Starting phenix.real_space_refine on Thu Aug 6 02:18:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t9f_41109/08_2026/8t9f_41109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t9f_41109/08_2026/8t9f_41109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t9f_41109/08_2026/8t9f_41109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t9f_41109/08_2026/8t9f_41109.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8t9f_41109/08_2026/8t9f_41109.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t9f_41109/08_2026/8t9f_41109.cif" model { file = "/net/cci-nas-00/data/ceres_data/8t9f_41109/08_2026/8t9f_41109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t9f_41109/08_2026/8t9f_41109.cif" } resolution = 2.6 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= 0.005 sd= 0.041 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 244 5.49 5 S 30 5.16 5 C 7475 2.51 5 N 2445 2.21 5 O 2938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 13132 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2060 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "I" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2484 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2518 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 698 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 785 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 781 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 835 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 2.22, per 1000 atoms: 0.17 Number of scatterers: 13132 At special positions: 0 Unit cell: (97.11, 117.611, 118.69, 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 30 16.00 P 244 15.00 O 2938 8.00 N 2445 7.00 C 7475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 554.4 milliseconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1928 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 14 sheets defined 64.7% alpha, 5.0% beta 122 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'K' and resid 73 through 88 Processing helix chain 'K' and resid 88 through 94 Processing helix chain 'K' and resid 134 through 148 Processing helix chain 'K' and resid 149 through 159 removed outlier: 3.995A pdb=" N ALA K 153 " --> pdb=" O HIS K 149 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER K 159 " --> pdb=" O LYS K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 169 Processing helix chain 'K' and resid 171 through 187 removed outlier: 3.779A pdb=" N TYR K 185 " --> pdb=" O HIS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 190 No H-bonds generated for 'chain 'K' and resid 188 through 190' Processing helix chain 'K' and resid 235 through 242 Processing helix chain 'K' and resid 266 through 271 removed outlier: 3.679A pdb=" N PHE K 270 " --> pdb=" O PRO K 267 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE K 271 " --> pdb=" O ALA K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 328 Processing helix chain 'K' and resid 329 through 333 Processing helix chain 'K' and resid 354 through 362 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.824A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.546A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.550A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.947A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.964A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.610A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 28 through 39 Processing helix chain 'G' and resid 47 through 76 removed outlier: 3.552A pdb=" N ALA G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 93 through 100 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 105 through 124 removed outlier: 3.870A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.532A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.555A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 47 through 76 removed outlier: 3.570A pdb=" N ALA C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 removed outlier: 3.609A pdb=" N ASP C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.934A pdb=" N ILE C 118 " --> pdb=" O HIS C 114 " (cutoff:3.500A) 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 104 through 123 removed outlier: 3.702A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 195 through 199 Processing sheet with id=AA2, first strand: chain 'K' and resid 230 through 234 removed