Starting phenix.real_space_refine on Thu May 15 09:32:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t9f_41109/05_2025/8t9f_41109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t9f_41109/05_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_41109/05_2025/8t9f_41109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t9f_41109/05_2025/8t9f_41109.map" model { file = "/net/cci-nas-00/data/ceres_data/8t9f_41109/05_2025/8t9f_41109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t9f_41109/05_2025/8t9f_41109.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} 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: 8.17, per 1000 atoms: 0.62 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: 3.57 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 6.57 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: 6.41 Time building geometry restraints manager: 4.14 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: 1.480 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.580 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (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 TRP 0.002 0.001 TRP K 264 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE H 66 TYR 0.009 0.001 TYR E 54 ARG 0.002 0.000 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.10964 ( 804) hydrogen bonds : angle 4.16749 ( 2064) covalent geometry : bond 0.00394 (13858) covalent geometry : angle 0.58902 (19738) *********************** 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 : 1.041 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: 0.8473 (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: 1.5522 time to fit residues: 372.4533 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 : 1.040 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 GLN K 207 GLN K 272 ASN K 273 HIS ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4026 r_free = 0.4026 target = 0.117108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.082663 restraints weight = 24297.350| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.63 r_work: 0.3239 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1446 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= 0.173 Angle : 0.530 8.541 19738 Z= 0.317 Chirality : 0.035 0.144 2236 Planarity : 0.004 0.036 1658 Dihedral : 29.557 178.438 3830 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.20 % Allowed : 13.98 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.26), residues: 1009 helix: 2.34 (0.21), residues: 638 sheet: -0.03 (0.70), residues: 44 loop : -1.00 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.007 0.001 HIS H 83 PHE 0.009 0.001 PHE K 332 TYR 0.010 0.001 TYR K 306 ARG 0.007 0.001 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 804) hydrogen bonds : angle 3.15986 ( 2064) covalent geometry : bond 0.00386 (13858) covalent geometry : angle 0.53009 (19738) *********************** 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 199 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: K 143 ARG cc_start: 0.6052 (ttp80) cc_final: 0.5727 (tmm160) REVERT: K 180 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8878 (mm-30) REVERT: K 187 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8818 (tpp80) REVERT: K 225 GLU cc_start: 0.8140 (pt0) cc_final: 0.7453 (tp30) REVERT: A 133 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: F 44 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8634 (mtpm) REVERT: G 25 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8785 (pp) REVERT: G 74 LYS cc_start: 0.8095 (tptt) cc_final: 0.7847 (mmmt) REVERT: D 42 TYR cc_start: 0.8426 (t80) cc_final: 0.8110 (t80) outliers start: 27 outliers final: 9 residues processed: 189 average time/residue: 1.5926 time to fit residues: 321.9954 Evaluate side-chains 177 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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 57 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.114322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.079471 restraints weight = 24481.050| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.63 r_work: 0.3163 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13858 Z= 0.259 Angle : 0.571 5.046 19738 Z= 0.342 Chirality : 0.038 0.137 2236 Planarity : 0.004 0.038 1658 Dihedral : 29.744 177.650 3828 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.08 % Allowed : 15.28 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.26), residues: 1009 helix: 2.25 (0.21), residues: 646 sheet: -0.15 (0.73), residues: 42 loop : -1.14 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 PHE 0.013 0.001 PHE K 281 TYR 0.015 0.002 TYR A 54 ARG 0.006 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.05326 ( 804) hydrogen bonds : angle 3.20795 ( 2064) covalent geometry : bond 0.00590 (13858) covalent geometry : angle 0.57122 (19738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8892 (mm-30) REVERT: K 225 GLU cc_start: 0.8297 (pt0) cc_final: 0.7537 (tp30) REVERT: A 133 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: F 24 ASP cc_start: 0.7636 (t0) cc_final: 0.7424 (t0) REVERT: F 44 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8689 (mtpp) REVERT: G 21 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8308 (tm-30) REVERT: G 25 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8946 (pp) REVERT: G 74 LYS cc_start: 0.8155 (tptt) cc_final: 0.7915 (mmmt) REVERT: E 120 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8451 (mmm) REVERT: C 67 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8207 (tp30) REVERT: C 74 LYS cc_start: 0.7373 (tppt) cc_final: 0.7152 (tppt) REVERT: C 79 LYS cc_start: 0.8530 (mmtp) cc_final: 0.8241 (mmtm) REVERT: D 42 TYR cc_start: 0.8427 (t80) cc_final: 0.8127 (t80) outliers start: 26 outliers final: 11 residues processed: 181 average time/residue: 1.5957 time to fit residues: 308.2098 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 : 1.071 ------------------------------------------------------------------------------- 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 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 109 VAL Chi-restraints excluded: chain C residue 118 ILE 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 28 optimal weight: 8.9990 chunk 112 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 94 optimal weight: 0.0670 chunk 68 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.116493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.082200 restraints weight = 24368.057| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.62 r_work: 0.3232 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13858 Z= 0.143 Angle : 0.530 7.496 19738 Z= 0.319 Chirality : 0.035 0.185 2236 Planarity : 0.004 0.057 1658 Dihedral : 29.691 177.628 3828 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.49 % Allowed : 15.05 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.27), residues: 1009 helix: 2.47 (0.21), residues: 639 sheet: -0.17 (0.74), residues: 42 loop : -1.03 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.007 0.001 PHE K 281 TYR 0.012 0.001 TYR B 88 ARG 0.009 0.001 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 804) hydrogen bonds : angle 3.03267 ( 2064) covalent geometry : bond 0.00306 (13858) covalent geometry : angle 0.52982 (19738) *********************** 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 197 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8884 (mm-30) REVERT: K 225 GLU cc_start: 0.8246 (pt0) cc_final: 0.7498 (tp30) REVERT: A 133 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: F 44 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8682 (mtpp) REVERT: F 93 GLN cc_start: 0.8789 (mp10) cc_final: 0.8534 (mp10) REVERT: G 21 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8289 (tm-30) REVERT: G 74 LYS cc_start: 0.8133 (tptt) cc_final: 0.7876 (mmmt) REVERT: C 67 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8174 (tp30) REVERT: C 74 LYS cc_start: 0.7163 (tppt) cc_final: 0.6901 (tppt) REVERT: C 79 LYS cc_start: 0.8504 (mmtp) cc_final: 0.8272 (mmtm) REVERT: D 42 TYR cc_start: 0.8357 (t80) cc_final: 0.8066 (t80) outliers start: 21 outliers final: 12 residues processed: 190 average time/residue: 1.5712 time to fit residues: 319.0730 Evaluate side-chains 181 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.114957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.080168 restraints weight = 24489.567| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.65 r_work: 0.3182 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2089 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= 0.217 Angle : 0.541 5.449 19738 Z= 0.325 Chirality : 0.036 0.136 2236 Planarity : 0.004 0.047 1658 Dihedral : 29.605 177.387 3828 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.25 % Allowed : 15.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.27), residues: 1009 helix: 2.45 (0.21), residues: 646 sheet: -0.29 (0.72), residues: 42 loop : -1.09 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 264 HIS 0.005 0.001 HIS H 83 PHE 0.008 0.001 PHE H 66 TYR 0.019 0.002 TYR D 83 ARG 0.009 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04741 ( 804) hydrogen bonds : angle 3.05488 ( 2064) covalent geometry : bond 0.00491 (13858) covalent geometry : angle 0.54068 (19738) *********************** 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 183 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8910 (mm-30) REVERT: K 225 GLU cc_start: 0.8272 (pt0) cc_final: 0.7490 (tp30) REVERT: A 133 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: F 44 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8708 (mtpp) REVERT: G 21 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8300 (tm-30) REVERT: G 74 LYS cc_start: 0.8171 (tptt) cc_final: 0.7926 (mmmt) REVERT: E 133 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: C 74 LYS cc_start: 0.7067 (tppt) cc_final: 0.6783 (tppt) REVERT: C 79 LYS cc_start: 0.8580 (mmtp) cc_final: 0.8325 (mmtm) REVERT: D 42 TYR cc_start: 0.8409 (t80) cc_final: 0.8155 (t80) REVERT: D 83 TYR cc_start: 0.7803 (m-80) cc_final: 0.7441 (m-80) outliers start: 19 outliers final: 12 residues processed: 176 average time/residue: 1.5842 time to fit residues: 297.8073 Evaluate side-chains 178 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 E residue 45 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 133 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 21 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.115633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.081044 restraints weight = 24613.607| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.65 r_work: 0.3201 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2084 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= 0.162 Angle : 0.527 5.357 19738 Z= 0.318 Chirality : 0.035 0.139 2236 Planarity : 0.004 0.048 1658 Dihedral : 29.611 177.510 3828 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.37 % Allowed : 15.