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.22), residues: 1457 helix: 2.77 (0.18), residues: 770 sheet: 0.96 (0.34), residues: 240 loop : -0.28 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG P 554 TYR 0.022 0.002 TYR D 42 PHE 0.010 0.001 PHE N 117 TRP 0.009 0.001 TRP N 185 HIS 0.016 0.002 HIS P 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (19018) covalent geometry : angle 0.68226 / 0.39 (27104) SS BOND : bond 0.00489 / 0.25 ( 4) SS BOND : angle 0.90955 / 0.55 ( 8) hydrogen bonds : bond 0.05300 / 3.62 ( 1166) hydrogen bonds : angle 3.78360 / 2.77 ( 3004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6366 (mt-10) REVERT: B 91 LYS cc_start: 0.9206 (tppt) cc_final: 0.8978 (ttpp) REVERT: C 56 GLU cc_start: 0.9232 (tt0) cc_final: 0.8761 (tt0) REVERT: C 92 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8752 (mt-10) REVERT: D 113 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8485 (mm-30) REVERT: E 50 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8804 (mt-10) REVERT: E 56 LYS cc_start: 0.8971 (ttpp) cc_final: 0.8765 (ttpt) REVERT: E 106 ASP cc_start: 0.8559 (m-30) cc_final: 0.8335 (m-30) REVERT: H 68 ASP cc_start: 0.9016 (t0) cc_final: 0.8619 (t0) REVERT: H 86 ARG cc_start: 0.8465 (mmt-90) cc_final: 0.8192 (mmt90) REVERT: M 30 MET cc_start: 0.8876 (ptp) cc_final: 0.8592 (ptp) REVERT: M 160 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8195 (mm) REVERT: M 222 ASP cc_start: 0.8460 (t70) cc_final: 0.7870 (t0) REVERT: N 154 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7938 (mp-120) REVERT: N 191 ARG cc_start: 0.8549 (ptm160) cc_final: 0.8034 (tmm-80) REVERT: N 222 ASP cc_start: 0.8067 (t70) cc_final: 0.7808 (t70) REVERT: O 119 ASN cc_start: 0.9090 (m110) cc_final: 0.8845 (m110) REVERT: O 122 GLU cc_start: 0.9603 (tp30) cc_final: 0.9260 (mm-30) REVERT: O 125 ARG cc_start: 0.9325 (mtm110) cc_final: 0.9083 (ttp80) REVERT: O 152 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8342 (m) outliers start: 35 outliers final: 10 residues processed: 266 average time/residue: 0.8243 time to fit residues: 238.9868 Evaluate side-chains 257 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain N residue 154 GLN Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain P residue 566 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 158 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 126 optimal weight: 0.3980 chunk 147 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 63 ASN M 95 ASN M 152 GLN N 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.122664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.076439 restraints weight = 33362.055| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.74 r_work: 0.2874 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19022 Z= 0.146 Angle : 0.632 12.875 27112 Z= 0.363 Chirality : 0.043 0.380 3081 Planarity : 0.005 0.059 2327 Dihedral : 28.533 176.801 5187 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.68 % Allowed : 17.04 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.22), residues: 1457 helix: 2.96 (0.18), residues: 770 sheet: 1.17 (0.34), residues: 240 loop : -0.18 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 33 TYR 0.015 0.001 TYR O 161 PHE 0.008 0.001 PHE P 566 TRP 0.007 0.001 TRP M 60 HIS 0.014 0.001 HIS P 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (19018) covalent geometry : angle 0.63179 / 0.36 (27104) SS BOND : bond 0.00355 / 0.18 ( 4) SS BOND : angle 0.62448 / 0.39 ( 8) hydrogen bonds : bond 0.04550 / 3.08 ( 1166) hydrogen bonds : angle 3.53100 / 2.58 ( 3004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6433 (mt-10) REVERT: B 91 LYS cc_start: 0.9213 (tppt) cc_final: 0.8996 (ttpp) REVERT: C 56 GLU cc_start: 0.9179 (tt0) cc_final: 0.8785 (tt0) REVERT: C 92 