Starting phenix.real_space_refine on Thu Sep 18 04:06:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d1z_30551/09_2025/7d1z_30551.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d1z_30551/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7d1z_30551/09_2025/7d1z_30551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d1z_30551/09_2025/7d1z_30551.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d1z_30551/09_2025/7d1z_30551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d1z_30551/09_2025/7d1z_30551.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.75, per 1000 atoms: 0.28 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: 1.08 Conformation dependent library (CDL) restraints added in 433.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.23 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: 3.12 Time building geometry restraints manager: 1.51 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.390 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (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 ARG 0.005 0.000 ARG G 88 TYR 0.015 0.002 TYR G 50 PHE 0.018 0.002 PHE K 275 TRP 0.004 0.001 TRP K 349 HIS 0.006 0.001 HIS K 299 Details of bonding type rmsd covalent geometry : bond 0.00746 (14152) covalent geometry : angle 0.73083 (20339) hydrogen bonds : bond 0.07813 ( 814) hydrogen bonds : angle 3.85048 ( 2059) *********************** 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 : 0.380 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: 0.2018 time to fit residues: 52.0296 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 : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS 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 49 HIS 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 = 0.3997 r_free = 0.3997 target = 0.150318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.091302 restraints weight = 20788.960| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.92 r_work: 0.2914 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14152 Z= 0.156 Angle : 0.630 27.107 20339 Z= 0.355 Chirality : 0.054 2.034 2297 Planarity : 0.004 0.029 1578 Dihedral : 30.754 160.388 4211 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.78 % Allowed : 12.92 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.27), residues: 911 helix: 1.41 (0.20), residues: 589 sheet: -3.29 (0.63), residues: 43 loop : -2.36 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 134 TYR 0.019 0.001 TYR K 274 PHE 0.012 0.001 PHE E 67 TRP 0.004 0.001 TRP K 349 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (14152) covalent geometry : angle 0.63048 (20339) hydrogen bonds : bond 0.03728 ( 814) hydrogen bonds : angle 3.17134 ( 2059) *********************** 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 178 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 0.400 Fit side-chains REVERT: A 59 GLU cc_start: 0.8448 (pp20) cc_final: 0.7660 (pp20) REVERT: B 88 TYR cc_start: 0.9209 (m-10) cc_final: 0.8954 (m-80) REVERT: B 93 GLN cc_start: 0.8349 (mm110) cc_final: 0.8062 (mm-40) REVERT: C 56 GLU cc_start: 0.8648 (tt0) cc_final: 0.8298 (tt0) REVERT: E 52 ARG cc_start: 0.8301 (ttm110) cc_final: 0.8037 (mtp-110) REVERT: G 71 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8263 (ttp80) REVERT: H 86 ARG cc_start: 0.8766 (mmt90) cc_final: 0.8402 (mmt90) REVERT: H 116 LYS cc_start: 0.9097 (tttt) cc_final: 0.8750 (ttmt) REVERT: H 121 TYR cc_start: 0.9282 (t80) cc_final: 0.8950 (t80) REVERT: F 31 LYS cc_start: 0.8943 (tttt) cc_final: 0.8706 (tttm) outliers start: 6 outliers final: 2 residues processed: 175 average time/residue: 0.1658 time to fit residues: 38.8218 Evaluate side-chains 161 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 ASP 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 47 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 50.0000 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.149088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089405 restraints weight = 21013.947| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.93 r_work: 0.2875 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14152 Z= 0.219 Angle : 0.646 27.146 20339 Z= 0.360 Chirality : 0.055 2.026 2297 Planarity : 0.004 0.030 1578 Dihedral : 30.740 160.554 4211 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.81 % Allowed : 13.95 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.28), residues: 911 helix: 2.04 (0.21), residues: 587 sheet: -3.16 (0.66), residues: 43 loop : -1.94 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.018 0.001 TYR K 274 PHE 0.011 0.002 PHE E 67 TRP 0.002 0.001 TRP K 349 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00499 (14152) covalent geometry : angle 0.64594 (20339) hydrogen bonds : bond 0.03881 ( 814) hydrogen bonds : angle 3.10605 ( 2059) *********************** 