outlier: 4.344A pdb=" N ALA K 261 " --> pdb=" O LEU K 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 272 through 273 removed outlier: 6.436A pdb=" N ASN K 272 " --> pdb=" O CYS K 305 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'K' and resid 279 through 283 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.437A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AB2, first strand: chain 'G' and resid 45 through 46 removed outlier: 6.597A pdb=" N ARG G 45 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 46 removed outlier: 6.529A pdb=" N ARG C 45 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 80 through 81 489 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 315 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 122 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2736 1.33 - 1.45: 4080 1.45 - 1.57: 6509 1.57 - 1.69: 486 1.69 - 1.81: 47 Bond restraints: 13858 Sorted by residual: bond pdb=" C1' DT J 28 " pdb=" N1 DT J 28 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.83e+01 bond pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " ideal model delta sigma weight residual 1.435 1.503 -0.068 1.30e-02 5.92e+03 2.75e+01 bond pdb=" C3' DT J 28 " pdb=" C2' DT J 28 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C5' DA I 120 " pdb=" C4' DA I 120 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.18e+01 bond pdb=" C3' DC I 26 " pdb=" C2' DC I 26 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 ... (remaining 13853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 18813 1.75 - 3.50: 872 3.50 - 5.25: 42 5.25 - 6.99: 8 6.99 - 8.74: 3 Bond angle restraints: 19738 Sorted by residual: angle pdb=" O4' DT J 28 " pdb=" C1' DT J 28 " pdb=" N1 DT J 28 " ideal model delta sigma weight residual 108.00 113.13 -5.13 7.00e-01 2.04e+00 5.38e+01 angle pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " pdb=" P DT J 28 " ideal model delta sigma weight residual 119.70 125.95 -6.25 1.20e+00 6.94e-01 2.71e+01 angle pdb=" O4' DT I 27 " pdb=" C4' DT I 27 " pdb=" C3' DT I 27 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT I 35 " pdb=" C4 DT I 35 " pdb=" O4 DT I 35 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" C4' DT J 28 " pdb=" O4' DT J 28 " pdb=" C1' DT J 28 " ideal model delta sigma weight residual 110.10 105.66 4.44 1.00e+00 1.00e+00 1.97e+01 ... (remaining 19733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 6486 35.14 - 70.28: 1186 70.28 - 105.42: 18 105.42 - 140.57: 1 140.57 - 175.71: 3 Dihedral angle restraints: 7694 sinusoidal: 4709 harmonic: 2985 Sorted by residual: dihedral pdb=" C4' DA J 110 " pdb=" C3' DA J 110 " pdb=" O3' DA J 110 " pdb=" P DC J 111 " ideal model delta sinusoidal sigma weight residual -140.00 35.71 -175.71 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 106 " pdb=" C3' DG J 106 " pdb=" O3' DG J 106 " pdb=" P DT J 107 " ideal model delta sinusoidal sigma weight residual 220.00 47.47 172.53 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 27 " pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " pdb=" P DT J 28 " ideal model delta sinusoidal sigma weight residual -140.00 15.85 -155.85 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 7691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1614 0.044 - 0.088: 506 0.088 - 0.132: 108 0.132 - 0.176: 5 0.176 - 0.220: 3 Chirality restraints: 2236 Sorted by residual: chirality pdb=" P DT J 28 " pdb=" OP1 DT J 28 " pdb=" OP2 DT J 28 " pdb=" O5' DT J 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.55 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C2' SAM K 401 " pdb=" C1' SAM K 401 " pdb=" C3' SAM K 401 " pdb=" O2' SAM K 401 " both_signs ideal model delta sigma weight residual False -2.76 -2.56 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" C3' DG J 106 " pdb=" C4' DG J 106 " pdb=" O3' DG J 106 " pdb=" C2' DG J 106 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 2233 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 27 " 0.050 2.00e-02 2.50e+03 2.91e-02 1.91e+01 pdb=" N1 DC J 27 " -0.039 2.00e-02 2.50e+03 pdb=" C2 DC J 27 " -0.034 2.00e-02 2.50e+03 pdb=" O2 DC J 27 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DC J 27 " 0.031 2.00e-02 2.50e+03 pdb=" C4 DC J 27 " -0.024 2.00e-02 2.50e+03 pdb=" N4 DC J 27 " 0.030 2.00e-02 2.50e+03 pdb=" C5 DC J 27 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DC J 27 