Starting phenix.real_space_refine on Sat Aug 23 15:25:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t9f_41109/08_2025/8t9f_41109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t9f_41109/08_2025/8t9f_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_2025/8t9f_41109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t9f_41109/08_2025/8t9f_41109.map" model { file = "/net/cci-nas-00/data/ceres_data/8t9f_41109/08_2025/8t9f_41109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t9f_41109/08_2025/8t9f_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-2.0-5787/lib/python3.9/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: 3.39, per 1000 atoms: 0.26 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 455.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 2.16 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: 2.88 Time building geometry restraints manager: 1.49 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=" N GLN K 374 " pdb=" CA GLN K 374 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.38e+00 bond pdb=" C2 SAM K 401 " pdb=" N3 SAM K 401 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" N ASP K 372 " pdb=" CA ASP K 372 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.10e-02 8.26e+03 7.42e+00 bond pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " ideal model delta sigma weight residual 1.422 1.503 -0.081 3.00e-02 1.11e+03 7.33e+00 bond pdb=" C8 SAM K 401 " pdb=" N7 SAM K 401 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.05e+00 ... (remaining 13853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 19300 1.75 - 3.50: 397 3.50 - 5.25: 30 5.25 - 6.99: 8 6.99 - 8.74: 3 Bond angle restraints: 19738 Sorted by residual: angle pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " pdb=" P DT J 28 " ideal model delta sigma weight residual 120.20 125.95 -5.75 1.50e+00 4.44e-01 1.47e+01 angle pdb=" N ASP K 372 " pdb=" CA ASP K 372 " pdb=" C ASP K 372 " ideal model delta sigma weight residual 112.57 108.70 3.87 1.13e+00 7.83e-01 1.17e+01 angle pdb=" CA ASN K 370 " pdb=" C ASN K 370 " pdb=" O ASN K 370 " ideal model delta sigma weight residual 121.99 118.36 3.63 1.14e+00 7.69e-01 1.01e+01 angle pdb=" O4' DT J 28 " pdb=" C1' DT J 28 " pdb=" N1 DT J 28 " ideal model delta sigma weight residual 108.40 113.13 -4.73 1.50e+00 4.44e-01 9.96e+00 angle pdb=" CA SER K 371 " pdb=" C SER K 371 " pdb=" O SER K 371 " ideal model delta sigma weight residual 121.56 118.19 3.37 1.09e+00 8.42e-01 9.55e+00 ... (remaining 19733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 6504 35.14 - 70.28: 1200 70.28 - 105.42: 18 105.42 - 140.57: 1 140.57 - 175.71: 3 Dihedral angle restraints: 7726 sinusoidal: 4741 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 7723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1742 0.042 - 0.084: 398 0.084 - 0.126: 90 0.126 - 0.167: 4 0.167 - 0.209: 2 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 2.35 -2.55 -0.21 2.00e-01 2.50e+01 1.09e+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=" C1' SAM K 401 " pdb=" C2' SAM K 401 " pdb=" N9 SAM K 401 " pdb=" O4' SAM K 401 " both_signs ideal model delta sigma weight residual False 2.30 2.46 -0.16 2.00e-01 2.50e+01 6.70e-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: 3.130 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: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.550 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:9.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.004 0.081 13858 Z= 0.191 Angle : 0.589 8.743 19738 Z= 0.351 Chirality : 0.037 0.209 2236 Planarity : 0.004 0.049 1658 Dihedral : 25.251 175.707 5798 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 aren 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 covalent geometry : bond 0.00394 (13858) covalent geometry : angle 0.58902 (19738) hydrogen bonds : bond 0.10964 ( 804) hydrogen bonds : angle 4.16749 ( 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 : 0.416 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8720 (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: 0.8473 (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: 0.8977 time to fit residues: 214.2654 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 : 0.429 ------------------------------------------------------------------------------- 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: 10.0000 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4033 r_free = 0.4033 target = 0.117510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.083159 restraints weight = 24487.577| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.63 r_work: 0.3250 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13858 Z= 0.165 Angle : 0.526 8.661 19738 Z= 0.315 Chirality : 0.035 0.174 2236 Planarity : 0.004 0.037 1658 Dihedral : 29.534 178.051 3830 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.08 % Allowed : 14.34 % 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 aren not related in a simple way. whole: 1.81 (0.26), residues: 1009 helix: 2.34 (0.21), residues: 