Starting phenix.real_space_refine on Thu Jul 31 22:29:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d1z_30551/07_2025/7d1z_30551.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d1z_30551/07_2025/7d1z_30551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d1z_30551/07_2025/7d1z_30551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d1z_30551/07_2025/7d1z_30551.map" model { file = "/net/cci-nas-00/data/ceres_data/7d1z_30551/07_2025/7d1z_30551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d1z_30551/07_2025/7d1z_30551.cif" } resolution = 3.15 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1358 atoms to isotropic. 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 288 5.49 5 S 20 5.16 5 C 7463 2.51 5 N 2499 2.21 5 O 3057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 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: 13327 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 699 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 Time building chain proxies: 7.59, per 1000 atoms: 0.57 Number of scatterers: 13327 At special positions: 0 Unit cell: (118.65, 99.75, 123.9, 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 20 16.00 P 288 15.00 O 3057 8.00 N 2499 7.00 C 7463 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: 2.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 64.5% alpha, 5.6% beta 138 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 7.06 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.805A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.544A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.399A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 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 103 through 124 removed outlier: 3.557A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.409A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.632A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 194 through 211 Processing helix chain 'K' and resid 254 through 264 removed outlier: 3.805A pdb=" N GLU K 259 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA K 260 " --> pdb=" O LYS K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 Processing helix chain 'K' and resid 348 through 352 removed outlier: 3.729A pdb=" N LYS K 351 " --> pdb=" O PRO K 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.595A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.784A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.876A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.807A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.863A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.199A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 218 through 223 removed outlier: 3.735A pdb=" N GLY K 227 " --> pdb=" O ILE K 223 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU K 330 " --> pdb=" O ALA K 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 240 through 244 removed outlier: 3.693A pdb=" N ASP K 240 " --> pdb=" O ALA K 322 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU K 320 " --> pdb=" O VAL K 242 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE K 321 " --> pdb=" O GLN K 306 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN K 306 " --> pdb=" O ILE K 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 248 through 250 removed outlier: 3.849A pdb=" N CYS K 283 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 276 through 277 Processing sheet with id=AB6, first strand: chain 'K' and resid 310 through 312 removed outlier: 3.966A pdb=" N VAL K 315 " --> pdb=" O ILE K 312 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 7.87 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2477 1.33 - 1.45: 4477 1.45 - 1.57: 6590 1.57 - 1.69: 576 1.69 - 1.81: 32 Bond restraints: 14152 Sorted by residual: bond pdb=" CA ALA F 76 " pdb=" C ALA F 76 " ideal model delta sigma weight residual 1.523 1.491 0.033 1.80e-02 3.09e+03 3.26e+00 bond pdb=" C LEU E 61 " pdb=" N ILE E 62 " ideal model delta sigma weight residual 1.334 1.315 0.019 1.29e-02 6.01e+03 2.08e+00 bond pdb=" CB ARG A 131 " pdb=" CG ARG A 131 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB ARG D 79 " pdb=" CG ARG D 79 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CB THR C 59 " pdb=" CG2 THR C 59 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 14147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.42: 20325 5.42 - 10.85: 11 10.85 - 16.27: 1 16.27 - 21.70: 1 21.70 - 27.12: 1 Bond angle restraints: 20339 Sorted by residual: angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP1 DG J 21 " ideal model delta sigma weight residual 108.00 80.88 27.12 3.00e+00 1.11e-01 8.17e+01 angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.71 106.59 7.12 9.50e-01 1.11e+00 5.61e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 108.00 87.24 20.76 3.00e+00 1.11e-01 4.79e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" O5' DG J 21 " ideal model delta sigma weight residual 104.00 97.98 6.02 1.50e+00 4.44e-01 1.61e+01 angle pdb=" C HIS F 75 " pdb=" N ALA F 76 " pdb=" CA ALA F 76 " ideal model delta sigma weight residual 122.31 114.58 7.73 2.00e+00 2.50e-01 1.49e+01 ... (remaining 20334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.83: 6034 31.83 - 63.67: 1699 63.67 - 95.50: 49 95.50 - 127.34: 0 127.34 - 159.17: 2 Dihedral angle restraints: 7784 sinusoidal: 5097 harmonic: 2687 Sorted by residual: dihedral pdb=" CA ALA G 12 " pdb=" C ALA G 12 " pdb=" N LYS G 13 " pdb=" CA LYS G 13 " ideal model delta harmonic sigma weight residual 180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 60.83 159.17 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 7781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.410: 2296 0.410 - 0.819: 0 0.819 - 1.229: 0 1.229 - 1.639: 0 1.639 - 2.048: 1 Chirality restraints: 2297 Sorted by residual: chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.35 0.30 2.05 2.00e-01 2.50e+01 1.05e+02 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA VAL A 117 " pdb=" N VAL A 117 " pdb=" C VAL A 117 " pdb=" CB VAL A 117 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 2294 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.028 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA I -35 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " 0.027 2.00e-02 2.50e+03 1.12e-02 3.76e+00 pdb=" N9 DG I 28 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.026 2.00e-02 2.50e+03 1.09e-02 3.57e+00 pdb=" N9 DG I 26 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " -0.002 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 453 2.67 - 3.23: 11697 3.23 - 3.79: 25151 3.79 - 4.34: 32751 4.34 - 4.90: 46742 Nonbonded interactions: 116794 Sorted by model distance: nonbonded pdb=" O ALA K 255 " pdb=" OH TYR K 274 " model vdw 2.118 3.040 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.179 3.120 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.194 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.254 3.040 ... (remaining 116789 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' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = (chain 'D' and resid 33 through 124) 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 39.270 Find NCS groups from input model: 0.310 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:4.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.007 0.047 14152 Z= 0.327 Angle : 0.731 27.121 20339 Z= 0.423 Chirality : 0.058 2.048 2297 Planarity : 0.003 0.035 1578 Dihedral : 28.096 159.170 6056 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.13 (0.24), residues: 911 helix: -0.32 (0.19), residues: 582 sheet: -3.86 (0.67), residues: 28 loop : -3.32 (0.28), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 349 HIS 0.006 0.001 HIS K 299 PHE 0.018 0.002 PHE K 275 TYR 0.015 0.002 TYR G 50 ARG 0.005 0.000 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.07813 ( 814) hydrogen bonds : angle 3.85048 ( 2059) covalent geometry : bond 0.00746 (14152) covalent geometry : angle 0.73083 (20339) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.943 Fit side-chains REVERT: A 59 GLU cc_start: 0.8147 (pp20) cc_final: 0.7642 (pp20) REVERT: B 88 TYR cc_start: 0.9097 (m-10) cc_final: 0.8748 (m-80) REVERT: C 75 LYS cc_start: 0.8629 (mttp) cc_final: 0.8408 (mtpt) REVERT: D 43 LYS cc_start: 0.8950 (mttt) cc_final: 0.8716 (mttm) REVERT: D 116 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8440 (ttmm) REVERT: E 50 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7909 (mt-10) REVERT: H 46 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8561 (mmtm) REVERT: H 116 LYS cc_start: 0.8901 (tttt) cc_final: 0.8639 (ttmt) REVERT: K 288 ARG cc_start: 0.5444 (ttp80) cc_final: 0.5186 (ttp80) REVERT: K 334 TYR cc_start: 0.7132 (p90) cc_final: 0.6896 (p90) REVERT: F 31 LYS cc_start: 0.9004 (tttt) cc_final: 0.8697 (tttm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.4534 time to fit residues: 117.0239 Evaluate side-chains 158 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.2980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.0170 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS B 93 GLN D 82 HIS D 84 ASN D 95 GLN E 68 GLN E 113 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 84 ASN K 347 HIS F 75 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.151208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.092547 restraints weight = 20715.950| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.90 r_work: 0.2940 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14152 Z= 0.148 Angle : 0.625 27.058 20339 Z= 0.352 Chirality : 0.055 2.035 2297 Planarity : 0.004 0.031 1578 Dihedral : 30.572 160.849 4211 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.90 % Allowed : 12.66 % Favored : 86.43 % 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: 0.45 (0.27), residues: 911 helix: 1.66 (0.20), residues: 590 sheet: -3.24 (0.64), residues: 43 loop : -2.17 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 349 HIS 0.004 0.001 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.020 0.001 TYR K 274 ARG 0.005 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 814) hydrogen bonds : angle 3.06158 ( 2059) covalent geometry : bond 0.00317 (14152) covalent geometry : angle 0.62456 (20339) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8356 (pp20) cc_final: 0.7550 (pp20) REVERT: A 77 ASP cc_start: 0.8534 (t0) cc_final: 0.8101 (t0) REVERT: A 79 LYS cc_start: 0.8591 (tttm) cc_final: 0.8374 (tttm) REVERT: B 88 TYR cc_start: 0.9168 (m-10) cc_final: 0.8908 (m-80) REVERT: B 93 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8114 (mm-40) REVERT: C 56 GLU cc_start: 0.8653 (tt0) cc_final: 0.8261 (tt0) REVERT: D 72 ARG cc_start: 0.8959 (mtt180) cc_final: 0.8527 (mtp180) REVERT: E 52 ARG cc_start: 0.8339 (ttm110) cc_final: 0.8019 (mtp-110) REVERT: H 86 ARG cc_start: 0.8761 (mmt90) cc_final: 0.8405 (mmt90) REVERT: H 116 LYS cc_start: 0.9077 (tttt) cc_final: 0.8752 (ttmt) REVERT: H 121 TYR cc_start: 0.9294 (t80) cc_final: 0.8968 (t80) REVERT: K 208 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5942 (tm-30) REVERT: K 218 MET cc_start: 0.3458 (mpp) cc_final: 0.2723 (mtm) REVERT: F 31 LYS cc_start: 0.8927 (tttt) cc_final: 0.8698 (tttm) REVERT: F 92 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8538 (mmm160) outliers start: 7 outliers final: 2 residues processed: 186 average time/residue: 0.3905 time to fit residues: 98.4910 Evaluate side-chains 167 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 320 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.150446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.091293 restraints weight = 20908.601| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.92 r_work: 0.2916 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14152 Z= 0.174 Angle : 0.621 27.160 20339 Z= 0.348 Chirality : 0.055 2.025 2297 Planarity : 0.003 0.032 1578 Dihedral : 30.588 160.741 4211 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.81 % Allowed : 14.99 % Favored : 83.20 % 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: 1.20 (0.28), residues: 911 helix: 2.25 (0.21), residues: 587 sheet: -3.19 (0.65), residues: 43 loop : -1.81 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS C 31 PHE 0.010 0.001 PHE E 67 TYR 0.016 0.001 TYR K 274 ARG 0.005 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 814) hydrogen bonds : angle 2.98714 ( 2059) covalent geometry : bond 0.00388 (14152) covalent geometry : angle 0.62080 (20339) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 1.437 Fit side-chains REVERT: B 88 TYR cc_start: 0.9184 (m-10) cc_final: 0.8957 (m-80) REVERT: B 93 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8189 (mm-40) REVERT: C 56 GLU