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8726 (mt-10) REVERT: D 113 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8502 (mm-30) REVERT: E 50 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8816 (mt-10) REVERT: E 56 LYS cc_start: 0.9040 (ttpp) cc_final: 0.8728 (ttpt) REVERT: E 106 ASP cc_start: 0.8589 (m-30) cc_final: 0.8369 (m-30) REVERT: E 120 MET cc_start: 0.8404 (mtt) cc_final: 0.7797 (mtt) REVERT: G 73 ASN cc_start: 0.8609 (t160) cc_final: 0.8296 (t160) REVERT: G 75 LYS cc_start: 0.8999 (mptp) cc_final: 0.8756 (mmmt) REVERT: H 68 ASP cc_start: 0.9071 (t0) cc_final: 0.8626 (t0) REVERT: H 86 ARG cc_start: 0.8399 (mmt-90) cc_final: 0.8131 (mmt90) REVERT: M 30 MET cc_start: 0.8892 (ptp) cc_final: 0.8594 (ptp) REVERT: M 95 ASN cc_start: 0.9115 (m-40) cc_final: 0.8811 (m-40) REVERT: M 222 ASP cc_start: 0.8470 (t70) cc_final: 0.7847 (t0) REVERT: N 91 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8863 (p) REVERT: N 154 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7969 (mp-120) REVERT: N 222 ASP cc_start: 0.8134 (t70) cc_final: 0.7808 (t70) REVERT: O 119 ASN cc_start: 0.9089 (m110) cc_final: 0.8730 (m110) REVERT: O 121 ARG cc_start: 0.9007 (tmm-80) cc_final: 0.8585 (tmm-80) REVERT: O 122 GLU cc_start: 0.9642 (tp30) cc_final: 0.9259 (mm-30) REVERT: O 125 ARG cc_start: 0.9317 (mtm110) cc_final: 0.9101 (ttp80) REVERT: O 127 LYS cc_start: 0.9543 (ptpp) cc_final: 0.9272 (mmtt) REVERT: P 554 ARG cc_start: 0.9208 (ptp-170) cc_final: 0.8998 (ptt-90) REVERT: P 557 LEU cc_start: 0.9636 (pp) cc_final: 0.9032 (pp) REVERT: P 560 ARG cc_start: 0.9377 (ttm110) cc_final: 0.9040 (mtm110) outliers start: 31 outliers final: 11 residues processed: 265 average time/residue: 0.7361 time to fit residues: 213.0556 Evaluate side-chains 260 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 246 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 154 GLN Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain P residue 566 PHE Chi-restraints excluded: chain P residue 588 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 79 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 49 HIS E 68 GLN G 73 ASN G 104 GLN H 95 GLN N 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.118442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.071212 restraints weight = 33131.047| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.75 r_work: 0.2769 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 19022 Z= 0.283 Angle : 0.711 11.229 27112 Z= 0.391 Chirality : 0.048 0.275 3081 Planarity : 0.005 0.063 2327 Dihedral : 28.955 177.389 5187 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.46 % Allowed : 16.18 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.22), residues: 1457 helix: 2.70 (0.18), residues: 770 sheet: 1.00 (0.33), residues: 252 loop : -0.17 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 33 TYR 0.015 0.002 TYR D 42 PHE 0.018 0.002 PHE O 133 TRP 0.009 0.002 TRP M 60 HIS 0.013 0.002 HIS P 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.28 (19018) covalent geometry : angle 0.71124 / 0.39 (27104) SS BOND : bond 0.00397 / 0.20 ( 4) SS BOND : angle 1.19065 / 0.69 ( 8) hydrogen bonds : bond 0.05574 / 3.79 ( 1166) hydrogen bonds : angle 3.61791 / 2.66 ( 3004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: C 92 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8744 (mt-10) REVERT: D 113 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8590 (mm-30) REVERT: E 50 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8784 (mt-10) REVERT: E 106 ASP cc_start: 0.8626 (m-30) cc_final: 0.8404 (m-30) REVERT: E 133 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6692 (mt-10) REVERT: G 73 ASN cc_start: 0.8676 (t0) cc_final: 0.8282 (t0) REVERT: G 75 LYS cc_start: 0.9040 (mptp) cc_final: 0.8784 (mmmt) REVERT: H 68 ASP