638 sheet: -0.01 (0.70), residues: 44 loop : -0.99 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 79 TYR 0.012 0.001 TYR K 306 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 covalent geometry : bond 0.00365 (13858) covalent geometry : angle 0.52642 (19738) hydrogen bonds : bond 0.04203 ( 804) hydrogen bonds : angle 3.14243 ( 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 198 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: K 143 ARG cc_start: 0.6082 (ttp80) cc_final: 0.5801 (tmm160) REVERT: K 180 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8880 (mm-30) REVERT: K 187 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8810 (tpp80) REVERT: K 225 GLU cc_start: 0.8133 (pt0) cc_final: 0.7444 (tp30) REVERT: A 133 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: F 44 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8631 (mtpm) REVERT: G 25 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8767 (pp) REVERT: G 74 LYS cc_start: 0.8067 (tptt) cc_final: 0.7834 (mmmt) REVERT: D 42 TYR cc_start: 0.8424 (t80) cc_final: 0.8110 (t80) outliers start: 26 outliers final: 8 residues processed: 188 average time/residue: 0.8755 time to fit residues: 175.2069 Evaluate side-chains 177 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 25 LEU 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 E residue 86 SER 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: 7.9990 chunk 10 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3996 r_free = 0.3996 target = 0.115343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.080588 restraints weight = 24539.318| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.64 r_work: 0.3188 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13858 Z= 0.213 Angle : 0.541 4.991 19738 Z= 0.326 Chirality : 0.036 0.136 2236 Planarity : 0.004 0.038 1658 Dihedral : 29.650 177.864 3828 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.84 % Allowed : 15.28 % Favored : 81.87 % 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 aren not related in a simple way. whole: 1.82 (0.27), residues: 1009 helix: 2.35 (0.21), residues: 646 sheet: -0.10 (0.74), residues: 42 loop : -1.08 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 39 TYR 0.013 0.002 TYR A 54 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 covalent geometry : bond 0.00482 (13858) covalent geometry : angle 0.54146 (19738) hydrogen bonds : bond 0.04788 ( 804) hydrogen bonds : angle 3.11114 ( 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 194 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8877 (mm-30) REVERT: K 225 GLU cc_start: 0.8249 (pt0) cc_final: 0.7514 (tp30) REVERT: A 133 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: F 44 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8677 (mtpp) REVERT: G 21 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8300 (tm-30) REVERT: G 74 LYS cc_start: 0.8146 (tptt) cc_final: 0.7921 (mmmt) REVERT: H 80 ARG cc_start: 0.8797 (ttm110) cc_final: 0.8530 (ttp80) REVERT: E 120 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8420 (mmm) REVERT: C 67 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: C 79 LYS cc_start: 0.8489 (mmtp) cc_final: 0.8180 (mmtm) REVERT: D 42 TYR cc_start: 0.8415 (t80) cc_final: 0.8143 (t80) outliers start: 24 outliers final: 10 residues processed: 184 average time/residue: 0.8858 time to fit residues: 173.4333 Evaluate side-chains 172 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.9980 chunk 121 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 0.4980 chunk 67 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 110 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4019 r_free = 0.4019 target = 0.116699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.082329 restraints weight = 24557.089| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.64 r_work: 0.3230 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13858 Z= 0.141 Angle : 0.525 7.734 19738 Z= 0.316 Chirality : 0.035 0.183 2236 Planarity : 0.004 0.045 1658 Dihedral : 29.624 177.647 3828 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.90 % Allowed : 15.88 % 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 aren not related in a simple way. whole: 1.98 (0.27), residues: 1009 helix: 2.51 (0.21), residues: 639 sheet: -0.14 (0.74), residues: 42 loop : -1.00 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 39 TYR 0.016 0.001 TYR H 84 PHE 0.006 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 covalent geometry : bond 0.00303 (13858) covalent geometry : angle 0.52519 (19738) hydrogen bonds : bond 0.04045 ( 804) hydrogen bonds : angle 3.01897 ( 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: 16 poor density : 168 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8874 (mm-30) REVERT: K 187 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8894 (tpp80) REVERT: K 225 GLU cc_start: 0.8245 (pt0) cc_final: 0.7461 (tp30) REVERT: A 133 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: F 44 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8679 (mtpp) REVERT: G 21 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8248 (tm-30) REVERT: G 25 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8825 (pp) REVERT: G 74 LYS cc_start: 0.8056 (tptt) cc_final: 0.7821 (mmmt) REVERT: H 80 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8507 (ttp80) REVERT: C 67 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8163 (tp30) REVERT: C 79 LYS cc_start: 0.8439 (mmtp) cc_final: 0.8206 (mmtm) REVERT: D 42 TYR cc_start: 0.8413 (t80) cc_final: 0.8129 (t80) outliers start: 16 outliers final: 10 residues processed: 178 average time/residue: 0.8239 time to fit residues: 156.1333 Evaluate side-chains 177 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 25 LEU Chi-restraints excluded: chain G residue 38 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4010 r_free = 0.4010 target = 0.116274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.081601 restraints weight = 24620.261| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.65 r_work: 0.3214 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13858 Z= 0.177 Angle : 0.516 5.201 19738 Z= 0.311 Chirality : 0.035 0.136 2236 Planarity : 0.004 0.042 1658 Dihedral : 29.476 178.194 3828 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.25 % Allowed : 16.00 % Favored : 81.75 % 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 aren not related in a simple way. whole: 2.04 (0.27), residues: 1009 helix: 2.52 (0.21), residues: 649 sheet: -0.22 (0.74), residues: 42 loop : -0.98 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 39 TYR 0.021 0.002 TYR K 92 PHE 0.007 0.001 PHE K 281 TRP 0.011 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 Details of bonding type rmsd covalent geometry : bond 0.00397 (13858) covalent geometry : angle 0.51622 (19738) hydrogen bonds : bond 0.04133 ( 804) hydrogen bonds : angle 2.93632 ( 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 187 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8883 (mm-30) REVERT: K 225 GLU cc_start: 0.8245 (pt0) cc_final: 0.7466 (tp30) REVERT: A 133 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: F 44 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8727 (mtpm) REVERT: G 21 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8262 (tm-30) REVERT: G 25 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8836 (pp) REVERT: G 74 LYS cc_start: 0.8046 (tptt) cc_final: 0.7807 (mmmt) REVERT: H 80 ARG cc_start: 0.8778 (ttm110) cc_final: 0.8548 (ttp80) REVERT: C 67 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8109 (tp30) REVERT: C 79 LYS cc_start: 0.8510 (mmtp) cc_final: 0.8302 (mmtm) REVERT: D 42 TYR cc_start: 0.8376 (t80) cc_final: 0.8121 (t80) outliers start: 19 outliers final: 12 residues processed: 180 average time/residue: 0.8853 time to fit residues: 169.1998 Evaluate side-chains 175 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 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 80 ARG 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: 0.9990 chunk 24 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4018 r_free = 0.4018 target = 0.116657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.082188 restraints weight = 24481.512| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.64 r_work: 0.3231 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2054 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 : 0.510 5.960 19738 Z= 0.308 Chirality : 0.034 0.136 2236 Planarity : 0.004 0.055 1658 Dihedral : 29.454 177.967 3828 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.13 % Allowed : 16.59 % 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 aren not related in a simple way. whole: 2.08 (0.27), residues: 1009 helix: 2.54 (0.21), residues: 649 sheet: -0.16 (0.74), residues: 42 loop : -0.95 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 39 TYR 0.014 0.001 TYR D 83 PHE 0.007 0.001 PHE F 61 TRP 0.010 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 Details of bonding type rmsd covalent geometry : bond 0.00345 (13858) covalent geometry : angle 0.50957 (19738) hydrogen bonds : bond 0.03884 ( 804) hydrogen bonds : angle 2.92088 ( 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: 18 poor density : 166 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8877 (mm-30) REVERT: K 225 GLU cc_start: 0.8209 (pt0) cc_final: 0.7442 (tp30) REVERT: A 133 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: F 44 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8709 (mtpm) REVERT: G 21 GLN cc_start: 0.8761 (tt0) cc_final: 0.8268 (tm-30) REVERT: G 25 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8821 (pp) REVERT: G 74 LYS cc_start: 0.8030 (tptt) cc_final: 0.7795 (mmmt) REVERT: H 80 ARG cc_start: 0.8775 (ttm110) cc_final: 0.8547 (ttp80) REVERT: D 42 TYR cc_start: 0.8388 (t80) cc_final: 0.8135 (t80) outliers start: 18 outliers final: 13 residues processed: 177 average time/residue: 0.8884 time to fit residues: 167.0248 Evaluate side-chains 178 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 17 