cc_start: 0.8686 (tt0) cc_final: 0.8302 (tt0) REVERT: D 71 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7889 (tm-30) REVERT: E 52 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8006 (mtp-110) REVERT: H 86 ARG cc_start: 0.8723 (mmt90) cc_final: 0.8391 (mmt90) REVERT: H 116 LYS cc_start: 0.9017 (tttt) cc_final: 0.8686 (ttmt) REVERT: H 121 TYR cc_start: 0.9294 (t80) cc_final: 0.8990 (t80) REVERT: F 31 LYS cc_start: 0.8994 (tttt) cc_final: 0.8770 (tttm) outliers start: 14 outliers final: 11 residues processed: 177 average time/residue: 0.3779 time to fit residues: 89.8907 Evaluate side-chains 167 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 47 GLN H 49 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.151203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092450 restraints weight = 20742.620| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.88 r_work: 0.2927 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14152 Z= 0.166 Angle : 0.612 27.067 20339 Z= 0.341 Chirality : 0.054 2.027 2297 Planarity : 0.003 0.035 1578 Dihedral : 30.447 161.881 4211 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.20 % Allowed : 15.12 % Favored : 82.69 % 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: 1.60 (0.28), residues: 911 helix: 2.53 (0.21), residues: 585 sheet: -3.06 (0.68), residues: 46 loop : -1.51 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS K 299 PHE 0.010 0.001 PHE E 67 TYR 0.014 0.001 TYR K 274 ARG 0.005 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 814) hydrogen bonds : angle 2.91572 ( 2059) covalent geometry : bond 0.00367 (14152) covalent geometry : angle 0.61178 (20339) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8651 (t0) cc_final: 0.8332 (t0) REVERT: A 79 LYS cc_start: 0.8602 (tttm) cc_final: 0.8330 (tttm) REVERT: B 88 TYR cc_start: 0.9186 (m-10) cc_final: 0.8959 (m-80) REVERT: C 56 GLU cc_start: 0.8660 (tt0) cc_final: 0.8274 (tt0) REVERT: D 71 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7908 (tm-30) REVERT: E 52 ARG cc_start: 0.8324 (ttm110) cc_final: 0.8069 (mtp-110) REVERT: G 91 GLU cc_start: 0.8666 (tt0) cc_final: 0.8397 (tm-30) REVERT: H 37 TYR cc_start: 0.9385 (m-80) cc_final: 0.9078 (m-80) REVERT: H 86 ARG cc_start: 0.8765 (mmt90) cc_final: 0.8408 (mmt90) REVERT: H 116 LYS cc_start: 0.9004 (tttt) cc_final: 0.8676 (ttmt) REVERT: H 121 TYR cc_start: 0.9287 (t80) cc_final: 0.9056 (t80) REVERT: K 208 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5950 (tm-30) REVERT: K 218 MET cc_start: 0.4010 (mpp) cc_final: 0.3038 (mtm) REVERT: K 285 ASP cc_start: 0.5570 (t0) cc_final: 0.5262 (m-30) REVERT: F 31 LYS cc_start: 0.8996 (tttt) cc_final: 0.8784 (tttm) outliers start: 17 outliers final: 12 residues processed: 193 average time/residue: 0.3218 time to fit residues: 85.8579 Evaluate side-chains 191 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.0470 chunk 108 optimal weight: 20.0000 chunk 95 optimal weight: 50.0000 chunk 63 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.153011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093976 restraints weight = 21221.613| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.00 r_work: 0.2966 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14152 Z= 0.139 Angle : 0.604 27.090 20339 Z= 0.336 Chirality : 0.054 2.029 2297 Planarity : 0.003 0.037 1578 Dihedral : 30.296 162.529 4211 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.68 % Allowed : 18.35 % Favored : 79.97 % 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: 1.91 (0.28), residues: 911 helix: 2.66 (0.21), residues: 589 sheet: -2.78 (0.72), residues: 46 loop : -1.20 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 349 HIS 0.003 0.001 HIS K 299 PHE 0.009 0.001 PHE E 67 TYR 0.018 0.001 TYR K 274 ARG 0.009 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 814) hydrogen bonds : angle 2.83525 ( 2059) covalent geometry : bond 0.00293 (14152) covalent geometry : angle 0.60360 (20339) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8625 (t0) cc_final: 0.8304 (t0) REVERT: B 88 TYR cc_start: 0.9180 (m-10) cc_final: 0.8950 (m-80) REVERT: B 93 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8127 (mm-40) REVERT: C 56 GLU cc_start: 0.8642 (tt0) cc_final: 