cc_start: 0.9144 (t0) cc_final: 0.8811 (t0) REVERT: M 30 MET cc_start: 0.8983 (ptp) cc_final: 0.8647 (ptp) REVERT: M 36 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: M 113 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8360 (t) REVERT: M 191 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8785 (ptm-80) REVERT: M 222 ASP cc_start: 0.8533 (t70) cc_final: 0.7900 (t0) REVERT: N 22 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8458 (tmtt) REVERT: N 91 SER cc_start: 0.9215 (OUTLIER) cc_final: 0.8874 (p) REVERT: N 222 ASP cc_start: 0.8067 (t70) cc_final: 0.7748 (t70) REVERT: O 121 ARG cc_start: 0.9058 (tmm-80) cc_final: 0.8566 (tmm-80) REVERT: O 122 GLU cc_start: 0.9651 (tp30) cc_final: 0.9136 (tp30) REVERT: O 125 ARG cc_start: 0.9314 (mtm110) cc_final: 0.9067 (ttp80) REVERT: O 149 MET cc_start: 0.7103 (tmt) cc_final: 0.6698 (ppp) outliers start: 40 outliers final: 16 residues processed: 274 average time/residue: 0.7615 time to fit residues: 227.8573 Evaluate side-chains 273 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 191 ARG Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain P residue 530 ASP Chi-restraints excluded: chain P residue 566 PHE Chi-restraints excluded: chain P residue 588 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 15 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 156 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 163 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 104 GLN ** M 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.119907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.073166 restraints weight = 32823.559| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.73 r_work: 0.2804 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19022 Z= 0.164 Angle : 0.661 14.265 27112 Z= 0.366 Chirality : 0.045 0.276 3081 Planarity : 0.005 0.080 2327 Dihedral : 28.960 177.397 5187 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.60 % Allowed : 18.60 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.22), residues: 1457 helix: 2.79 (0.18), residues: 770 sheet: 1.09 (0.33), residues: 252 loop : -0.10 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 33 TYR 0.014 0.002 TYR H 42 PHE 0.018 0.001 PHE P 566 TRP 0.011 0.001 TRP N 185 HIS 0.008 0.001 HIS P 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (19018) covalent geometry : angle 0.66051 / 0.37 (27104) SS BOND : bond 0.00300 / 0.15 ( 4) SS BOND : angle 0.72092 / 0.43 ( 8) hydrogen bonds : bond 0.04637 / 3.12 ( 1166) hydrogen bonds : angle 3.50985 / 2.58 ( 3004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: C 56 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8760 (tt0) REVERT: C 92 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8716 (mt-10) REVERT: D 113 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8481 (mm-30) REVERT: E 50 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8784 (mt-10) REVERT: E 106 ASP cc_start: 0.8591 (m-30) cc_final: 0.8359 (m-30) REVERT: E 133 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6536 (mt-10) REVERT: G 73 ASN cc_start: 0.8624 (t0) cc_final: 0.8213 (t0) REVERT: G 75 LYS cc_start: 0.9037 (mptp) cc_final: 0.8794 (mmmt) REVERT: H 68 ASP cc_start: 0.9155 (t0) cc_final: 0.8821 (t0) REVERT: M 30 MET cc_start: 0.9008 (ptp) cc_final: 0.8665 (ptp) REVERT: M 36 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8347 (pm20) REVERT: M 113 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8262 (t) REVERT: M 191 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8769 (ptm-80) REVERT: M 222 ASP cc_start: 0.8533 (t70) cc_final: 0.7893 (t0) REVERT: N 22 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8412 (tmtt) REVERT: N 222 ASP cc_start: 0.8144 (t70) cc_final: 0.7789 (t70) REVERT: O 119 ASN cc_start: 0.9047 (m110) cc_final: 