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.27), residues: 1009 helix: 2.48 (0.21), residues: 646 sheet: -0.21 (0.77), residues: 36 loop : -1.07 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.003 0.001 HIS H 83 PHE 0.007 0.001 PHE F 61 TYR 0.023 0.002 TYR H 84 ARG 0.016 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 804) hydrogen bonds : angle 3.02832 ( 2064) covalent geometry : bond 0.00358 (13858) covalent geometry : angle 0.52676 (19738) *********************** 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 188 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8909 (mm-30) REVERT: K 225 GLU cc_start: 0.8262 (pt0) cc_final: 0.7466 (tp30) REVERT: A 133 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: F 44 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8704 (mtpp) REVERT: G 21 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8311 (tm-30) REVERT: G 25 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8874 (pp) REVERT: G 74 LYS cc_start: 0.8152 (tptt) cc_final: 0.7911 (mmmt) REVERT: E 115 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8220 (mptt) REVERT: C 67 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8159 (tp30) REVERT: C 74 LYS cc_start: 0.7161 (tppt) cc_final: 0.6873 (tppt) REVERT: C 79 LYS cc_start: 0.8546 (mmtp) cc_final: 0.8329 (mmtm) REVERT: D 42 TYR cc_start: 0.8383 (t80) cc_final: 0.8149 (t80) outliers start: 20 outliers final: 14 residues processed: 181 average time/residue: 1.6667 time to fit residues: 323.1798 Evaluate side-chains 178 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS 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 H residue 79 SER Chi-restraints excluded: chain E residue 45 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.115960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.081368 restraints weight = 24532.704| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.65 r_work: 0.3210 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2113 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= 0.166 Angle : 0.522 5.460 19738 Z= 0.314 Chirality : 0.035 0.148 2236 Planarity : 0.004 0.057 1658 Dihedral : 29.564 177.724 3828 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.37 % Allowed : 15.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.27), residues: 1009 helix: 2.52 (0.21), residues: 646 sheet: -0.16 (0.77), residues: 36 loop : -1.05 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 PHE 0.007 0.001 PHE F 61 TYR 0.020 0.001 TYR H 84 ARG 0.011 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 804) hydrogen bonds : angle 2.97559 ( 2064) covalent geometry : bond 0.00370 (13858) covalent geometry : angle 0.52152 (19738) *********************** 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 184 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8915 (mm-30) REVERT: K 225 GLU cc_start: 0.8290 (pt0) cc_final: 0.7471 (tp30) REVERT: A 133 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: F 44 LYS cc_start: 0.8938 (mtpt) cc_final: 0.8702 (mtpp) REVERT: G 21 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8300 (tm-30) REVERT: G 25 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8877 (pp) REVERT: G 74 LYS cc_start: 0.8136 (tptt) cc_final: 0.7893 (mmmt) REVERT: E 115 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8214 (mptt) REVERT: C 67 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: C 74 LYS cc_start: 0.7101 (tppt) cc_final: 0.6815 (tppt) REVERT: C 79 LYS cc_start: 0.8549 (mmtp) cc_final: 0.8337 (mmtm) REVERT: D 42 TYR cc_start: 0.8373 (t80) cc_final: 0.8136 (t80) outliers start: 20 outliers final: 15 residues processed: 176 average time/residue: 1.6906 time to fit residues: 318.1461 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 : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS 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 45 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 278 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.114111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.079411 restraints weight = 24408.103| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.63 r_work: 0.3167 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2329 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= 0.241 Angle : 0.555 5.546 19738 Z= 0.332 Chirality : 0.037 0.145 2236 Planarity : 0.004 0.054 1658 Dihedral : 29.610 177.224 3828 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.01 % Allowed : 16.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.27), residues: 1009 helix: 2.38 (0.21), residues: 646 sheet: -0.30 (0.76), residues: 36 loop : -1.08 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 264 HIS 0.006 0.001 HIS H 83 PHE 0.008 0.001 PHE K 281 TYR 0.023 0.002 TYR K 92 ARG 0.012 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 804) hydrogen bonds : angle 3.08734 ( 2064) covalent geometry : bond 0.00548 (13858) covalent geometry : angle 0.55501 (19738) *********************** 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 174 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 1.044 Fit side-chains REVERT: K 180 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8923 (mm-30) REVERT: K 225 GLU cc_start: 0.8387 (pt0) cc_final: 0.7595 (tp30) REVERT: A 133 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: F 44 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8726 (mtpp) REVERT: G 21 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8247 (tm-30) REVERT: G 25 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8936 (pp) REVERT: G 74 LYS cc_start: 0.8174 (tptt) cc_final: 0.7921 (mmmt) REVERT: H 80 ARG cc_start: 0.8765 (ttm110) cc_final: 0.8515 (ttp80) REVERT: E 115 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8292 (mptt) REVERT: C 67 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8191 (tp30) REVERT: C 74 LYS cc_start: 0.7377 (tppt) cc_final: 0.7099 (tppt) REVERT: D 42 TYR cc_start: 0.8396 (t80) cc_final: 0.8140 (t80) outliers start: 17 outliers final: 14 residues processed: 167 average time/residue: 1.7092 time to fit residues: 303.4072 Evaluate side-chains 172 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 45 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.115342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.080788 