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3995 r_free = 0.3995 target = 0.115336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080666 restraints weight = 24376.089| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.63 r_work: 0.3194 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13858 Z= 0.199 Angle : 0.527 6.276 19738 Z= 0.316 Chirality : 0.036 0.142 2236 Planarity : 0.004 0.050 1658 Dihedral : 29.491 176.654 3828 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.78 % Allowed : 16.94 % 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 aren not related in a simple way. whole: 2.02 (0.27), residues: 1009 helix: 2.49 (0.21), residues: 649 sheet: -0.23 (0.73), residues: 42 loop : -0.95 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 39 TYR 0.017 0.002 TYR D 83 PHE 0.007 0.001 PHE H 66 TRP 0.010 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 Details of bonding type rmsd covalent geometry : bond 0.00449 (13858) covalent geometry : angle 0.52672 (19738) hydrogen bonds : bond 0.04508 ( 804) hydrogen bonds : angle 2.98379 ( 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 182 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8881 (mm-30) REVERT: K 225 GLU cc_start: 0.8282 (pt0) cc_final: 0.7474 (tp30) REVERT: A 133 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: F 44 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8676 (mtpm) REVERT: G 21 GLN cc_start: 0.8739 (tt0) cc_final: 0.8270 (tm-30) REVERT: G 25 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8884 (pp) REVERT: G 74 LYS cc_start: 0.8145 (tptt) cc_final: 0.7913 (mmmt) REVERT: H 80 ARG cc_start: 0.8782 (ttm110) cc_final: 0.8559 (ttp80) REVERT: C 67 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8182 (tp30) REVERT: C 74 LYS cc_start: 0.7257 (tppt) cc_final: 0.6988 (tppt) REVERT: D 42 TYR cc_start: 0.8368 (t80) cc_final: 0.8101 (t80) outliers start: 15 outliers final: 13 residues processed: 177 average time/residue: 0.8945 time to fit residues: 168.1232 Evaluate side-chains 179 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3987 r_free = 0.3987 target = 0.114904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.080290 restraints weight = 24281.325| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.63 r_work: 0.3187 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13858 Z= 0.213 Angle : 0.541 6.586 19738 Z= 0.324 Chirality : 0.036 0.146 2236 Planarity : 0.004 0.059 1658 Dihedral : 29.465 176.745 3828 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.25 % Allowed : 16.59 % Favored : 81.16 % 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 aren not related in a simple way. whole: 1.98 (0.27), residues: 1009 helix: 2.48 (0.21), residues: 646 sheet: -0.22 (0.77), residues: 36 loop : -0.98 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 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 covalent geometry : bond 0.00483 (13858) covalent geometry : angle 0.54064 (19738) hydrogen bonds : bond 0.04603 ( 804) hydrogen bonds : angle 2.98935 ( 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 180 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.377 Fit side-chains REVERT: K 180 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8908 (mm-30) REVERT: K 225 GLU cc_start: 0.8317 (pt0) cc_final: 0.7498 (tp30) REVERT: A 133 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: F 44 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8715 (mtpm) REVERT: G 21 GLN cc_start: 0.8737 (tt0) cc_final: 0.8279 (tm-30) REVERT: G 25 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8893 (pp) REVERT: G 74 LYS cc_start: 0.8123 (tptt) cc_final: 0.7866 (mmmt) REVERT: H 80 ARG cc_start: 0.8787 (ttm110) cc_final: 0.8581 (ttp80) REVERT: C 67 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: C 74 LYS cc_start: 0.7246 (tppt) cc_final: 0.6993 (tppt) REVERT: D 42 TYR cc_start: 0.8398 (t80) cc_final: 0.8156 (t80) outliers start: 19 outliers final: 13 residues processed: 173 average time/residue: 0.8980 time to fit residues: 164.9228 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 : 0.299 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 278 ASN D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.114108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079478 restraints weight = 24576.771| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.63 r_work: 0.3167 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13858 Z= 0.246 Angle : 0.564 5.307 19738 Z= 0.336 Chirality : 0.037 0.160 2236 Planarity : 0.004 0.062 1658 Dihedral : 29.521 174.962 3828 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.01 % Allowed : 17.06 % Favored : 80.92 % 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 aren not related in a simple way. whole: 1.90 (0.27), residues: 1009 helix: 2.41 (0.21), residues: 646 sheet: -0.29 (0.77), residues: 36 loop : -0.98 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 39 TYR 0.026 0.002 TYR D 83 PHE 0.008 0.001 PHE H 66 TRP 0.012 0.002 TRP K 264 HIS 0.004 0.001 HIS H 83 Details of bonding type rmsd covalent geometry : bond 0.00560 (13858) covalent geometry : angle 0.56356 (19738) hydrogen bonds : bond 0.05022 ( 804) hydrogen bonds : angle 3.07112 ( 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 171 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.292 Fit side-chains REVERT: K 180 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8920 (mm-30) REVERT: K 225 GLU cc_start: 0.8374 (pt0) cc_final: 0.7597 (tp30) REVERT: A 133 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: F 44 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8720 (mtpp) REVERT: G 21 GLN cc_start: 0.8729 (tt0) cc_final: 0.8278 (tm-30) REVERT: G 25 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8943 (pp) REVERT: G 74 LYS cc_start: 0.8157 (tptt) cc_final: 0.7885 (mmmt) REVERT: H 80 ARG cc_start: 0.8763 (ttm110) cc_final: 0.8559 (ttp80) REVERT: E 41 TYR cc_start: 0.9107 (m-80) cc_final: 0.8886 (m-80) REVERT: E 115 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8260 (mptt) REVERT: C 67 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8171 (tp30) REVERT: C 74 LYS cc_start: 0.7216 (tppt) cc_final: 0.6967 (tppt) REVERT: D 42 TYR cc_start: 0.8358 (t80) cc_final: 0.8143 (t80) outliers start: 17 outliers final: 13 residues processed: 163 average time/residue: 0.7674 time to fit residues: 132.8672 Evaluate side-chains 170 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 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 115 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 7 optimal weight: 0.0370 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.115315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.080612 restraints weight = 24592.855| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.67 r_work: 0.3200 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13858 Z= 0.165 Angle : 0.539 6.946 19738 Z= 0.324 Chirality : 0.035 0.162 2236 Planarity : 0.004 0.071 1658 Dihedral : 29.503 175.688 3828 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.90 % Allowed : 17.54 % Favored : 80.57 % 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 aren not related in a simple way. whole: 2.05 (0.27), residues: 1009 helix: 2.54 (0.21), residues: 640 sheet: -0.21 (0.78), residues: 36 loop : -0.91 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 39 TYR 0.022 0.002 TYR K 92 PHE 0.007 0.001 PHE H 66 TRP 0.009 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 Details of bonding type rmsd covalent geometry : bond 0.00365 (13858) covalent geometry : angle 0.53860 (19738) hydrogen bonds : bond 0.04230 ( 804) hydrogen bonds : angle 3.00030 ( 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 175 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.247 Fit side-chains REVERT: K 180 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8939 (mm-30) REVERT: K 225 GLU cc_start: 0.8363 (pt0) cc_final: 0.7523 (tp30) REVERT: A 133 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: F 44 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8747 (mtpm) REVERT: G 21 GLN cc_start: 0.8731 (tt0) cc_final: 0.8273 (tm-30) REVERT: G 74 LYS cc_start: 0.8137 (tptt) cc_final: 0.7862 (mmmt) REVERT: H 80 ARG cc_start: 0.8767 (ttm110) cc_final: 0.8561 (ttp80) REVERT: E 41 TYR cc_start: 0.9084 (m-80) cc_final: 0.8863 (m-80) REVERT: E 115 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8223 (mptt) REVERT: C 67 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: C 74 LYS cc_start: 0.7020 (tppt) cc_final: 0.6749 (tppt) REVERT: D 42 TYR cc_start: 0.8358 (t80) cc_final: 0.8072 (t80) outliers start: 16 outliers final: 13 residues processed: 168 average time/residue: 0.7435 time to fit residues: 132.5687 Evaluate side-chains 171 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 86 SER Chi-restraints excluded: chain E residue 115 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 85 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 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 = 0.4004 r_free = 0.4004 target = 0.115745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.081351 restraints weight = 24486.950| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.64 r_work: 0.3211 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13858 Z= 0.171 Angle : 0.531 6.550 19738 Z= 0.319 Chirality : 0.035 0.154 2236 Planarity : 0.004 0.066 1658 Dihedral : 29.389 176.762 3828 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.01 % Allowed : 18.01 % Favored : 79.98 % 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 aren not related in a simple way. whole: 2.08 (0.27), residues: 1009 helix: 2.57 (0.21), residues: 640 sheet: -0.20 (0.78), residues: 36 loop : -0.89 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 39 TYR 0.039 0.002 TYR D 83 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 covalent geometry : bond 0.00381 (13858) covalent geometry : angle 0.53080 (19738) hydrogen bonds : bond 0.04053 ( 804) hydrogen bonds : angle 2.95786 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6518.85 seconds wall clock time: 111 minutes 17.32 seconds (6677.32 seconds total)