0.8785 (m110) REVERT: O 121 ARG cc_start: 0.9028 (tmm-80) cc_final: 0.8652 (tmm-80) REVERT: P 554 ARG cc_start: 0.9184 (ptp-170) cc_final: 0.8872 (ptt-90) REVERT: P 556 ARG cc_start: 0.8883 (ttm110) cc_final: 0.8623 (ttm110) REVERT: P 569 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8933 (tt) REVERT: P 580 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: P 585 LYS cc_start: 0.8256 (mptm) cc_final: 0.8050 (pptt) outliers start: 30 outliers final: 13 residues processed: 264 average time/residue: 0.6956 time to fit residues: 200.6572 Evaluate side-chains 269 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 191 ARG Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain P residue 530 ASP Chi-restraints excluded: chain P residue 566 PHE Chi-restraints excluded: chain P residue 569 LEU Chi-restraints excluded: chain P residue 580 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 137 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 171 optimal weight: 40.0000 chunk 60 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 104 GLN H 63 ASN N 96 ASN O 124 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.120847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074446 restraints weight = 32868.237| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.78 r_work: 0.2825 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19022 Z= 0.141 Angle : 0.624 12.478 27112 Z= 0.351 Chirality : 0.043 0.277 3081 Planarity : 0.004 0.075 2327 Dihedral : 28.858 177.415 5187 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.34 % Allowed : 18.77 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.22), residues: 1457 helix: 2.90 (0.18), residues: 776 sheet: 1.24 (0.34), residues: 252 loop : -0.03 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 37 TYR 0.015 0.001 TYR O 161 PHE 0.009 0.001 PHE P 566 TRP 0.005 0.001 TRP M 60 HIS 0.009 0.001 HIS P 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (19018) covalent geometry : angle 0.62362 / 0.35 (27104) SS BOND : bond 0.00260 / 0.13 ( 4) SS BOND : angle 0.47554 / 0.29 ( 8) hydrogen bonds : bond 0.04247 / 2.86 ( 1166) hydrogen bonds : angle 3.40136 / 2.49 ( 3004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8739 (tt0) REVERT: C 92 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8714 (mt-10) REVERT: D 113 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8502 (mm-30) REVERT: E 50 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8810 (mt-10) REVERT: E 106 ASP cc_start: 0.8561 (m-30) cc_final: 0.8341 (m-30) REVERT: E 120 MET cc_start: 0.8381 (mtt) cc_final: 0.7849 (mtt) REVERT: E 133 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6585 (mt-10) REVERT: G 71 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7869 (ttm110) REVERT: G 73 ASN cc_start: 0.8606 (t0) cc_final: 0.8166 (t0) REVERT: G 75 LYS cc_start: 0.9027 (mptp) cc_final: 0.8792 (mmmt) REVERT: G 104 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8705 (mm-40) REVERT: H 68 ASP cc_start: 0.9153 (t0) cc_final: 0.8826 (t0) REVERT: M 30 MET cc_start: 0.9008 (ptp) cc_final: 0.8641 (ptp) REVERT: M 36 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: M 113 SER cc_start: 0.8498 (OUTLIER) cc_final: 0.8245 (t) REVERT: M 222 ASP cc_start: 0.8516 (t70) cc_final: 0.7900 (t0) REVERT: N 22 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8415 (tmtt) REVERT: N 47 ASP cc_start: 0.9339 (t0) cc_final: 0.9046 (t0) REVERT: N 222 ASP cc_start: 0.8137 (t70) cc_final: 0.7795 (t70) REVERT: N 236 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7442 (t) REVERT: O 119 ASN cc_start: 0.9054 (m110) cc_final: 0.8737 (m110) REVERT: O 121 ARG cc_start: 0.9021 (tmm-80) cc_final: 0.8636 (tmm-80) REVERT: O 125 ARG cc_start: 0.9250 (mtm110) cc_final: 0.9012 (mtp85) REVERT: O 136 LEU cc_start: 0.9348 (tm) cc_final: 