Starting phenix.real_space_refine on Fri Jul 3 07:56:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t9f_41109/07_2026/8t9f_41109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t9f_41109/07_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_41109/07_2026/8t9f_41109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t9f_41109/07_2026/8t9f_41109.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8t9f_41109/07_2026/8t9f_41109.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t9f_41109/07_2026/8t9f_41109.cif" model { file = "/net/cci-nas-00/data/ceres_data/8t9f_41109/07_2026/8t9f_41109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t9f_41109/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.86, per 1000 atoms: 0.22 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: 1.10 Conformation dependent library (CDL) restraints added in 445.1 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: 1.86 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: 2.66 Time building geometry restraints manager: 1.50 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: 18833 1.75 - 3.50: 852 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=" 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 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+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: 2.360 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.450 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: 0.010 Load rotamer database and sin/cos tables:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- 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 : 0.726 8.743 19738 Z= 0.628 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 0.72559 / 0.63 (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 : 0.379 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: 0.8081 (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: 0.7940 time to fit residues: 190.4838 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 : 0.372 ------------------------------------------------------------------------------- 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: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.117461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.083043 restraints weight = 24547.062| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.65 r_work: 0.3212 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1229 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= 0.153 Angle : 0.597 8.205 19738 Z= 0.351 Chirality : 0.045 0.273 2236 Planarity : 0.004 0.042 1658 Dihedral : 29.799 176.666 3798 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 1.69 (0.26), residues: 1009 helix: 2.26 (0.21), residues: 638 sheet: -0.09 (0.71), residues: 44 loop : -1.06 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 39 TYR 0.014 0.001 TYR H 84 PHE 0.008 0.001 PHE K 183 TRP 0.008 0.001 TRP K 264 HIS 0.007 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (13858) covalent geometry : angle 0.59660 / 0.35 (19738) hydrogen bonds : bond 0.05011 / 3.35 ( 804) hydrogen bonds : angle 3.38063 / 2.38 ( 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 194 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8836 (mm-30) REVERT: K 187 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8829 (tpp80) REVERT: K 225 GLU cc_start: 0.8207 (pt0) cc_final: 0.7429 (tp30) REVERT: A 59 GLU cc_start: 0.8711 (pm20) cc_final: 0.8483 (pm20) REVERT: F 44 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8732 (mtpp) REVERT: G 25 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8760 (pp) REVERT: G 67 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8118 (tp30) REVERT: G 74 LYS cc_start: 0.7994 (tptt) cc_final: 0.7744 (mmmt) REVERT: H 69 ASP cc_start: 0.8973 (t0) cc_final: 0.8762 (t0) REVERT: E 120 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8385 (mtm) REVERT: C 67 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8454 (tp30) REVERT: D 42 TYR cc_start: 0.8458 (t80) cc_final: 0.8091 (t80) outliers start: 24 outliers final: 8 residues processed: 184 average time/residue: 0.7376 time to fit residues: 144.6487 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 : 0.286 ------------------------------------------------------------------------------- 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: 4.9990 chunk 10 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 117 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.117659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.083199 restraints weight = 24652.541| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.64 r_work: 0.3247 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1505 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= 0.142 Angle : 0.559 7.711 19738 Z= 0.332 Chirality : 0.043 0.285 2236 Planarity : 0.004 0.056 1658 Dihedral : 29.902 175.358 3796 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.37 % Allowed : 15.05 % Favored : 82.58 % 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: 2.41 (0.21), residues: 639 sheet: -0.27 (0.70), residues: 44 loop : -0.94 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 39 TYR 0.018 0.001 TYR H 84 PHE 0.007 0.001 PHE K 332 TRP 0.007 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (13858) covalent geometry : angle 0.55932 / 0.33 (19738) hydrogen bonds : bond 0.04607 / 3.12 ( 804) hydrogen bonds : angle 3.16261 / 2.25 ( 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 190 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8863 (mm-30) REVERT: K 187 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8846 (tpp80) REVERT: K 225 GLU cc_start: 0.8163 (pt0) cc_final: 0.7461 (tp30) REVERT: F 44 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8697 (mtpm) REVERT: G 25 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8784 (pp) REVERT: G 74 LYS cc_start: 0.8020 (tptt) cc_final: 0.7785 (mmmt) REVERT: G 93 ASP cc_start: 0.8625 (t0) cc_final: 0.8334 (t0) REVERT: H 69 ASP cc_start: 0.8957 (t0) cc_final: 0.8714 (t0) REVERT: C 67 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8335 (tp30) REVERT: D 42 TYR cc_start: 0.8432 (t80) cc_final: 0.8114 (t80) outliers start: 20 outliers final: 8 residues processed: 182 average time/residue: 0.7236 time to fit residues: 140.5610 Evaluate side-chains 173 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 121 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 84 optimal weight: 0.0670 chunk 36 optimal weight: 10.0000 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.117223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.082738 restraints weight = 24592.156| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.64 r_work: 0.3238 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1613 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= 0.146 Angle : 0.559 7.973 19738 Z= 0.329 Chirality : 0.043 0.285 2236 Planarity : 0.004 0.048 1658 Dihedral : 29.951 175.270 3796 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.61 % Allowed : 15.05 % 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: 1.92 (0.27), residues: 1009 helix: 2.43 (0.21), residues: 639 sheet: -0.14 (0.77), residues: 36 loop : -0.93 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 143 TYR 0.017 0.001 TYR H 84 PHE 0.007 0.001 PHE H 66 TRP 0.008 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (13858) covalent geometry : angle 0.55894 / 0.33 (19738) hydrogen bonds : bond 0.04570 / 3.09 ( 804) hydrogen bonds : angle 3.09044 / 2.21 ( 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 187 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: K 150 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7308 (tt) REVERT: K 180 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8864 (mm-30) REVERT: K 187 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8745 (tpp80) REVERT: K 225 GLU cc_start: 0.8165 (pt0) cc_final: 0.7405 (tp30) REVERT: A 133 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: F 44 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8646 (mtpm) REVERT: G 25 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8842 (pp) REVERT: G 67 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8090 (tp30) REVERT: G 74 LYS cc_start: 0.8035 (tptt) cc_final: 0.7816 (mmmt) REVERT: H 69 ASP cc_start: 0.8957 (t0) cc_final: 0.8720 (t0) REVERT: C 67 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8274 (tp30) REVERT: D 42 TYR cc_start: 0.8452 (t80) cc_final: 0.8140 (t80) outliers start: 22 outliers final: 11 residues processed: 179 average time/residue: 0.7670 time to fit residues: 146.5488 Evaluate side-chains 180 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 0.5980 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.115906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.081066 restraints weight = 24585.215| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.64 r_work: 0.3200 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13858 Z= 0.179 Angle : 0.583 7.662 19738 Z= 0.338 Chirality : 0.044 0.285 2236 Planarity : 0.004 0.058 1658 Dihedral : 29.996 174.185 3796 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.08 % Allowed : 14.81 % 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: 1.83 (0.27), residues: 1009 helix: 2.38 (0.21), residues: 639 sheet: -0.22 (0.76), residues: 36 loop : -1.01 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 79 TYR 0.020 0.002 TYR H 84 PHE 0.009 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 0.00360 / 0.18 (13858) covalent geometry : angle 0.58262 / 0.34 (19738) hydrogen bonds : bond 0.05155 / 3.49 ( 804) hydrogen bonds : angle 3.12817 / 2.24 ( 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 186 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: K 150 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7419 (tt) REVERT: K 180 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8875 (mm-30) REVERT: K 187 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8752 (tpp80) REVERT: K 225 GLU cc_start: 0.8219 (pt0) cc_final: 0.7450 (tp30) REVERT: A 133 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: F 44 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8711 (mtpm) REVERT: G 25 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8877 (pp) REVERT: G 67 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8133 (tp30) REVERT: G 74 LYS cc_start: 0.8089 (tptt) cc_final: 0.7861 (mmmt) REVERT: H 69 ASP cc_start: 0.9024 (t0) cc_final: 0.8764 (t0) REVERT: H 80 ARG cc_start: 0.8744 (ttm110) cc_final: 0.8460 (ttp80) REVERT: E 120 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8428 (mmm) REVERT: C 67 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8266 (tp30) REVERT: D 42 TYR cc_start: 0.8410 (t80) cc_final: 0.8143 (t80) outliers start: 26 outliers final: 12 residues processed: 174 average time/residue: 0.7094 time to fit residues: 131.9367 Evaluate side-chains 175 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 24 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.116124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.081536 restraints weight = 24374.568| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.62 r_work: 0.3211 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1769 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= 0.153 Angle : 0.574 7.714 19738 Z= 0.334 Chirality : 0.044 0.281 2236 Planarity : 0.004 0.054 1658 Dihedral : 29.997 174.760 3796 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.13 % Allowed : 15.64 % 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: 1.89 (0.27), residues: 1009 helix: 2.43 (0.21), residues: 639 sheet: -0.23 (0.76), residues: 36 loop : -0.99 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 39 TYR 0.019 0.002 TYR H 84 PHE 0.007 0.001 PHE K 281 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 0.00292 / 0.15 (13858) covalent geometry : angle 0.57399 / 0.33 (19738) hydrogen bonds : bond 0.04850 / 3.28 ( 804) hydrogen bonds : angle 3.11849 / 2.24 ( 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 179 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8909 (mm-30) REVERT: K 187 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8778 (tpp80) REVERT: K 225 GLU cc_start: 0.8170 (pt0) cc_final: 0.7416 (tp30) REVERT: A 133 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: F 44 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8724 (mtpm) REVERT: G 67 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8121 (tp30) REVERT: G 74 LYS cc_start: 0.8078 (tptt) cc_final: 0.7846 (mmmt) REVERT: H 69 ASP cc_start: 0.8992 (t0) cc_final: 0.8731 (t0) REVERT: H 80 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8482 (ttp80) REVERT: C 67 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8266 (tp30) REVERT: D 42 TYR cc_start: 0.8415 (t80) cc_final: 0.8152 (t80) outliers start: 18 outliers final: 10 residues processed: 171 average time/residue: 0.8033 time to fit residues: 146.5817 Evaluate side-chains 173 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain A residue 133 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 17 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.116411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.081864 restraints weight = 24337.837| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.63 r_work: 0.3218 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1814 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= 0.150 Angle : 0.562 7.005 19738 Z= 0.328 Chirality : 0.043 0.280 2236 Planarity : 0.004 0.058 1658 Dihedral : 29.973 175.846 3796 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.37 % Allowed : 15.40 % 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: 1.94 (0.27), residues: 1009 helix: 2.47 (0.21), residues: 639 sheet: -0.22 (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 0.022 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 0.00285 / 0.15 (13858) covalent geometry : angle 0.56242 / 0.33 (19738) hydrogen bonds : bond 0.04599 / 3.12 ( 804) hydrogen bonds : angle 3.07627 / 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: 20 poor density : 161 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: K 150 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7449 (tt) REVERT: K 180 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8913 (mm-30) REVERT: K 185 TYR cc_start: 0.9135 (m-80) cc_final: 0.8918 (m-80) REVERT: K 187 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8773 (tpp80) REVERT: K 225 GLU cc_start: 0.8149 (pt0) cc_final: 0.7414 (tp30) REVERT: A 133 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: F 44 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8707 (mtpm) REVERT: G 25 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8822 (pp) REVERT: G 67 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8125 (tp30) REVERT: G 74 LYS cc_start: 0.8075 (tptt) cc_final: 0.7844 (mmmt) REVERT: H 69 ASP cc_start: 0.8987 (t0) cc_final: 0.8725 (t0) REVERT: H 80 ARG cc_start: 0.8744 (ttm110) cc_final: 0.8517 (ttp80) REVERT: C 67 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: D 42 TYR cc_start: 0.8412 (t80) cc_final: 0.8143 (t80) outliers start: 20 outliers final: 11 residues processed: 174 average time/residue: 0.8017 time to fit residues: 148.8106 Evaluate side-chains 177 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 50.0000 chunk 13 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3975 r_free = 0.3975 target = 0.114095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.079141 restraints weight = 24176.635| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.62 r_work: 0.3154 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13858 Z= 0.282 Angle : 0.645 6.897 19738 Z= 0.364 Chirality : 0.048 0.289 2236 Planarity : 0.005 0.057 1658 Dihedral : 29.983 172.811 3796 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.61 % Allowed : 15.40 % 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: 1.62 (0.27), residues: 1009 helix: 2.22 (0.20), residues: 646 sheet: -0.50 (0.69), residues: 42 loop : -1.16 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 39 TYR 0.024 0.002 TYR D 83 PHE 0.013 0.002 PHE K 281 TRP 0.012 0.002 TRP K 264 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.28 (13858) covalent geometry : angle 0.64514 / 0.36 (19738) hydrogen bonds : bond 0.06470 / 4.37 ( 804) hydrogen bonds : angle 3.27004 / 2.36 ( 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 181 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: K 150 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7689 (tt) REVERT: K 180 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8902 (mm-30) REVERT: K 187 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8908 (tpp80) REVERT: K 225 GLU cc_start: 0.8319 (pt0) cc_final: 0.7528 (tp30) REVERT: A 133 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: F 44 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8750 (mtpp) REVERT: G 67 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8147 (tp30) REVERT: G 74 LYS cc_start: 0.8192 (tptt) cc_final: 0.7957 (mmmt) REVERT: G 93 ASP cc_start: 0.8731 (t0) cc_final: 0.8440 (t0) REVERT: E 120 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8566 (mmm) REVERT: C 67 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: D 42 TYR cc_start: 0.8406 (t80) cc_final: 0.8137 (t80) outliers start: 22 outliers final: 12 residues processed: 173 average