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 63 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C GLU B 63 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU B 63 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN B 64 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 59 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C LYS B 59 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS B 59 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 60 " 0.012 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 5 2.16 - 2.84: 3786 2.84 - 3.53: 17560 3.53 - 4.21: 34723 4.21 - 4.90: 53586 Nonbonded interactions: 109660 Sorted by model distance: nonbonded pdb=" OH TYR K 306 " pdb=" OD1 ASP K 309 " model vdw 1.469 3.040 nonbonded pdb=" CD2 LEU K 150 " pdb=" CE1 PHE K 183 " model vdw 1.636 3.760 nonbonded pdb=" O GLU K 325 " pdb=" CE2 PHE K 332 " model vdw 2.081 3.340 nonbonded pdb=" CD2 LEU K 150 " pdb=" CD1 PHE K 183 " model vdw 2.084 3.760 nonbonded pdb=" CD2 LEU K 150 " pdb=" CZ PHE K 183 " model vdw 2.106 3.760 ... (remaining 109655 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 135) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.970 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.700 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13858 Z= 0.484 Angle : 0.733 8.743 19738 Z= 0.635 Chirality : 0.043 0.220 2236 Planarity : 0.004 0.049 1658 Dihedral : 25.222 175.707 5766 Min Nonbonded Distance : 1.469 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.25), residues: 1009 helix: 1.75 (0.20), residues: 635 sheet: 0.01 (0.71), residues: 44 loop : -1.20 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 257 TYR 0.009 0.001 TYR E 54 PHE 0.008 0.001 PHE H 66 TRP 0.002 0.001 TRP K 264 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.48 (13858) covalent geometry : angle 0.73272 / 0.64 (19738) hydrogen bonds : bond 0.10964 / 7.14 ( 804) hydrogen bonds : angle 4.16749 / 2.87 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8728 (mm-30) REVERT: K 225 GLU cc_start: 0.7675 (pt0) cc_final: 0.7339 (tp30) REVERT: A 81 ASP cc_start: 0.8311 (m-30) cc_final: 0.8080 (m-30) REVERT: F 44 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8474 (mtpp) REVERT: D 42 TYR cc_start: 0.8146 (t80) cc_final: 0.7929 (t80) outliers start: 0 outliers final: 1 residues processed: 225 average time/residue: 0.6655 time to fit residues: 160.1565 Evaluate side-chains 166 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 271 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 50.0000 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 134 GLN K 207 GLN K 272 ASN K 273 HIS B 18 HIS B 25 ASN A 85 GLN F 93 GLN G 26 GLN H 110 HIS E 68 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.117411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.083000 restraints weight = 24534.554| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.64 r_work: 0.3210 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13858 Z= 0.152 Angle : 0.605 8.206 19738 Z= 0.353 Chirality : 0.045 0.300 2236 Planarity : 0.004 0.047 1658 Dihedral : 29.749 175.758 3798 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.84 % Allowed : 14.10 % Favored : 83.06 % 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: 1.71 (0.26), residues: 1009 helix: 2.28 (0.21), residues: 638 sheet: -0.12 (0.71), residues: 44 loop : -1.06 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 143 TYR 0.015 0.001 TYR H 84 PHE 0.008 0.001 PHE K 332 TRP 0.010 0.001 TRP K 264 HIS 0.007 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (13858) covalent geometry : angle 0.60466 / 0.35 (19738) hydrogen bonds : bond 0.04983 / 3.33 ( 804) hydrogen bonds : angle 3.37181 / 2.37 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8824 (mm-30) REVERT: K 187 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8835 (tpp80) REVERT: K 225 GLU cc_start: 0.8210 (pt0) cc_final: 0.7430 (tp30) REVERT: A 59 GLU cc_start: 0.8711 (pm20) cc_final: 0.8485 (pm20) REVERT: F 44 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8715 (mtpp) REVERT: G 25 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8769 (pp) REVERT: G 67 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8111 (tp30) REVERT: G 74 LYS cc_start: 0.8002 (tptt) cc_final: 0.7764 (mmmt) REVERT: H 69 ASP cc_start: 0.8984 (t0) cc_final: 0.8774 (t0) REVERT: E 120 