Starting phenix.real_space_refine on Mon Dec 30 11:15:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t9f_41109/12_2024/8t9f_41109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t9f_41109/12_2024/8t9f_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_41109/12_2024/8t9f_41109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t9f_41109/12_2024/8t9f_41109.map" model { file = "/net/cci-nas-00/data/ceres_data/8t9f_41109/12_2024/8t9f_41109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t9f_41109/12_2024/8t9f_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-5532/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: 8.10, 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: 3.27 Conformation dependent library (CDL) restraints added in 1.2 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: 5.76 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: 5.83 Time building geometry restraints manager: 3.75 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: 2.870 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.490 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.220 ------------------------------------------------------------------------------- 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= 0.221 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 *********************** 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 : 1.071 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: 1.6859 time to fit residues: 404.5776 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 : 1.209 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 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= 0.213 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 *********************** 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 : 1.032 Fit side-chains revert: symmetry clash REVERT: K 143 ARG cc_start: 0.5947 (ttp80) cc_final: 0.5642 (tmm160) REVERT: K 187 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8770 (tpp80) REVERT: K 225 GLU cc_start: 0.7771 (pt0) cc_final: 0.7378 (tp30) REVERT: A 133 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: F 44 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8427 (mtpm) REVERT: G 25 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8865 (pp) REVERT: G 74 LYS cc_start: 0.8115 (tptt) cc_final: 0.7878 (mmmt) REVERT: D 42 TYR cc_start: 0.8152 (t80) cc_final: 0.7939 (t80) outliers start: 27 outliers final: 9 residues processed: 189 average time/residue: 1.6853 time to fit residues: 339.9039 Evaluate side-chains 176 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 62 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1871 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= 0.287 Angle : 0.549 5.071 19738 Z= 0.329 Chirality : 0.037 0.139 2236 Planarity : 0.004 0.038 1658 Dihedral : 29.659 178.010 3828 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.84 % Allowed : 15.40 % 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: 1.80 (0.27), residues: 1009 helix: 2.34 (0.21), residues: 646 sheet: -0.11 (0.73), residues: 42 loop : -1.09 (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 0.010 0.001 PHE K 281 TYR 0.013 0.002 TYR A 54 ARG 0.006 0.001 ARG C 39 *********************** 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 191 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: K 187 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8701 (tpp80) REVERT: K 225 GLU cc_start: 0.7911 (pt0) cc_final: 0.7430 (tp30) REVERT: A 133 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: F 44 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8447 (mtpp) REVERT: G 21 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8099 (tm-30) REVERT: G 74 LYS cc_start: 0.8185 (tptt) cc_final: 0.7968 (mmmt) REVERT: E 120 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8509 (mmm) REVERT: C 67 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: C 74 LYS cc_start: 0.7423 (tppt) cc_final: 0.7223 (tppt) REVERT: C 79 LYS cc_start: 0.8339 (mmtp) cc_final: 0.8061 (mmtm) outliers start: 24 outliers final: 10 residues processed: 181 average time/residue: 1.6958 time to fit residues: 327.1203 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 : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1890 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= 0.213 Angle : 0.535 8.003 19738 Z= 0.322 Chirality : 0.035 0.187 2236 Planarity : 0.004 0.048 1658 Dihedral : 29.636 177.810 3828 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.37 % Allowed : 15.64 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.48 (0.21), residues: 639 sheet: -0.21 (0.73), residues: 42 loop : -1.03 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 264 HIS 0.003 0.001 HIS H 83 PHE 0.007 0.001 PHE H 66 TYR 0.016 0.001 TYR H 84 ARG 0.008 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: K 187 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8784 (tpp80) REVERT: K 225 GLU cc_start: 0.7880 (pt0) cc_final: 0.7416 (tp30) REVERT: K 226 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8829 (mm) REVERT: A 133 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: F 44 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8470 (mtpp) REVERT: G 21 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8130 (tm-30) REVERT: G 25 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8909 (pp) REVERT: G 