Starting phenix.real_space_refine on Thu Jul 31 01:40:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t9f_41109/07_2025/8t9f_41109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t9f_41109/07_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_41109/07_2025/8t9f_41109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t9f_41109/07_2025/8t9f_41109.map" model { file = "/net/cci-nas-00/data/ceres_data/8t9f_41109/07_2025/8t9f_41109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t9f_41109/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.95, per 1000 atoms: 0.61 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: 3.10 Conformation dependent library (CDL) restraints added in 1.1 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: 5.66 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: 5.07 Time building geometry restraints manager: 3.71 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: 2.640 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.180 Find NCS groups from input model: 0.300 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:10.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.640 ------------------------------------------------------------------------------- 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 : 1.175 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: 1.6860 time to fit residues: 404.2894 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 : 1.088 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.082662 restraints weight = 24297.350| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.63 r_work: 0.3238 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 : 1.179 Fit side-chains revert: symmetry clash REVERT: K 143 ARG cc_start: 0.6038 (ttp80) cc_final: 0.5717 (tmm160) REVERT: K 180 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8879 (mm-30) REVERT: K 187 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8815 (tpp80) REVERT: K 225 GLU cc_start: 0.8141 (pt0) cc_final: 0.7451 (tp30) REVERT: A 133 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: F 44 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8633 (mtpm) REVERT: G 25 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8784 (pp) REVERT: G 74 LYS cc_start: 0.8095 (tptt) cc_final: 0.7847 (mmmt) REVERT: D 42 TYR cc_start: 0.8427 (t80) cc_final: 0.8110 (t80) outliers start: 27 outliers final: 9 residues processed: 189 average time/residue: 1.6549 time to fit residues: 334.1525 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 : 1.039 ------------------------------------------------------------------------------- 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: 0.7980 chunk 77 optimal weight: 0.0040 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.114629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.079784 restraints weight = 24479.789| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.64 r_work: 0.3169 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1950 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= 0.243 Angle : 0.563 5.036 19738 Z= 0.337 Chirality : 0.038 0.137 2236 Planarity : 0.004 0.038 1658 Dihedral : 29.721 177.864 3828 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: 1.73 (0.27), residues: 1009 helix: 2.29 (0.21), residues: 646 sheet: -0.16 (0.73), residues: 42 loop : -1.13 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.006 0.001 HIS H 83 PHE 0.012 0.001 PHE K 281 TYR 0.015 0.002 TYR A 54 ARG 0.007 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.05192 ( 804) hydrogen bonds : angle 3.17840 ( 2064) covalent geometry : bond 0.00554 (13858) covalent geometry : angle 0.56333 (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 : 1.062 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8883 (mm-30) REVERT: K 225 GLU cc_start: 0.8283 (pt0) cc_final: 0.7527 (tp30) REVERT: A 133 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: F 44 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8691 (mtpp) REVERT: G 21 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8319 (tm-30) REVERT: G 74 LYS cc_start: 0.8166 (tptt) cc_final: 0.7931 (mmmt) REVERT: E 120 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8448 (mmm) REVERT: C 67 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8211 (tp30) REVERT: C 79 LYS cc_start: 0.8505 (mmtp) cc_final: 0.8203 (mmtm) REVERT: D 42 TYR cc_start: 0.8422 (t80) cc_final: 0.8125 (t80) outliers start: 26 outliers final: 11 residues processed: 180 average time/residue: 1.6286 time to fit residues: 312.8027 Evaluate side-chains 172 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 35 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 94 optimal weight: 0.0040 chunk 68 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.116980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.082731 restraints weight = 24460.708| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.63 r_work: 0.3240 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1962 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= 0.153 Angle : 0.512 6.711 19738 Z= 0.309 Chirality : 0.034 0.135 2236 Planarity : 0.004 0.044 1658 Dihedral : 29.477 178.023 3828 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.37 % Allowed : 15.40 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.21), residues: 639 sheet: -0.15 (0.74), residues: 42 loop : -1.00 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.006 0.001 PHE H 66 TYR 0.010 0.001 TYR B 88 ARG 0.007 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 804) hydrogen bonds : angle 2.91161 ( 2064) covalent geometry : bond 0.00339 (13858) covalent geometry : angle 0.51153 (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 195 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8884 (mm-30) REVERT: K 187 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8751 (tpp80) REVERT: K 225 GLU cc_start: 0.8220 (pt0) cc_final: 0.7442 (tp30) REVERT: A 133 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: F 44 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8662 (mtpp) REVERT: F 93 GLN cc_start: 0.8809 (mp10) cc_final: 0.8540 (mp10) REVERT: G 21 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8333 (tm-30) REVERT: G 25 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8825 (pp) REVERT: G 74 LYS cc_start: 0.8014 (tptt) cc_final: 0.7788 (mmmt) REVERT: C 79 LYS cc_start: 0.8498 (mmtp) cc_final: 0.8286 (mmtm) REVERT: D 42 TYR cc_start: 0.8412 (t80) cc_final: 0.8133 (t80) outliers start: 20 outliers final: 9 residues processed: 187 average time/residue: 1.6000 time to fit residues: 319.7785 Evaluate side-chains 179 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 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 86 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 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: 0.7980 chunk 21 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 GLN ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.116449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.081931 restraints weight = 24570.502| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.65 r_work: 0.3219 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2098 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= 0.168 Angle : 0.513 6.147 19738 Z= 0.309 Chirality : 0.034 0.139 2236 Planarity : 0.004 0.039 1658 Dihedral : 29.439 179.578 3828 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.25 % Allowed : 16.11 % 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: 2.09 (0.27), residues: 1009 helix: 2.57 (0.21), residues: 649 sheet: -0.14 (0.79), residues: 36 loop : -0.99 (0.32), residues: 324 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 H 66 TYR 0.033 0.002 TYR D 83 ARG 0.010 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 804) hydrogen bonds : angle 2.89537 ( 2064) covalent geometry : bond 0.00376 (13858) covalent geometry : angle 0.51323 (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 191 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8903 (mm-30) REVERT: K 187 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8734 (tpp80) REVERT: K 225 GLU cc_start: 0.8236 (pt0) cc_final: 0.7452 (tp30) REVERT: K 226 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8890 (mm) REVERT: A 133 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: F 44 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8659 (mtpm) REVERT: F 93 GLN cc_start: 0.8795 (mp10) cc_final: 0.8488 (mp10) REVERT: G 21 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8327 (tm-30) REVERT: G 25 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8847 (pp) REVERT: G 74 LYS cc_start: 0.8101 (tptt) cc_final: 0.7867 (mmmt) REVERT: C 67 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8156 (tp30) REVERT: D 42 TYR cc_start: 0.8373 (t80) cc_final: 0.8129 (t80) REVERT: D 83 TYR cc_start: 0.7692 (m-80) cc_final: 0.7317 (m-80) outliers start: 19 outliers final: 11 residues processed: 183 average time/residue: 1.6302 time to fit residues: 318.3210 Evaluate side-chains 182 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain K residue 226 LEU 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 45 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 67 GLU 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: 1.9990 chunk 103 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 72 optimal weight: 0.0770 chunk 57 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.116576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.082170 restraints weight = 24817.028| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.66 r_work: 0.3227 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2205 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= 0.163 Angle : 0.505 5.424 19738 Z= 0.304 Chirality : 0.034 0.139 2236 Planarity : 0.004 0.043 1658 Dihedral : 29.380 178.289 3828 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.50 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 (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: 2.14 (0.27), residues: 1009 helix: 2.61 (0.21), residues: 649 sheet: -0.14 (0.79), residues: 36 loop : -0.96 (0.32), residues: 324 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 H 66 TYR 0.021 0.001 TYR D 83 ARG 0.012 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 804) hydrogen bonds : angle 2.85558 ( 2064) covalent geometry : bond 0.00364 (13858) covalent geometry : angle 0.50455 (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 187 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8912 (mm-30) REVERT: K 225 GLU cc_start: 0.8270 (pt0) cc_final: 0.7460 (tp30) REVERT: K 226 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8891 (mm) REVERT: A 133 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: F 44 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8676 (mtpm) REVERT: F 93 GLN cc_start: 0.8804 (mp10) cc_final: 0.8590 (mp10) REVERT: G 21 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8333 (tm-30) REVERT: G 25 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8831 (pp) REVERT: G 74 LYS cc_start: 0.8019 (tptt) cc_final: 0.7798 (mmmt) REVERT: D 42 TYR cc_start: 0.8349 (t80) cc_final: 0.8101 (t80) outliers start: 15 outliers final: 12 residues processed: 181 average time/residue: 1.6949 time to fit residues: 327.2454 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 : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU 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 45 THR 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 53 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 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 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 = 0.116464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.082502 restraints weight = 24709.894| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.63 r_work: 0.3232 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2301 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= 0.167 Angle : 0.516 7.931 19738 Z= 0.309 Chirality : 0.034 0.140 2236 Planarity : 0.004 0.051 1658 Dihedral : 29.335 177.839 3828 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.49 % Allowed : 16.71 % 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: 2.14 (0.27), residues: 1009 helix: 2.60 (0.20), residues: 649 sheet: -0.13 (0.79), residues: 36 loop : -0.94 (0.32), residues: 324 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 H 66 TYR 0.021 0.001 TYR K 92 ARG 0.011 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 804) hydrogen bonds : angle 2.85955 ( 2064) covalent geometry : bond 0.00374 (13858) covalent geometry : angle 0.51608 (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 189 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8918 (mm-30) REVERT: K 225 GLU cc_start: 0.8218 (pt0) cc_final: 0.7456 (tp30) REVERT: K 226 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8884 (mm) REVERT: A 133 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: F 44 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8688 (mtpm) REVERT: F 93 GLN cc_start: 0.8794 (mp10) cc_final: 0.8567 (mp10) REVERT: G 21 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8318 (tm-30) REVERT: G 25 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8827 (pp) REVERT: G 74 LYS cc_start: 0.8026 (tptt) cc_final: 0.7800 (mmmt) REVERT: E 115 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8092 (mptt) REVERT: C 67 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8160 (tp30) REVERT: D 42 TYR cc_start: 0.8369 (t80) cc_final: 0.8115 (t80) outliers start: 21 outliers final: 13 residues processed: 178 average time/residue: 2.1063 time to fit residues: 400.4903 Evaluate side-chains 185 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU 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 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: 0.9990 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 278 ASN K 316 ASN E 68 GLN D 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.113394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.078657 restraints weight = 24559.108| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.64 r_work: 0.3148 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13858 Z= 0.297 Angle : 0.587 6.265 19738 Z= 0.349 Chirality : 0.039 0.142 2236 Planarity : 0.005 0.059 1658 Dihedral : 29.592 174.561 3828 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.37 % Allowed : 16.94 % Favored : 80.69 % 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: 1.77 (0.26), residues: 1009 helix: 2.32 (0.20), residues: 646 sheet: -0.33 (0.77), residues: 36 loop : -1.08 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 264 HIS 0.005 0.001 HIS H 83 PHE 0.010 0.001 PHE K 281 TYR 0.023 0.002 TYR D 83 ARG 0.012 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.05662 ( 804) hydrogen bonds : angle 3.14913 ( 2064) covalent geometry : bond 0.00678 (13858) covalent geometry : angle 0.58676 (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 173 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.033 Fit side-chains REVERT: K 180 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8936 (mm-30) REVERT: K 187 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8768 (tpp80) REVERT: K 225 GLU cc_start: 0.8393 (pt0) cc_final: 0.7666 (tp30) REVERT: F 44 LYS cc_start: 0.9008 (mtpt) cc_final: 0.8766 (mtpp) REVERT: G 21 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8260 (tm-30) REVERT: G 74 LYS cc_start: 0.8177 (tptt) cc_final: 0.7915 (mmmt) REVERT: C 67 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8223 (tp30) REVERT: D 42 TYR cc_start: 0.8325 (t80) cc_final: 0.8124 (t80) outliers start: 20 outliers final: 13 residues processed: 165 average time/residue: 1.8124 time to fit residues: 317.9584 Evaluate side-chains 166 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 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: 0.7980 chunk 121 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 113 