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8362 (mmm) REVERT: C 67 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8413 (tp30) REVERT: D 42 TYR cc_start: 0.8445 (t80) cc_final: 0.8081 (t80) outliers start: 24 outliers final: 8 residues processed: 185 average time/residue: 0.7095 time to fit residues: 139.7921 Evaluate side-chains 174 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 83 optimal weight: 0.0970 chunk 15 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.116957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.082287 restraints weight = 24559.219| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.64 r_work: 0.3222 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13858 Z= 0.158 Angle : 0.585 7.970 19738 Z= 0.341 Chirality : 0.044 0.313 2236 Planarity : 0.004 0.059 1658 Dihedral : 29.865 174.595 3796 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.84 % Allowed : 14.45 % Favored : 82.70 % 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: 1.86 (0.27), residues: 1009 helix: 2.38 (0.21), residues: 639 sheet: -0.17 (0.72), residues: 42 loop : -0.97 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 39 TYR 0.016 0.002 TYR H 84 PHE 0.010 0.001 PHE K 332 TRP 0.008 0.001 TRP K 264 HIS 0.006 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (13858) covalent geometry : angle 0.58488 / 0.34 (19738) hydrogen bonds : bond 0.04931 / 3.34 ( 804) hydrogen bonds : angle 3.19211 / 2.28 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8852 (mm-30) REVERT: K 187 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8856 (tpp80) REVERT: K 225 GLU cc_start: 0.8161 (pt0) cc_final: 0.7451 (tp30) REVERT: F 44 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8661 (mtpm) REVERT: G 25 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8822 (pp) REVERT: G 74 LYS cc_start: 0.8057 (tptt) cc_final: 0.7821 (mmmt) REVERT: G 93 ASP cc_start: 0.8639 (t0) cc_final: 0.8352 (t0) REVERT: H 69 ASP cc_start: 0.8973 (t0) cc_final: 0.8733 (t0) REVERT: C 67 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8330 (tp30) REVERT: D 42 TYR cc_start: 0.8420 (t80) cc_final: 0.8118 (t80) outliers start: 24 outliers final: 11 residues processed: 183 average time/residue: 0.7573 time to fit residues: 148.2102 Evaluate side-chains 174 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 48 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 0.0270 chunk 121 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 84 optimal weight: 0.0270 chunk 36 optimal weight: 9.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 278 ASN F 93 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.116586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.082054 restraints weight = 24527.509| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.62 r_work: 0.3220 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13858 Z= 0.156 Angle : 0.583 7.771 19738 Z= 0.336 Chirality : 0.044 0.313 2236 Planarity : 0.004 0.053 1658 Dihedral : 29.922 174.091 3796 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.49 % Allowed : 15.17 % Favored : 82.35 % 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: 1.87 (0.27), residues: 1009 helix: 2.41 (0.21), residues: 639 sheet: -0.21 (0.77), residues: 36 loop : -0.98 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 143 TYR 0.018 0.001 TYR H 84 PHE 0.008 0.001 PHE K 281 TRP 0.009 0.001 TRP K 264 HIS 0.006 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (13858) covalent geometry : angle 0.58280 / 0.34 (19738) hydrogen bonds : bond 0.04729 / 3.20 ( 804) hydrogen bonds : angle 3.11675 / 2.23 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: K 150 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7397 (tt) REVERT: K 180 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8881 (mm-30) REVERT: K 187 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8745 (tpp80) REVERT: K 225 GLU cc_start: 0.8232 (pt0) cc_final: 0.7455 (tp30) REVERT: A 133 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: F 44 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8710 (mtpm) REVERT: G 25 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8833 (pp) REVERT: G 67 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8107 (tp30) REVERT: G 74 LYS cc_start: 0.8059 (tptt) cc_final: 0.7840 (mmmt) REVERT: H 69 ASP cc_start: 0.8986 (t0) cc_final: 0.8744 (t0) REVERT: C 67 