0.8237 (tt0) REVERT: D 99 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8386 (mtp85) REVERT: E 52 ARG cc_start: 0.8306 (ttm110) cc_final: 0.8069 (mtp-110) REVERT: G 91 GLU cc_start: 0.8675 (tt0) cc_final: 0.8457 (tm-30) REVERT: H 37 TYR cc_start: 0.9315 (m-80) cc_final: 0.8950 (m-80) REVERT: H 86 ARG cc_start: 0.8727 (mmt90) cc_final: 0.8374 (mmt90) REVERT: H 116 LYS cc_start: 0.8977 (tttt) cc_final: 0.8650 (ttmt) REVERT: K 208 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5899 (tm-30) REVERT: K 218 MET cc_start: 0.4163 (mpp) cc_final: 0.3020 (mtm) REVERT: K 285 ASP cc_start: 0.5588 (t0) cc_final: 0.5372 (m-30) REVERT: F 31 LYS cc_start: 0.8977 (tttt) cc_final: 0.8765 (tttm) REVERT: F 93 GLN cc_start: 0.8662 (mp10) cc_final: 0.8368 (mp10) outliers start: 13 outliers final: 8 residues processed: 187 average time/residue: 0.2889 time to fit residues: 74.6308 Evaluate side-chains 185 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 221 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 50.0000 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS G 84 GLN G 89 ASN G 104 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.150657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091538 restraints weight = 21026.215| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.87 r_work: 0.2912 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14152 Z= 0.190 Angle : 0.626 27.124 20339 Z= 0.345 Chirality : 0.055 2.020 2297 Planarity : 0.003 0.035 1578 Dihedral : 30.432 162.999 4211 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.45 % Allowed : 17.96 % Favored : 79.59 % 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 (0.28), residues: 911 helix: 2.65 (0.21), residues: 585 sheet: -2.79 (0.71), residues: 46 loop : -1.08 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS C 31 PHE 0.009 0.001 PHE C 25 TYR 0.017 0.001 TYR H 40 ARG 0.005 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 814) hydrogen bonds : angle 2.97091 ( 2059) covalent geometry : bond 0.00426 (14152) covalent geometry : angle 0.62601 (20339) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7601 (ptp-110) REVERT: B 84 MET cc_start: 0.8919 (mmm) cc_final: 0.8651 (mmm) REVERT: B 88 TYR cc_start: 0.9236 (m-10) cc_final: 0.8806 (m-80) REVERT: B 93 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8125 (mm-40) REVERT: C 56 GLU cc_start: 0.8681 (tt0) cc_final: 0.8323 (tt0) REVERT: D 71 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7941 (tm-30) REVERT: D 99 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.8424 (mtp85) REVERT: E 52 ARG cc_start: 0.8313 (ttm110) cc_final: 0.8067 (mtp-110) REVERT: G 91 GLU cc_start: 0.8680 (tt0) cc_final: 0.8459 (tm-30) REVERT: H 37 TYR cc_start: 0.9389 (m-80) cc_final: 0.9079 (m-80) REVERT: H 86 ARG cc_start: 0.8784 (mmt90) cc_final: 0.8405 (mmt90) REVERT: H 116 LYS cc_start: 0.9013 (tttt) cc_final: 0.8686 (ttmt) REVERT: K 208 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5965 (tm-30) REVERT: F 31 LYS cc_start: 0.9040 (tttt) cc_final: 0.8804 (tttm) outliers start: 19 outliers final: 14 residues processed: 183 average time/residue: 0.2890 time to fit residues: 73.1684 Evaluate side-chains 184 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 22 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.151981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092247 restraints weight = 21328.269| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.98 r_work: 0.2927 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14152 Z= 0.166 Angle : 0.617 27.074 20339 Z= 0.339 Chirality : 0.054 2.025 2297 Planarity : 0.003 0.035 1578 Dihedral : 30.282 163.525 4211 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.84 % Allowed : 18.48 % Favored : 78.68 % 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 (0.28), residues: 911 helix: 2.64 (0.21), residues: 589 sheet: -2.70 (0.71), residues: 46 loop : -0.91 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 349 HIS 0.004 0.001 HIS C 31 PHE 0.009 0.001 PHE E 67 TYR 0.016 0.001 TYR H 40 ARG 0.005 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 814) hydrogen bonds : angle 2.92882 ( 2059) covalent geometry : bond 0.00366 (14152) covalent geometry : angle 0.61667 (20339) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7584 (ptp-110) REVERT: A 77 ASP cc_start: 0.8661 (t0) cc_final: 0.8389 (t0) REVERT: B 88 TYR cc_start: 0.9224 (m-10) cc_final: 0.8998 (m-80) REVERT: B 93 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8057 (mm-40) REVERT: C 56 GLU cc_start: 0.8670 (tt0) cc_final: 0.8318 (tt0) REVERT: E 52 ARG cc_start: 0.8353 (ttm110) cc_final: 0.8106 (mtp-110) REVERT: G 91 GLU cc_start: 0.8690 (tt0) cc_final: 0.8477 (tm-30) REVERT: H 37 TYR cc_start: 0.9355 (m-80) cc_final: 0.9096 (m-80) REVERT: H 86 ARG cc_start: 0.8782 (mmt90) cc_final: 0.8418 (mmt90) REVERT: H 116 LYS cc_start: 0.9017 (tttt) cc_final: 0.8693 (ttmt) REVERT: H 121 TYR cc_start: 0.9227 (t80) cc_final: 0.8939 (t80) REVERT: K 208 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5954 (mm-30) REVERT: K 218 MET cc_start: 0.4369 (mpp) cc_final: 0.2925 (mtm) REVERT: F 31 LYS cc_start: 0.9028 (tttt) cc_final: 0.8796 (tttm) outliers start: 22 outliers final: 18 residues processed: 180 average time/residue: 0.2928 time to fit residues: 72.6086 Evaluate side-chains 185 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 22 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 106 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.151463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.091673 restraints weight = 21249.805| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.95 r_work: 0.2919 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14152 Z= 0.182 Angle : 0.629 27.120 20339 Z= 0.343 Chirality : 0.054 2.019 2297 Planarity : 0.003 0.034 1578 Dihedral : 30.274 163.924 4211 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.97 % Allowed : 18.35 % Favored : 78.68 % 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: 1.97 (0.28), residues: 911 helix: 2.60 (0.21), residues: 588 sheet: -2.71 (0.71), residues: 46 loop : -0.89 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS C 31 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.001 TYR K 334 ARG 0.005 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 814) hydrogen bonds : angle 2.95598 ( 2059) covalent geometry : bond 0.00409 (14152) covalent geometry : angle 0.62896 (20339) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7580 (ptp-110) REVERT: A 77 ASP cc_start: 0.8665 (t0) cc_final: 0.8382 (t0) REVERT: B 88 TYR cc_start: 0.9266 (m-10) cc_final: 0.9064 (m-80) REVERT: B 93 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8111 (mm-40) REVERT: C 56 GLU cc_start: 0.8680 (tt0) cc_final: 0.8322 (tt0) REVERT: D 71 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7996 (tm-30) REVERT: E 52 ARG cc_start: 0.8345 (ttm110) cc_final: 0.8109 (mtp-110) REVERT: G 91 GLU cc_start: 0.8704 (tt0) cc_final: 0.8489 (tm-30) REVERT: H 37 TYR cc_start: 0.9383 (m-80) cc_final: 0.9124 (m-80) REVERT: H 86 ARG cc_start: 0.8779 (mmt90) cc_final: 0.8418 (mmt90) REVERT: H 116 LYS cc_start: 0.9024 (tttt) cc_final: 0.8691 (ttmt) REVERT: H 121 TYR cc_start: 0.9261 (t80) cc_final: 0.8915 (t80) REVERT: K 218 MET cc_start: 0.4512 (mpp) cc_final: 0.3015 (mtm) REVERT: F 31 LYS cc_start: 0.9034 (tttt) cc_final: 0.8799 (tttm) outliers start: 23 outliers final: 19 residues processed: 177 average time/residue: 0.3452 time to fit residues: 86.4450 Evaluate side-chains 179 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.151004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.093122 restraints weight = 21097.510| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.15 r_work: 0.2895 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14152 Z= 0.200 Angle : 0.636 27.118 20339 Z= 0.346 Chirality : 0.055 2.019 2297 Planarity : 0.003 0.035 1578 Dihedral : 30.259 164.546 4211 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.58 % Allowed : 18.86 % Favored : 78.55 % 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: 1.93 (0.28), residues: 911 helix: 2.54 (0.21), residues: 588 sheet: -2.60 (0.72), residues: 46 loop : -0.84 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS C 31 PHE 0.009 0.001 PHE E 67 TYR 0.010 0.001 TYR C 57 ARG 0.005 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 814) hydrogen bonds : angle 3.00928 ( 2059) covalent geometry : bond 0.00452 (14152) covalent geometry : angle 