74 LYS cc_start: 0.8164 (tptt) cc_final: 0.7929 (mmmt) REVERT: C 67 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7904 (tp30) REVERT: C 74 LYS cc_start: 0.7300 (tppt) cc_final: 0.7031 (tppt) REVERT: C 79 LYS cc_start: 0.8378 (mmtp) cc_final: 0.8176 (mmtm) outliers start: 20 outliers final: 11 residues processed: 179 average time/residue: 1.7344 time to fit residues: 331.1255 Evaluate side-chains 179 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 86 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 106 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2143 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= 0.279 Angle : 0.540 4.913 19738 Z= 0.324 Chirality : 0.036 0.135 2236 Planarity : 0.004 0.041 1658 Dihedral : 29.582 177.188 3828 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.37 % Allowed : 16.11 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.27), residues: 1009 helix: 2.41 (0.20), residues: 646 sheet: -0.31 (0.73), residues: 42 loop : -1.10 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 PHE 0.008 0.001 PHE K 281 TYR 0.022 0.002 TYR K 92 ARG 0.010 0.001 ARG C 39 *********************** 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 184 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.249 Fit side-chains REVERT: K 187 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8726 (tpp80) REVERT: K 225 GLU cc_start: 0.7963 (pt0) cc_final: 0.7441 (tp30) REVERT: A 133 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: G 21 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8134 (tm-30) REVERT: G 25 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8959 (pp) REVERT: G 74 LYS cc_start: 0.8192 (tptt) cc_final: 0.7943 (mmmt) REVERT: H 80 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8306 (ttp80) REVERT: C 67 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7915 (tp30) outliers start: 20 outliers final: 13 residues processed: 176 average time/residue: 1.7684 time to fit residues: 331.6943 Evaluate side-chains 178 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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 42 TYR 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 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2157 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= 0.210 Angle : 0.528 6.687 19738 Z= 0.318 Chirality : 0.035 0.161 2236 Planarity : 0.004 0.054 1658 Dihedral : 29.553 178.692 3828 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.61 % Allowed : 16.23 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.99 (0.27), residues: 1009 helix: 2.53 (0.21), residues: 646 sheet: -0.23 (0.77), residues: 36 loop : -1.06 (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 0.015 0.001 TYR H 84 ARG 0.010 0.000 ARG C 39 *********************** 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 189 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 1.129 Fit side-chains REVERT: K 225 GLU cc_start: 0.7969 (pt0) cc_final: 0.7425 (tp30) REVERT: A 133 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: G 21 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8137 (tm-30) REVERT: G 25 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8951 (pp) REVERT: G 74 LYS cc_start: 0.8187 (tptt) cc_final: 0.7945 (mmmt) REVERT: H 80 ARG cc_start: 0.8524 (ttm110) cc_final: 0.8311 (ttp80) outliers start: 22 outliers final: 14 residues processed: 183 average time/residue: 1.7624 time to fit residues: 343.5295 Evaluate side-chains 176 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 42 TYR 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 13 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.0570 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2248 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= 0.194 Angle : 0.512 5.829 19738 Z= 0.308 Chirality : 0.034 0.148 2236 Planarity : 0.004 0.056 1658 Dihedral : 29.403 177.970 3828 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.37 % Allowed : 16.71 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.20), residues: 649 sheet: -0.21 (0.78), residues: 36 loop : -0.98 (0.32), residues: 324 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 0.016 0.001 TYR H 84 ARG 0.012 0.000 ARG C 39 *********************** 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 191 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 1.215 Fit side-chains REVERT: K 225 GLU cc_start: 0.7985 (pt0) cc_final: 0.7382 (tp30) REVERT: A 133 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: G 21 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8111 (tm-30) REVERT: G 25 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8880 (pp) REVERT: G 74 LYS cc_start: 0.8091 (tptt) cc_final: 0.7851 (mmmt) REVERT: E 115 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8106 (mptt) REVERT: C 67 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7841 (tp30) outliers start: 20 outliers final: 14 residues processed: 182 average time/residue: 1.7540 time to fit residues: 341.3822 Evaluate side-chains 182 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.0270 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2326 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= 0.190 Angle : 0.518 6.547 19738 Z= 0.310 Chirality : 0.034 0.148 2236 Planarity : 0.004 0.059 1658 Dihedral : 29.341 177.912 3828 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.37 % Allowed : 16.82 % 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: 2.12 (0.27), residues: 1009 helix: 2.58 (0.20), residues: 649 sheet: -0.18 (0.74), residues: 42 loop : -0.95 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 PHE 0.006 0.001 PHE F 61 TYR 0.020 0.002 TYR D 83 ARG 0.013 0.000 ARG C 39 *********************** 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 186 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.130 Fit side-chains REVERT: K 225 GLU cc_start: 0.8000 (pt0) cc_final: 0.7393 (tp30) REVERT: A 133 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: G 21 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8137 (tm-30) REVERT: G 25 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8886 (pp) REVERT: G 74 LYS cc_start: 0.8071 (tptt) cc_final: 0.7833 (mmmt) REVERT: E 115 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8106 (mptt) REVERT: C 67 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7835 (tp30) outliers start: 20 outliers final: 14 residues processed: 177 average time/residue: 1.7217 time to fit residues: 325.3944 Evaluate side-chains 181 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 42 TYR 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 103 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 113 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN C 21 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2385 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= 0.187 Angle : 0.516 5.710 19738 Z= 0.309 Chirality : 0.034 0.147 2236 Planarity : 0.004 0.062 1658 Dihedral : 29.277 178.210 3828 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.90 % Allowed : 17.65 % 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: 2.16 (0.27), residues: 1009 helix: 2.63 (0.21), residues: 642 sheet: -0.18 (0.79), residues: 36 loop : -0.88 (0.32), residues: 331 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 0.006 0.001 PHE F 61 TYR 0.021 0.002 TYR K 92 ARG 0.014 0.000 ARG C 39 *********************** 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 184 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.938 Fit side-chains REVERT: K 225 GLU cc_start: 0.7998 (pt0) cc_final: 0.7386 (tp30) REVERT: A 133 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: G 21 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8142 (tm-30) REVERT: G 25 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8891 (pp) REVERT: G 74 LYS cc_start: 0.8016 (tptt) cc_final: 0.7804 (mmmt) REVERT: E 115 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8105 (mptt) REVERT: C 67 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7830 (tp30) outliers start: 16 outliers final: 13 residues processed: 176 average time/residue: 1.7267 time to fit residues: 323.8884 Evaluate side-chains 180 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2424 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= 0.227 Angle : 0.541 10.018 19738 Z= 0.321 Chirality : 0.035 0.150 2236 Planarity : 0.004 0.060 1658 Dihedral : 29.303 177.600 3828 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.01 % Allowed : 17.89 % Favored : 80.09 % 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: 2.51 (0.20), residues: 649 sheet: -0.28 (0.78), residues: 36 loop : -0.93 (0.32), residues: 324 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 H 66 TYR 0.024 0.002 TYR H 84 ARG 0.015 0.000 ARG C 39 ********************** 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: 17 poor density : 155 time to evaluate : 1.111 Fit side-chains REVERT: K 225 GLU cc_start: 0.8037 (pt0) cc_final: 0.7402 (tp30) REVERT: A 133 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: G 21 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8074 (tm-30) REVERT: G 25 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8920 (pp) REVERT: G 74 LYS cc_start: 0.8100 (tptt) cc_final: 0.7879 (mmmt) REVERT: E 115 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8150 (mptt) REVERT: C 67 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7857 (tp30) outliers start: 17 outliers final: 13 residues processed: 163 average time/residue: 1.7856 time to fit residues: 309.4539 Evaluate side-chains 168 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 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 42 TYR 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 29 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.0270 chunk 27 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.114907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.080208 restraints weight = 24216.266| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.65 r_work: 0.3186 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13858 Z= 0.274 Angle : 0.557 9.585 19738 Z= 0.331 Chirality : 0.036 0.159 2236 Planarity : 0.004 0.063 1658 Dihedral : 29.400 177.082 3828 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.01 % Allowed : 17.65 % Favored : 80.33 % 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: 1.99 (0.27), residues: 1009 helix: 2.51 (0.20), residues: 640 sheet: -0.34 (0.77), residues: 36 loop : -0.95 (0.31), residues: 333 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 0.007 0.001 PHE H 66 TYR 0.034 0.002 TYR B 88 ARG 0.015 0.001 ARG C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5521.57 seconds wall clock time: 99 minutes 7.81 seconds (5947.81 seconds total)