0.9026 (pp) REVERT: O 149 MET cc_start: 0.7096 (tmt) cc_final: 0.6364 (ppp) REVERT: P 554 ARG cc_start: 0.9235 (ptp-170) cc_final: 0.8929 (ptt-90) REVERT: P 580 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7040 (mm-30) outliers start: 27 outliers final: 9 residues processed: 270 average time/residue: 0.8092 time to fit residues: 238.6116 Evaluate side-chains 269 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain P residue 566 PHE Chi-restraints excluded: chain P residue 580 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 88 optimal weight: 10.0000 chunk 137 optimal weight: 0.4980 chunk 26 optimal weight: 0.0060 chunk 105 optimal weight: 0.0030 chunk 70 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 24 optimal weight: 0.0770 overall best weight: 0.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 93 GLN E 68 GLN H 63 ASN O 124 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.122640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.076657 restraints weight = 33153.668| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.71 r_work: 0.2884 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19022 Z= 0.126 Angle : 0.613 12.144 27112 Z= 0.346 Chirality : 0.042 0.279 3081 Planarity : 0.005 0.087 2327 Dihedral : 28.747 177.622 5187 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.51 % Allowed : 18.43 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.22), residues: 1457 helix: 3.03 (0.18), residues: 776 sheet: 1.52 (0.35), residues: 240 loop : 0.01 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P 556 TYR 0.015 0.001 TYR D 42 PHE 0.011 0.001 PHE O 133 TRP 0.007 0.001 TRP M 60 HIS 0.010 0.001 HIS P 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.13 (19018) covalent geometry : angle 0.61291 / 0.35 (27104) SS BOND : bond 0.00251 / 0.13 ( 4) SS BOND : angle 0.38624 / 0.23 ( 8) hydrogen bonds : bond 0.03980 / 2.68 ( 1166) hydrogen bonds : angle 3.26852 / 2.39 ( 3004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: C 92 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8704 (mt-10) REVERT: E 50 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8828 (mt-10) REVERT: E 120 MET cc_start: 0.8300 (mtt) cc_final: 0.7728 (mtt) REVERT: E 133 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6521 (mt-10) REVERT: G 73 ASN cc_start: 0.8591 (t0) cc_final: 0.8232 (t0) REVERT: G 75 LYS cc_start: 0.9038 (mptp) cc_final: 0.8807 (mmmt) REVERT: G 104 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8689 (mm-40) REVERT: H 68 ASP cc_start: 0.9149 (t0) cc_final: 0.8852 (t0) REVERT: H 112 SER cc_start: 0.8922 (m) cc_final: 0.8682 (p) REVERT: M 30 MET cc_start: 0.9000 (ptp) cc_final: 0.8695 (ptp) REVERT: M 36 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: M 113 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8143 (t) REVERT: M 191 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8756 (ptm-80) REVERT: M 222 ASP cc_start: 0.8516 (t70) cc_final: 0.7885 (t0) REVERT: N 47 ASP cc_start: 0.9324 (t0) cc_final: 0.8981 (t0) REVERT: N 222 ASP cc_start: 0.8220 (t70) cc_final: 0.7867 (t70) REVERT: N 236 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7408 (t) REVERT: O 121 ARG cc_start: 0.8992 (tmm-80) cc_final: 0.8676 (tmm-80) REVERT: O 127 LYS cc_start: 0.9542 (ptpp) cc_final: 0.9202 (mmtt) REVERT: O 136 LEU cc_start: 0.9324 (tm) cc_final: 0.8993 (pp) REVERT: O 149 MET cc_start: 0.6954 (tmt) cc_final: 0.6306 (ppp) REVERT: P 554 ARG cc_start: 0.9252 (ptp-170) cc_final: 0.8906 (ptt-90) REVERT: P 580 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: P 597 LEU cc_start: 0.8155 (mm) cc_final: 0.7942 (tm) outliers start: 29 outliers final: 12 residues processed: 275 average time/residue: 0.8031 time to fit residues: 241.2757 Evaluate side-chains 268 