0.63605 (20339) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.105 Fit side-chains REVERT: A 42 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7595 (ptp-110) REVERT: B 84 MET cc_start: 0.9044 (mmm) cc_final: 0.8675 (mmm) REVERT: B 88 TYR cc_start: 0.9247 (m-10) cc_final: 0.8853 (m-80) REVERT: C 56 GLU cc_start: 0.8654 (tt0) cc_final: 0.8298 (tt0) REVERT: D 71 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8018 (tm-30) REVERT: E 52 ARG cc_start: 0.8373 (ttm110) cc_final: 0.8133 (mtp-110) REVERT: H 37 TYR cc_start: 0.9398 (m-80) cc_final: 0.9133 (m-80) REVERT: H 86 ARG cc_start: 0.8796 (mmt90) cc_final: 0.8417 (mmt90) REVERT: H 116 LYS cc_start: 0.9020 (tttt) cc_final: 0.8676 (ttmt) REVERT: H 121 TYR cc_start: 0.9271 (t80) cc_final: 0.8897 (t80) REVERT: F 31 LYS cc_start: 0.9045 (tttt) cc_final: 0.8817 (tttm) outliers start: 20 outliers final: 18 residues processed: 178 average time/residue: 0.2930 time to fit residues: 72.5484 Evaluate side-chains 182 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 62 optimal weight: 0.0670 chunk 113 optimal weight: 1.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.151930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093858 restraints weight = 21157.579| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.21 r_work: 0.2898 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14152 Z= 0.157 Angle : 0.629 27.091 20339 Z= 0.342 Chirality : 0.054 2.023 2297 Planarity : 0.004 0.045 1578 Dihedral : 30.230 164.938 4211 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.33 % Allowed : 19.25 % Favored : 78.42 % 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: 1.93 (0.28), residues: 911 helix: 2.54 (0.21), residues: 589 sheet: -2.68 (0.73), residues: 46 loop : -0.84 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS K 299 PHE 0.009 0.001 PHE E 67 TYR 0.012 0.001 TYR K 334 ARG 0.010 0.000 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 814) hydrogen bonds : angle 2.97553 ( 2059) covalent geometry : bond 0.00345 (14152) covalent geometry : angle 0.62866 (20339) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.079 Fit side-chains REVERT: A 42 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7593 (ptp-110) REVERT: B 84 MET cc_start: 0.9052 (mmm) cc_final: 0.8707 (mmm) REVERT: B 88 TYR cc_start: 0.9258 (m-10) cc_final: 0.8869 (m-80) REVERT: B 93 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8203 (mm-40) REVERT: C 56 GLU cc_start: 0.8694 (tt0) cc_final: 0.8330 (tt0) REVERT: D 71 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8040 (tm-30) REVERT: E 52 ARG cc_start: 0.8382 (ttm110) cc_final: 0.8114 (mtp-110) REVERT: H 37 TYR cc_start: 0.9394 (m-80) cc_final: 0.9084 (m-80) REVERT: H 86 ARG cc_start: 0.8815 (mmt90) cc_final: 0.8433 (mmt90) REVERT: H 116 LYS cc_start: 0.9016 (tttt) cc_final: 0.8668 (ttmt) REVERT: H 121 TYR cc_start: 0.9286 (t80) cc_final: 0.8899 (t80) REVERT: F 31 LYS cc_start: 0.9043 (tttt) cc_final: 0.8815 (tttm) outliers start: 18 outliers final: 17 residues processed: 176 average time/residue: 0.4339 time to fit residues: 105.6578 Evaluate side-chains 181 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.150473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.091551 restraints weight = 21161.887| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.08 r_work: 0.2870 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14152 Z= 0.218 Angle : 0.650 27.160 20339 Z= 0.351 Chirality : 0.055 2.015 2297 Planarity : 0.004 0.039 1578 Dihedral : 30.304 165.096 4211 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.58 % Allowed : 19.12 % Favored : 78.29 % 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 (0.28), residues: 911 helix: 2.50 (0.21), residues: 588 sheet: -2.64 (0.73), residues: 43 loop : -0.92 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 349 HIS 0.003 0.001 HIS C 31 PHE 0.010 0.002 PHE C 25 TYR 0.010 0.001 TYR C 57 ARG 0.005 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 814) hydrogen bonds : angle 3.05646 ( 2059) covalent geometry : bond 0.00497 (14152) covalent geometry : angle 0.64962 (20339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7533.03 seconds wall clock time: 135 minutes 51.73 seconds (8151.73 seconds total)