time/residue: 0.8215 time to fit residues: 151.2598 Evaluate side-chains 173 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 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 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: 10.0000 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.115520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.080670 restraints weight = 24421.482| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.64 r_work: 0.3192 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2035 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= 0.147 Angle : 0.598 8.771 19738 Z= 0.344 Chirality : 0.045 0.271 2236 Planarity : 0.005 0.072 1658 Dihedral : 30.003 175.032 3796 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.49 % Allowed : 15.88 % 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: 1.77 (0.27), residues: 1009 helix: 2.34 (0.21), residues: 646 sheet: -0.39 (0.75), residues: 36 loop : -1.11 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 39 TYR 0.033 0.002 TYR H 84 PHE 0.008 0.001 PHE D 65 TRP 0.008 0.001 TRP K 264 HIS 0.003 0.001 HIS K 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (13858) covalent geometry : angle 0.59844 / 0.34 (19738) hydrogen bonds : bond 0.04995 / 3.39 ( 804) hydrogen bonds : angle 3.15521 / 2.27 ( 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 183 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: K 150 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7642 (tt) REVERT: K 180 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8907 (mm-30) REVERT: K 187 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8876 (tpp80) REVERT: K 225 GLU cc_start: 0.8315 (pt0) cc_final: 0.7506 (tp30) REVERT: A 133 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: F 44 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8757 (mtpp) REVERT: G 74 LYS cc_start: 0.8138 (tptt) cc_final: 0.7904 (mmmt) REVERT: C 67 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8248 (tp30) REVERT: D 42 TYR cc_start: 0.8379 (t80) cc_final: 0.8085 (t80) outliers start: 21 outliers final: 12 residues processed: 175 average time/residue: 0.6955 time to fit residues: 129.9853 Evaluate side-chains 175 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 79 SER Chi-restraints excluded: chain E residue 45 THR 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 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: 0.2980 chunk 89 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.115835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.081100 restraints weight = 24477.850| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.63 r_work: 0.3200 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2020 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= 0.140 Angle : 0.589 6.902 19738 Z= 0.340 Chirality : 0.044 0.275 2236 Planarity : 0.004 0.074 1658 Dihedral : 29.996 175.775 3796 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.37 % Allowed : 16.35 % Favored : 81.28 % 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: 1.83 (0.27), residues: 1009 helix: 2.39 (0.21), residues: 646 sheet: -0.35 (0.75), residues: 36 loop : -1.08 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 39 TYR 0.043 0.002 TYR H 84 PHE 0.007 0.001 PHE F 61 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 0.00251 / 0.14 (13858) covalent geometry : angle 0.58928 / 0.34 (19738) hydrogen bonds : bond 0.04753 / 3.22 ( 804) hydrogen bonds : angle 3.13556 / 2.25 ( 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 180 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.406 Fit side-chains REVERT: K 150 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7565 (tt) REVERT: K 180 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8887 (mm-30) REVERT: K 187 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8771 (tpp80) REVERT: K 225 GLU cc_start: 0.8264 (pt0) cc_final: 0.7468 (tp30) REVERT: A 133 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: F 44 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8723 (mtpp) REVERT: G 25 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8908 (pp) REVERT: G 74 LYS cc_start: 0.8136 (tptt) cc_final: 0.7892 (mmmt) REVERT: C 67 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8220 (tp30) REVERT: D 42 TYR cc_start: 0.8409 (t80) cc_final: 0.8112 (t80) outliers start: 20 outliers final: 14 residues processed: 173 average time/residue: 0.7498 time to fit residues: 138.3597 Evaluate side-chains 178 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 75 ASP 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 45 THR 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: 0.0970 chunk 97 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.115569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.080844 restraints weight = 24374.820| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.64 r_work: 0.3199 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13858 Z= 0.167 Angle : 0.586 6.862 19738 Z= 0.338 Chirality : 0.044 0.277 2236 Planarity : 0.004 0.067 1658 Dihedral : 29.946 175.964 3796 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.90 % Allowed : 16.82 % Favored : 81.28 % 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: 1.84 (0.27), residues: 1009 helix: 2.41 (0.21), residues: 646 sheet: -0.36 (0.75), residues: 36 loop : -1.11 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 39 TYR 0.034 0.002 TYR H 84 PHE 0.008 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 0.00332 / 0.17 (13858) covalent geometry : angle 0.58595 / 0.34 (19738) hydrogen bonds : bond 0.04888 / 3.31 ( 804) hydrogen bonds : angle 3.10560 / 2.23 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6110.10 seconds wall clock time: 104 minutes 21.59 seconds (6261.59 seconds total)