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 191 ARG Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain P residue 566 PHE Chi-restraints excluded: chain P residue 580 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 85 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 172 optimal weight: 50.0000 chunk 105 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 130 optimal weight: 0.0370 chunk 145 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN H 63 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.119397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.072869 restraints weight = 32810.298| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.72 r_work: 0.2792 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19022 Z= 0.219 Angle : 0.658 14.910 27112 Z= 0.363 Chirality : 0.044 0.271 3081 Planarity : 0.005 0.071 2327 Dihedral : 28.988 178.057 5187 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.16 % Allowed : 19.55 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.22), residues: 1457 helix: 2.87 (0.18), residues: 776 sheet: 1.31 (0.34), residues: 252 loop : 0.06 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 49 TYR 0.019 0.002 TYR D 42 PHE 0.010 0.001 PHE E 67 TRP 0.008 0.001 TRP M 60 HIS 0.008 0.001 HIS P 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (19018) covalent geometry : angle 0.65832 / 0.36 (27104) SS BOND : bond 0.00314 / 0.16 ( 4) SS BOND : angle 1.06146 / 0.63 ( 8) hydrogen bonds : bond 0.04814 / 3.27 ( 1166) hydrogen bonds : angle 3.44440 / 2.53 ( 3004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8670 (mt-10) REVERT: D 113 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8444 (mm-30) REVERT: E 50 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8793 (mt-10) REVERT: E 133 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6266 (mt-10) REVERT: G 73 ASN cc_start: 0.8665 (t0) cc_final: 0.8241 (t0) REVERT: G 75 LYS cc_start: 0.9025 (mptp) cc_final: 0.8800 (mmmt) REVERT: G 104 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8749 (mm-40) REVERT: H 68 ASP cc_start: 0.9182 (t0) cc_final: 0.8843 (t0) REVERT: M 30 MET cc_start: 0.8994 (ptp) cc_final: 0.8608 (ptp) REVERT: M 36 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8282 (pm20) REVERT: M 113 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8160 (m) REVERT: M 191 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8775 (ptm-80) REVERT: M 222 ASP cc_start: 0.8525 (t70) cc_final: 0.7896 (t0) REVERT: N 22 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8360 (tmtt) REVERT: N 47 ASP cc_start: 0.9317 (t0) cc_final: 0.8989 (t0) REVERT: N 222 ASP cc_start: 0.8122 (t70) cc_final: 0.7738 (t70) REVERT: N 236 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7330 (t) REVERT: O 121 ARG cc_start: 0.9031 (tmm-80) cc_final: 0.8657 (tmm-80) REVERT: O 136 LEU cc_start: 0.9282 (tm) cc_final: 0.8977 (pp) REVERT: O 149 MET cc_start: 0.7067 (tmt) cc_final: 0.6402 (ppp) REVERT: P 554 ARG cc_start: 0.9252 (ptp-170) cc_final: 0.8916 (ptt-90) REVERT: P 572 MET cc_start: 0.8715 (mmm) cc_final: 0.8477 (pp-130) outliers start: 25 outliers final: 10 residues processed: 261 average time/residue: 0.7624 time to fit residues: 217.3922 Evaluate side-chains 262 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 191 ARG Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 136 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN H 63 ASN ** O 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.120104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.073614 restraints weight = 32732.196| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.73 r_work: 0.2822 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19022 Z= 0.155 Angle : 0.648 14.646 27112 Z= 0.357 Chirality : 0.043 0.277 3081 Planarity : 0.005 0.083 2327 Dihedral : 28.996 178.138 5187 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.99 % Allowed : 20.16 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.22), residues: 1457 helix: 2.90 (0.18), residues: 776 sheet: 1.34 (0.34), residues: 252 loop : 0.07 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 49 TYR 0.017 0.002 TYR F 88 PHE 0.007 0.001 PHE O 133 TRP 0.007 0.001 TRP M 60 HIS 0.010 0.001 HIS P 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (19018) covalent geometry : angle 0.64750 / 0.36 (27104) SS BOND : bond 0.00314 / 0.16 ( 4) SS BOND : angle 0.68070 / 0.41 ( 8) hydrogen bonds : bond 0.04343 / 2.94 ( 1166) hydrogen bonds : angle 3.40968 / 2.50 ( 3004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8673 (mt-10) REVERT: D 113 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8387 (mm-30) REVERT: E 50 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8801 (mt-10) REVERT: E 120 MET cc_start: 0.8416 (mtt) cc_final: 0.7920 (mtt) REVERT: E 133 GLU cc_start: 0.6596 (mt-10) cc_final: 0.6273 (mt-10) REVERT: G 73 ASN cc_start: 0.8659 (t0) cc_final: 0.8212 (t0) REVERT: G 75 LYS cc_start: 0.9020 (mptp) cc_final: 0.8807 (mmmt) REVERT: G 104 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8694 (mm-40) REVERT: H 68 ASP cc_start: 0.9169 (t0) cc_final: 0.8834 (t0) REVERT: M 30 MET cc_start: 0.8989 (ptp) cc_final: 0.8614 (ptp) REVERT: M 36 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8378 (pm20) REVERT: M 37 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7752 (ttm-80) REVERT: M 113 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.8141 (m) REVERT: M 191 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8757 (ptm-80) REVERT: M 222 ASP cc_start: 0.8518 (t70) cc_final: 0.7890 (t0) REVERT: N 22 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8334 (tmtt) REVERT: N 47 ASP cc_start: 0.9319 (t0) cc_final: 0.8984 (t0) REVERT: N 222 ASP cc_start: 0.8173 (t70) cc_final: 0.7811 (t70) REVERT: N 236 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7328 (t) REVERT: O 121 ARG cc_start: 0.9034 (tmm-80) cc_final: 0.8664 (tmm-80) REVERT: O 127 LYS cc_start: 0.9536 (OUTLIER) cc_final: 0.9227 (mmtt) REVERT: O 136 LEU cc_start: 0.9282 (tm) cc_final: 0.9017 (pp) REVERT: O 149 MET cc_start: 0.7089 (tmt) cc_final: 0.6424 (ppp) REVERT: P 554 ARG cc_start: 0.9259 (ptp-170) cc_final: 0.8925 (ptt-90) REVERT: P 572 MET cc_start: 0.8738 (mmm) cc_final: 0.8520 (pp-130) outliers start: 23 outliers final: 12 residues processed: 259 average time/residue: 0.7048 time to fit residues: 200.1697 Evaluate side-chains 265 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 191 ARG Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 127 LYS Chi-restraints excluded: chain O residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 84 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** O 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.120148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.073347 restraints weight = 32885.316| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.73 r_work: 0.2824 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19022 Z= 0.167 Angle : 0.656 17.563 27112 Z= 0.360 Chirality : 0.043 0.283 3081 Planarity : 0.005 0.088 2327 Dihedral : 28.981 178.229 5187 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.64 % Allowed : 20.76 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.22), residues: 1457 helix: 2.89 (0.18), residues: 776 sheet: 1.34 (0.34), residues: 252 loop : 0.08 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 49 TYR 0.018 0.002 TYR H 83 PHE 0.007 0.001 PHE A 67 TRP 0.007 0.001 TRP M 60 HIS 0.008 0.001 HIS P 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (19018) covalent geometry : angle 0.65588 / 0.36 (27104) SS BOND : bond 0.00304 / 0.16 ( 4) SS BOND : angle 0.66033 / 0.39 ( 8) hydrogen bonds : bond 0.04292 / 2.90 ( 1166) hydrogen bonds : angle 3.42110 / 2.50 ( 3004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 254 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8674 (mt-10) REVERT: D 113 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8388 (mm-30) REVERT: E 50 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8799 (mt-10) REVERT: E 120 MET cc_start: 0.8417 (mtt) cc_final: 0.7903 (mtt) REVERT: E 133 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6314 (mt-10) REVERT: G 73 ASN cc_start: 0.8662 (t0) cc_final: 0.7966 (t0) REVERT: G 75 LYS cc_start: 0.9028 (mptp) cc_final: 0.8768 (mmmt) REVERT: G 104 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8684 (mm-40) REVERT: H 68 ASP cc_start: 0.9172 (t0) cc_final: 0.8846 (t0) REVERT: M 30 MET cc_start: 0.8991 (ptp) cc_final: 0.8622 (ptp) REVERT: M 36 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8300 (pm20) REVERT: M 37 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.7807 (ttm-80) REVERT: M 113 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8148 (m) REVERT: M 191 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8750 (ptm-80) REVERT: M 222 ASP cc_start: 0.8519 (t70) cc_final: 0.7882 (t0) REVERT: N 22 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8336 (tmtt) REVERT: N 30 MET cc_start: 0.8725 (ptm) cc_final: 0.8402 (ppp) REVERT: N 47 ASP cc_start: 0.9320 (t0) cc_final: 0.8908 (t0) REVERT: N 222 ASP cc_start: 0.8165 (t70) cc_final: 0.7805 (t70) REVERT: N 236 THR cc_start: 0.7771 (OUTLIER) cc_final: 0.7258 (t) REVERT: O 121 ARG cc_start: 0.9035 (tmm-80) cc_final: 0.8656 (tmm-80) REVERT: O 127 LYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9231 (mmtt) REVERT: O 149 MET cc_start: 0.7035 (tmt) cc_final: 0.6294 (ppp) REVERT: P 572 MET cc_start: 0.8720 (mmm) cc_final: 0.8515 (pp-130) outliers start: 19 outliers final: 11 residues processed: 263 average time/residue: 0.7733 time to fit residues: 222.6688 Evaluate side-chains 265 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 248 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 113 SER Chi-restraints excluded: chain M residue 191 ARG Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain N residue 200 ILE Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 257 ASP Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain O residue 118 ARG Chi-restraints excluded: chain O residue 127 LYS Chi-restraints excluded: chain O residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 112 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** O 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.120280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.073879 restraints weight = 32872.361| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.71 r_work: 0.2829 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19022 Z= 0.163 Angle : 0.648 15.243 27112 Z= 0.357 Chirality : 0.043 0.299 3081 Planarity : 0.005 0.099 2327 Dihedral : 28.961 178.487 5187 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.82 % Allowed : 21.11 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.22), residues: 1457 helix: 2.89 (0.18), residues: 776 sheet: 1.33 (0.34), residues: 252 loop : 0.11 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 49 TYR 0.016 0.001 TYR D 42 PHE 0.009 0.001 PHE O 133 TRP 0.008 0.001 TRP M 60 HIS 0.008 0.001 HIS P 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (19018) covalent geometry : angle 0.64836 / 0.36 (27104) SS BOND : bond 0.00315 / 0.16 ( 4) SS BOND : angle 0.68300 / 0.40 ( 8) hydrogen bonds : bond 0.04215 / 2.85 ( 1166) hydrogen bonds : angle 3.40546 / 2.49 ( 3004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9977.76 seconds wall clock time: 169 minutes 37.49 seconds (10177.49 seconds total)