restraints weight = 24374.090| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.63 r_work: 0.3201 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2320 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= 0.166 Angle : 0.541 7.202 19738 Z= 0.325 Chirality : 0.035 0.155 2236 Planarity : 0.004 0.063 1658 Dihedral : 29.581 175.636 3828 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.25 % Allowed : 16.35 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.27), residues: 1009 helix: 2.55 (0.21), residues: 640 sheet: -0.24 (0.77), residues: 36 loop : -1.07 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.002 0.001 HIS K 98 PHE 0.007 0.001 PHE H 66 TYR 0.025 0.002 TYR H 84 ARG 0.014 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 804) hydrogen bonds : angle 3.00477 ( 2064) covalent geometry : bond 0.00369 (13858) covalent geometry : angle 0.54124 (19738) *********************** 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: 19 poor density : 164 time to evaluate : 1.138 Fit side-chains REVERT: K 180 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8923 (mm-30) REVERT: K 225 GLU cc_start: 0.8358 (pt0) cc_final: 0.7497 (tp30) REVERT: A 133 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: F 44 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8719 (mtpp) REVERT: G 21 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8242 (tm-30) REVERT: G 25 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8911 (pp) REVERT: G 74 LYS cc_start: 0.8189 (tptt) cc_final: 0.7943 (mmmt) REVERT: H 80 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8525 (ttp80) REVERT: E 115 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8223 (mptt) REVERT: C 67 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8186 (tp30) REVERT: C 74 LYS cc_start: 0.7070 (tppt) cc_final: 0.6825 (tppt) REVERT: D 42 TYR cc_start: 0.8386 (t80) cc_final: 0.8135 (t80) outliers start: 19 outliers final: 14 residues processed: 174 average time/residue: 1.6253 time to fit residues: 302.0386 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 : 1.192 ------------------------------------------------------------------------------- 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 45 THR 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 117 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.115142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.080496 restraints weight = 24406.153| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.65 r_work: 0.3196 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2379 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= 0.196 Angle : 0.539 6.421 19738 Z= 0.323 Chirality : 0.036 0.151 2236 Planarity : 0.004 0.060 1658 Dihedral : 29.435 176.636 3828 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.13 % Allowed : 16.47 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.27), residues: 1009 helix: 2.57 (0.20), residues: 640 sheet: -0.26 (0.77), residues: 36 loop : -1.05 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.008 0.001 PHE H 66 TYR 0.023 0.002 TYR H 84 ARG 0.014 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 804) hydrogen bonds : angle 2.96799 ( 2064) covalent geometry : bond 0.00442 (13858) covalent geometry : angle 0.53937 (19738) ********************** 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 172 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 1.156 Fit side-chains REVERT: K 180 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8929 (mm-30) REVERT: K 225 GLU cc_start: 0.8348 (pt0) cc_final: 0.7499 (tp30) REVERT: A 133 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: F 44 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8678 (mtpm) REVERT: G 21 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8251 (tm-30) REVERT: G 25 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8895 (pp) REVERT: G 74 LYS cc_start: 0.8113 (tptt) cc_final: 0.7853 (mmmt) REVERT: H 80 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8539 (ttp80) REVERT: E 115 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8134 (mptt) REVERT: C 67 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8191 (tp30) REVERT: D 42 TYR cc_start: 0.8408 (t80) cc_final: 0.8150 (t80) outliers start: 18 outliers final: 14 residues processed: 165 average time/residue: 1.7035 time to fit residues: 299.2572 Evaluate side-chains 170 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 45 THR 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 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 23 optimal weight: 0.0170 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.115814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.081381 restraints weight = 24599.556| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.64 r_work: 0.3212 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2384 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= 0.160 Angle : 0.539 8.783 19738 Z= 0.322 Chirality : 0.035 0.144 2236 Planarity : 0.004 0.066 1658 Dihedral : 29.434 176.835 3828 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.13 % Allowed : 17.06 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.27), residues: 1009 helix: 2.58 (0.20), residues: 640 sheet: -0.21 (0.78), residues: 36 loop : -1.02 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 PHE 0.007 0.001 PHE F 61 TYR 0.052 0.002 TYR D 83 ARG 0.014 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 804) hydrogen bonds : angle 2.94562 ( 2064) covalent geometry : bond 0.00355 (13858) covalent geometry : angle 0.53886 (19738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12309.44 seconds wall clock time: 211 minutes 14.13 seconds (12674.13 seconds total)