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 177 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.395 Fit side-chains REVERT: B 88 TYR cc_start: 0.9220 (m-10) cc_final: 0.8945 (m-80) REVERT: B 93 GLN cc_start: 0.8394 (mm110) cc_final: 0.8122 (mm-40) REVERT: C 56 GLU cc_start: 0.8663 (tt0) cc_final: 0.8309 (tt0) REVERT: D 71 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7976 (tm-30) REVERT: D 101 LEU cc_start: 0.9325 (mm) cc_final: 0.9116 (mm) REVERT: E 52 ARG cc_start: 0.8321 (ttm110) cc_final: 0.8019 (mtp-110) REVERT: G 71 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8272 (ttp80) REVERT: H 52 THR cc_start: 0.8991 (m) cc_final: 0.8691 (t) REVERT: H 86 ARG cc_start: 0.8799 (mmt90) cc_final: 0.8416 (mmt90) REVERT: H 116 LYS cc_start: 0.9026 (tttt) cc_final: 0.8687 (ttmt) REVERT: H 121 TYR cc_start: 0.9301 (t80) cc_final: 0.9007 (t80) REVERT: K 208 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5983 (tm-30) REVERT: K 218 MET cc_start: 0.3677 (mpp) cc_final: 0.2664 (mtm) REVERT: F 31 LYS cc_start: 0.9029 (tttt) cc_final: 0.8776 (tttm) outliers start: 14 outliers final: 10 residues processed: 168 average time/residue: 0.1647 time to fit residues: 37.1030 Evaluate side-chains 164 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 51 ASP 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 F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.147108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087076 restraints weight = 21005.572| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.96 r_work: 0.2842 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 14152 Z= 0.287 Angle : 0.673 27.130 20339 Z= 0.373 Chirality : 0.057 2.026 2297 Planarity : 0.004 0.040 1578 Dihedral : 30.913 160.593 4211 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.45 % Allowed : 14.60 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.28), residues: 911 helix: 2.08 (0.21), residues: 585 sheet: -3.09 (0.68), residues: 43 loop : -1.73 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 88 TYR 0.017 0.002 TYR K 274 PHE 0.013 0.002 PHE C 25 TRP 0.002 0.001 TRP K 349 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00660 (14152) covalent geometry : angle 0.67310 (20339) hydrogen bonds : bond 0.04363 ( 814) hydrogen bonds : angle 3.19717 ( 2059) *********************** 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 179 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.424 Fit side-chains REVERT: A 42 ARG cc_start: 0.7934 (mtp85) cc_final: 0.7627 (ptp-110) REVERT: B 88 TYR cc_start: 0.9267 (m-10) cc_final: 0.9016 (m-80) REVERT: D 71 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8023 (tm-30) REVERT: D 99 ARG cc_start: 0.8825 (mtm-85) cc_final: 0.8411 (mtp85) REVERT: D 101 LEU cc_start: 0.9362 (mm) cc_final: 0.9120 (mm) REVERT: E 50 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8263 (mt-10) REVERT: E 52 ARG cc_start: 0.8320 (ttm110) cc_final: 0.8033 (mtp-110) REVERT: H 52 THR cc_start: 0.9039 (m) cc_final: 0.8769 (t) REVERT: H 86 ARG cc_start: 0.8846 (mmt90) cc_final: 0.8421 (mmt90) REVERT: H 116 LYS cc_start: 0.9061 (tttt) cc_final: 0.8717 (ttmt) REVERT: K 208 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.5986 (tm-30) REVERT: F 31 LYS cc_start: 0.9060 (tttt) cc_final: 0.8780 (tttm) outliers start: 19 outliers final: 17 residues processed: 171 average time/residue: 0.1605 time to fit residues: 36.9035 Evaluate side-chains 180 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN 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 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 Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 0.0770 chunk 87 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 103 optimal weight: 50.0000 chunk 23 optimal weight: 0.0000 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 108 ASN H 47 GLN H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.153064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094440 restraints weight = 21368.375| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.97 r_work: 0.2974 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2366 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= 0.144 Angle : 0.604 26.862 20339 Z= 0.339 Chirality : 0.054 2.032 2297 Planarity : 0.003 0.038 1578 Dihedral : 30.145 162.422 4211 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.81 % Allowed : 15.76 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.29), residues: 911 helix: 2.56 (0.21), residues: 592 sheet: -2.94 (0.72), residues: 46 loop : -1.26 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.014 0.001 TYR H 40 PHE 0.011 0.001 PHE E 67 TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS K 299 Details of bonding type rmsd covalent geometry : bond 0.00306 (14152) covalent geometry : angle 0.60414 (20339) hydrogen bonds : bond 