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: D 42 TYR cc_start: 0.8409 (t80) cc_final: 0.8112 (t80) outliers start: 21 outliers final: 11 residues processed: 176 average time/residue: 0.7855 time to fit residues: 147.5941 Evaluate side-chains 176 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.115419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.080571 restraints weight = 24530.238| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.64 r_work: 0.3186 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13858 Z= 0.196 Angle : 0.610 7.512 19738 Z= 0.348 Chirality : 0.046 0.312 2236 Planarity : 0.004 0.055 1658 Dihedral : 29.930 172.887 3796 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.08 % Allowed : 15.28 % Favored : 81.64 % 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: 1.74 (0.27), residues: 1009 helix: 2.30 (0.21), residues: 646 sheet: -0.30 (0.76), residues: 36 loop : -1.09 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 79 TYR 0.019 0.002 TYR H 84 PHE 0.010 0.001 PHE K 281 TRP 0.009 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.20 (13858) covalent geometry : angle 0.61035 / 0.35 (19738) hydrogen bonds : bond 0.05415 / 3.67 ( 804) hydrogen bonds : angle 3.17200 / 2.28 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8881 (mm-30) REVERT: K 225 GLU cc_start: 0.8238 (pt0) cc_final: 0.7460 (tp30) REVERT: A 133 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: F 44 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8737 (mtpp) REVERT: G 25 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8915 (pp) REVERT: G 67 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8129 (tp30) REVERT: G 74 LYS cc_start: 0.8122 (tptt) cc_final: 0.7887 (mmmt) REVERT: H 69 ASP cc_start: 0.9023 (t0) cc_final: 0.8779 (t0) REVERT: H 80 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8466 (ttp80) REVERT: E 120 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8435 (mmm) REVERT: C 67 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8278 (tp30) REVERT: D 42 TYR cc_start: 0.8421 (t80) cc_final: 0.8149 (t80) outliers start: 26 outliers final: 11 residues processed: 174 average time/residue: 0.7991 time to fit residues: 148.3790 Evaluate side-chains 172 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 113 optimal weight: 0.0060 chunk 66 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.116259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.081463 restraints weight = 24357.508| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.64 r_work: 0.3213 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13858 Z= 0.134 Angle : 0.588 7.424 19738 Z= 0.338 Chirality : 0.045 0.302 2236 Planarity : 0.004 0.052 1658 Dihedral : 29.923 173.770 3796 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.37 % Allowed : 15.64 % Favored : 81.99 % 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: 1.89 (0.27), residues: 1009 helix: 2.44 (0.21), residues: 639 sheet: -0.33 (0.76), residues: 36 loop : -0.99 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 39 TYR 0.021 0.002 TYR B 88 PHE 0.008 0.001 PHE K 281 TRP 0.009 0.001 TRP K 264 HIS 0.003 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (13858) covalent geometry : angle 0.58771 / 0.34 (19738) hydrogen bonds : bond 0.04728 / 3.21 ( 804) hydrogen bonds : angle 3.13930 / 2.25 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8890 (mm-30) REVERT: K 225 GLU cc_start: 0.8207 (pt0) cc_final: 0.7423 (tp30) REVERT: A 133 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: F 44 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8714 (mtpp) REVERT: G 25 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8893 (pp) REVERT: G 67 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: G 74 LYS cc_start: 0.8093 (tptt) cc_final: 0.7854 (mmmt) REVERT: H 69 ASP cc_start: 0.8993 (t0) cc_final: 0.8728 (t0) REVERT: H 80 ARG cc_start: 0.8751 (ttm110) cc_final: 0.8474 (ttp80) REVERT: C 67 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: D 42 TYR cc_start: 0.8411 (t80) cc_final: 0.8147 (t80) outliers start: 20 outliers final: 12 residues processed: 176 average time/residue: 0.7889 time to fit residues: 148.4095 Evaluate side-chains 176 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 17 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 85 optimal weight: 0.0020 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 