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.115082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.080780 restraints weight = 24406.321| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.59 r_work: 0.3197 rms_B_bonded: 2.84 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: 0.8537 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13858 Z= 0.162 Angle : 0.546 7.013 19738 Z= 0.328 Chirality : 0.035 0.167 2236 Planarity : 0.004 0.068 1658 Dihedral : 29.577 175.436 3828 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.78 % Allowed : 17.77 % Favored : 80.45 % 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: 2.45 (0.20), residues: 646 sheet: -0.29 (0.78), residues: 36 loop : -1.03 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.003 0.001 HIS K 98 PHE 0.006 0.001 PHE H 66 TYR 0.022 0.002 TYR H 84 ARG 0.014 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 804) hydrogen bonds : angle 3.04126 ( 2064) covalent geometry : bond 0.00356 (13858) covalent geometry : angle 0.54552 (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 179 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 1.114 Fit side-chains REVERT: K 180 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8900 (mm-30) REVERT: K 187 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8808 (tpp80) REVERT: K 225 GLU cc_start: 0.8328 (pt0) cc_final: 0.7581 (tp30) REVERT: F 44 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8722 (mtpp) REVERT: F 93 GLN cc_start: 0.8766 (mp10) cc_final: 0.8520 (mp10) REVERT: G 21 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8336 (tm-30) REVERT: G 74 LYS cc_start: 0.8181 (tptt) cc_final: 0.7918 (mmmt) REVERT: C 67 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8174 (tp30) REVERT: D 42 TYR cc_start: 0.8366 (t80) cc_final: 0.8113 (t80) outliers start: 15 outliers final: 13 residues processed: 172 average time/residue: 1.8968 time to fit residues: 347.1549 Evaluate side-chains 174 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 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: 0.2980 chunk 4 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 97 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.115086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.080546 restraints weight = 24430.257| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.63 r_work: 0.3190 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2520 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 : 0.544 6.408 19738 Z= 0.326 Chirality : 0.036 0.155 2236 Planarity : 0.004 0.066 1658 Dihedral : 29.447 176.264 3828 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.78 % Allowed : 18.25 % 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 (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: 2.52 (0.20), residues: 646 sheet: -0.30 (0.78), residues: 36 loop : -1.00 (0.32), residues: 327 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 0.007 0.001 PHE H 66 TYR 0.023 0.002 TYR K 92 ARG 0.016 0.001 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 804) hydrogen bonds : angle 2.97100 ( 2064) covalent geometry : bond 0.00442 (13858) covalent geometry : angle 0.54369 (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 175 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 1.186 Fit side-chains REVERT: K 180 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8908 (mm-30) REVERT: K 225 GLU cc_start: 0.8375 (pt0) cc_final: 0.7590 (tp30) REVERT: F 44 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8725 (mtpp) REVERT: F 93 GLN cc_start: 0.8783 (mp10) cc_final: 0.8556 (mp10) REVERT: G 21 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8268 (tm-30) REVERT: G 74 LYS cc_start: 0.8134 (tptt) cc_final: 0.7869 (mmmt) REVERT: H 80 ARG cc_start: 0.8743 (ttm110) cc_final: 0.8436 (ttp80) REVERT: C 67 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8178 (tp30) REVERT: D 42 TYR cc_start: 0.8351 (t80) cc_final: 0.8135 (t80) outliers start: 15 outliers final: 13 residues processed: 169 average time/residue: 1.7677 time to fit residues: 317.6673 Evaluate side-chains 172 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 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: 2.9990 chunk 66 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.115465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.081118 restraints weight = 24567.487| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.62 r_work: 0.3204 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13858 Z= 0.171 Angle : 0.540 6.755 19738 Z= 0.323 Chirality : 0.035 0.144 2236 Planarity : 0.004 0.067 1658 Dihedral : 29.442 176.485 3828 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.66 % Allowed : 18.48 % Favored : 79.86 % 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: 2.08 (0.27), residues: 1009 helix: 2.60 (0.20), residues: 640 sheet: -0.26 (0.78), residues: 36 loop : -0.97 (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 0.007 0.001 PHE H 66 TYR 0.025 0.001 TYR H 84 ARG 0.015 0.000 ARG C 39 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 804) hydrogen bonds : angle 2.95284 ( 2064) covalent geometry : bond 0.00383 (13858) covalent geometry : angle 0.53970 (19738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13238.68 seconds wall clock time: 229 minutes 54.38 seconds (13794.38 seconds total)