0.03377 ( 814) hydrogen bonds : angle 2.82386 ( 2059) *********************** 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 206 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.387 Fit side-chains REVERT: A 42 ARG cc_start: 0.7787 (mtp85) cc_final: 0.7473 (ptp-110) REVERT: C 36 LYS cc_start: 0.9186 (mttt) cc_final: 0.8981 (mtpt) REVERT: C 56 GLU cc_start: 0.8625 (tt0) cc_final: 0.8266 (tt0) REVERT: E 52 ARG cc_start: 0.8281 (ttm110) cc_final: 0.8034 (mtp-110) REVERT: E 125 GLN cc_start: 0.8987 (mt0) cc_final: 0.8724 (mt0) REVERT: G 91 GLU cc_start: 0.8661 (tt0) cc_final: 0.8417 (tm-30) REVERT: H 37 TYR cc_start: 0.9338 (m-80) cc_final: 0.9112 (m-80) REVERT: H 76 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8119 (mm-30) REVERT: H 86 ARG cc_start: 0.8737 (mmt90) cc_final: 0.8374 (mmt90) REVERT: H 116 LYS cc_start: 0.8979 (tttt) cc_final: 0.8696 (ttpt) REVERT: K 208 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5991 (tm-30) REVERT: K 221 ASP cc_start: 0.1766 (p0) cc_final: 0.0275 (m-30) REVERT: F 31 LYS cc_start: 0.8966 (tttt) cc_final: 0.8744 (tttm) outliers start: 14 outliers final: 8 residues processed: 196 average time/residue: 0.1469 time to fit residues: 39.7019 Evaluate side-chains 181 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 68 GLN 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 D residue 51 ASP Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 50.0000 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.148571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.089003 restraints weight = 20922.519| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.93 r_work: 0.2867 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14152 Z= 0.263 Angle : 0.662 27.232 20339 Z= 0.365 Chirality : 0.056 2.015 2297 Planarity : 0.004 0.054 1578 Dihedral : 30.668 162.818 4211 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.58 % Allowed : 17.96 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.28), residues: 911 helix: 2.43 (0.21), residues: 585 sheet: -2.87 (0.72), residues: 46 loop : -1.27 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.028 0.002 TYR B 88 PHE 0.011 0.002 PHE G 25 TRP 0.002 0.001 TRP K 349 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00605 (14152) covalent geometry : angle 0.66238 (20339) hydrogen bonds : bond 0.04091 ( 814) hydrogen bonds : angle 3.09596 ( 2059) *********************** 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 186 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.353 Fit side-chains REVERT: A 42 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7571 (ptp-110) REVERT: A 77 ASP cc_start: 0.8631 (t0) cc_final: 0.8339 (t0) REVERT: B 53 GLU cc_start: 0.8368 (tp30) cc_final: 0.8164 (tp30) REVERT: E 50 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8212 (mt-10) REVERT: E 52 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8061 (mtp-110) REVERT: G 91 GLU cc_start: 0.8711 (tt0) cc_final: 0.8469 (tm-30) REVERT: H 52 THR cc_start: 0.9016 (m) cc_final: 0.8731 (t) REVERT: H 86 ARG cc_start: 0.8809 (mmt90) cc_final: 0.8411 (mmt90) REVERT: H 116 LYS cc_start: 0.9052 (tttt) cc_final: 0.8708 (ttmt) REVERT: H 121 TYR cc_start: 0.9276 (t80) cc_final: 0.8951 (t80) REVERT: K 208 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5954 (tm-30) REVERT: F 31 LYS cc_start: 0.9069 (tttt) cc_final: 0.8803 (tttm) outliers start: 20 outliers final: 16 residues processed: 179 average time/residue: 0.1410 time to fit residues: 34.9905 Evaluate side-chains 184 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 73 THR 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 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 209 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 101 optimal weight: 30.0000 chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN H 47 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.151261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.091831 restraints weight = 21099.899| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.99 r_work: 0.2925 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2351 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= 0.163 Angle : 0.619 27.038 20339 Z= 0.344 Chirality : 0.054 2.026 2297 Planarity : 0.004 0.038 1578 Dihedral : 30.302 162.626 4211 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.58 % Allowed : 18.09 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.28), residues: 911 helix: 2.59 (0.21), residues: 589 sheet: -2.79 (0.72), residues: 46 loop : -1.07 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.039 0.001 TYR B 88 PHE 0.010 0.001 PHE E 67 TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS K 299 Details of bonding type rmsd covalent geometry : bond 0.00359 (14152) covalent geometry : angle 0.61876 (20339) hydrogen bonds : bond 0.03485 ( 814) hydrogen