103 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.116510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.081901 restraints weight = 24353.662| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.63 r_work: 0.3221 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 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 : 0.003 0.030 13858 Z= 0.141 Angle : 0.575 7.610 19738 Z= 0.331 Chirality : 0.044 0.305 2236 Planarity : 0.004 0.059 1658 Dihedral : 29.877 174.944 3796 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.25 % Allowed : 15.52 % Favored : 82.23 % 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: 1.95 (0.27), residues: 1009 helix: 2.49 (0.21), residues: 639 sheet: -0.31 (0.76), residues: 36 loop : -0.98 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 39 TYR 0.018 0.001 TYR H 84 PHE 0.007 0.001 PHE F 61 TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (13858) covalent geometry : angle 0.57485 / 0.33 (19738) hydrogen bonds : bond 0.04522 / 3.06 ( 804) hydrogen bonds : angle 3.07521 / 2.21 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8911 (mm-30) REVERT: K 225 GLU cc_start: 0.8234 (pt0) cc_final: 0.7433 (tp30) REVERT: A 133 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: F 44 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8719 (mtpm) REVERT: G 25 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8881 (pp) REVERT: G 67 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8112 (tp30) REVERT: G 74 LYS cc_start: 0.8080 (tptt) cc_final: 0.7845 (mmmt) REVERT: H 69 ASP cc_start: 0.8981 (t0) cc_final: 0.8730 (t0) REVERT: H 80 ARG cc_start: 0.8748 (ttm110) cc_final: 0.8485 (ttp80) REVERT: C 67 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8164 (tp30) REVERT: D 42 TYR cc_start: 0.8404 (t80) cc_final: 0.8136 (t80) outliers start: 19 outliers final: 13 residues processed: 174 average time/residue: 0.8214 time to fit residues: 152.4543 Evaluate side-chains 178 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 50.0000 chunk 13 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.115949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.081251 restraints weight = 24221.357| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.63 r_work: 0.3206 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13858 Z= 0.165 Angle : 0.582 7.550 19738 Z= 0.334 Chirality : 0.044 0.306 2236 Planarity : 0.004 0.058 1658 Dihedral : 29.850 174.109 3796 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.01 % Allowed : 15.88 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.27), residues: 1009 helix: 2.43 (0.21), residues: 646 sheet: -0.34 (0.75), residues: 36 loop : -1.04 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 39 TYR 0.021 0.002 TYR D 83 PHE 0.008 0.001 PHE H 66 TRP 0.010 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (13858) covalent geometry : angle 0.58161 / 0.33 (19738) hydrogen bonds : bond 0.04825 / 3.27 ( 804) hydrogen bonds : angle 3.09156 / 2.23 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: K 225 GLU cc_start: 0.8237 (pt0) cc_final: 0.7433 (tp30) REVERT: A 133 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: F 44 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8714 (mtpp) REVERT: G 25 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8922 (pp) REVERT: G 67 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8113 (tp30) REVERT: G 74 LYS cc_start: 0.8095 (tptt) cc_final: 0.7850 (mmmt) REVERT: H 69 ASP cc_start: 0.8991 (t0) cc_final: 0.8734 (t0) REVERT: H 80 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8517 (ttp80) REVERT: C 67 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8174 (tp30) REVERT: D 42 TYR cc_start: 0.8423 (t80) cc_final: 0.8151 (t80) outliers start: 17 outliers final: 12 residues processed: 171 average time/residue: 0.8061 time to fit residues: 146.9257 Evaluate side-chains 174 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.116084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.081345 restraints weight = 24549.077| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.63 r_work: 0.3210 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13858 Z= 0.155 Angle : 0.588 7.549 19738 Z= 0.336 Chirality : 0.044 0.303 2236 Planarity : 0.004 0.060 1658 Dihedral : 29.842 174.550 3796 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.90 % Allowed : 16.59 % Favored : 81.52 % 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: 1.91 (0.27), residues: 1009 helix: 2.45 (0.21), residues: 646 sheet: -0.32 (0.76), residues: 36 loop : -1.04 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 39 TYR 0.024 0.002 TYR D 83 PHE 0.008 0.001 PHE K 281 TRP 0.010 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (13858) covalent geometry : angle 0.58767 / 0.34 (19738) hydrogen bonds : bond 0.04650 / 3.15 ( 804) hydrogen bonds : angle 3.06046 / 2.20 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: K 225 GLU cc_start: 0.8279 (pt0) cc_final: 0.7461 (tp30) REVERT: A 133 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: F 44 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8735 (mtpm) REVERT: G 25 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8917 (pp) REVERT: G 67 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8130 (tp30) REVERT: G 74 LYS cc_start: 0.8097 (tptt) cc_final: 0.7842 (mmmt) REVERT: H 69 ASP cc_start: 0.9002 (t0) cc_final: 0.8745 (t0) REVERT: H 80 ARG cc_start: 0.8748 (ttm110) cc_final: 0.8509 (ttp80) REVERT: C 67 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8177 (tp30) REVERT: D 42 TYR cc_start: 0.8380 (t80) cc_final: 0.8106 (t80) outliers start: 16 outliers final: 12 residues processed: 172 average time/residue: 0.7979 time to fit residues: 146.4763 Evaluate side-chains 174 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.116304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.081638 restraints weight = 24543.144| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.63 r_work: 0.3213 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13858 Z= 0.143 Angle : 0.585 7.377 19738 Z= 0.335 Chirality : 0.044 0.301 2236 Planarity : 0.004 0.060 1658 Dihedral : 29.839 174.582 3796 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.01 % Allowed : 16.59 % 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: 1.93 (0.27), residues: 1009 helix: 2.46 (0.21), residues: 646 sheet: -0.32 (0.76), residues: 36 loop : -1.04 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 39 TYR 0.029 0.002 TYR D 83 PHE 0.007 0.001 PHE F 61 TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (13858) covalent geometry : angle 0.58516 / 0.34 (19738) hydrogen bonds : bond 0.04572 / 3.10 ( 804) hydrogen bonds : angle 3.05555 / 2.20 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: K 225 GLU cc_start: 0.8283 (pt0) cc_final: 0.7477 (tp30) REVERT: A 133 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: F 44 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8726 (mtpm) REVERT: G 25 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8915 (pp) REVERT: G 67 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: G 74 LYS cc_start: 0.8088 (tptt) cc_final: 0.7833 (mmmt) REVERT: H 69 ASP cc_start: 0.8993 (t0) cc_final: 0.8739 (t0) REVERT: H 80 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8497 (ttp80) REVERT: C 67 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8164 (tp30) REVERT: D 42 TYR cc_start: 0.8382 (t80) cc_final: 0.8107 (t80) outliers start: 17 outliers final: 12 residues processed: 169 average time/residue: 0.7745 time to fit residues: 139.6778 Evaluate side-chains 173 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 85 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.114752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.079845 restraints weight = 24345.334| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.62 r_work: 0.3175 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13858 Z= 0.215 Angle : 0.624 6.978 19738 Z= 0.352 Chirality : 0.047 0.305 2236 Planarity : 0.005 0.059 1658 Dihedral : 29.855 172.628 3796 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.78 % Allowed : 16.82 % 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: 1.77 (0.27), residues: 1009 helix: 2.34 (0.20), residues: 646 sheet: -0.42 (0.75), residues: 36 loop : -1.12 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 39 TYR 0.032 0.002 TYR D 83 PHE 0.010 0.001 PHE K 281 TRP 0.010 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 (13858) covalent geometry : angle 0.62438 / 0.35 (19738) hydrogen bonds : bond 0.05669 / 3.83 ( 804) hydrogen bonds : angle 3.16421 / 2.28 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5822.86 seconds wall clock time: 99 minutes 33.62 seconds (5973.62 seconds total)