bonds : angle 2.93215 ( 2059) *********************** 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 187 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.379 Fit side-chains REVERT: A 42 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7552 (ptp-110) REVERT: E 52 ARG cc_start: 0.8341 (ttm110) cc_final: 0.8111 (mtp-110) REVERT: G 91 GLU cc_start: 0.8699 (tt0) cc_final: 0.8475 (tm-30) REVERT: H 37 TYR cc_start: 0.9412 (m-80) cc_final: 0.8971 (m-80) REVERT: H 76 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8077 (mm-30) REVERT: H 86 ARG cc_start: 0.8786 (mmt90) cc_final: 0.8414 (mmt90) REVERT: H 116 LYS cc_start: 0.9001 (tttt) cc_final: 0.8664 (ttmt) REVERT: H 121 TYR cc_start: 0.9253 (t80) cc_final: 0.8894 (t80) REVERT: K 208 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5938 (tm-30) REVERT: F 31 LYS cc_start: 0.9016 (tttt) cc_final: 0.8789 (tttm) outliers start: 20 outliers final: 15 residues processed: 178 average time/residue: 0.1408 time to fit residues: 34.9717 Evaluate side-chains 178 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 50 ILE 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 D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN 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 Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 30.0000 chunk 4 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.152285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.092982 restraints weight = 20973.749| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.99 r_work: 0.2944 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2553 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= 0.151 Angle : 0.614 27.077 20339 Z= 0.340 Chirality : 0.054 2.025 2297 Planarity : 0.004 0.036 1578 Dihedral : 30.206 164.112 4211 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.20 % Allowed : 19.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.29), residues: 911 helix: 2.68 (0.21), residues: 589 sheet: -2.78 (0.72), residues: 46 loop : -0.89 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.035 0.001 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.002 0.000 TRP K 349 HIS 0.004 0.001 HIS K 317 Details of bonding type rmsd covalent geometry : bond 0.00330 (14152) covalent geometry : angle 0.61374 (20339) hydrogen bonds : bond 0.03377 ( 814) hydrogen bonds : angle 2.89377 ( 2059) *********************** 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 187 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.363 Fit side-chains REVERT: A 42 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7533 (ptp-110) REVERT: C 36 LYS cc_start: 0.9073 (mtmt) cc_final: 0.8837 (mttp) REVERT: E 52 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8113 (mtp-110) REVERT: G 91 GLU cc_start: 0.8672 (tt0) cc_final: 0.8452 (tm-30) REVERT: H 37 TYR cc_start: 0.9387 (m-80) cc_final: 0.8991 (m-80) REVERT: H 76 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8114 (mm-30) REVERT: H 86 ARG cc_start: 0.8753 (mmt90) cc_final: 0.8375 (mmt90) REVERT: H 116 LYS cc_start: 0.8992 (tttt) cc_final: 0.8659 (ttmt) REVERT: F 31 LYS cc_start: 0.9021 (tttt) cc_final: 0.8800 (tttm) REVERT: F 93 GLN cc_start: 0.8723 (mp-120) cc_final: 0.8347 (mp10) outliers start: 17 outliers final: 15 residues processed: 176 average time/residue: 0.1366 time to fit residues: 33.7479 Evaluate side-chains 177 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR 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 D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain F residue 22 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 30.0000 chunk 39 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.151341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.091519 restraints weight = 21238.591| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.97 r_work: 0.2915 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.004 0.040 14152 Z= 0.183 Angle : 0.631 27.129 20339 Z= 0.346 Chirality : 0.054 2.019 2297 Planarity : 0.004 0.037 1578 Dihedral : 30.236 164.710 4211 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.71 % Allowed : 18.48 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.28), residues: 911 helix: 2.65 (0.21), residues: 585 sheet: -2.67 (0.72), residues: 46 loop : -0.85 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.032 0.001 TYR B 88 PHE 0.009 0.001 PHE A 67 TRP 0.003 0.001 TRP K 349 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00412 (14152) covalent geometry : angle 0.63067 (20339) hydrogen bonds : bond 0.03631 ( 814) hydrogen bonds : angle 2.95782 ( 2059) *********************** 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 178 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.376 Fit side-chains REVERT: A 42 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7562 (ptp-110) REVERT: C 36 LYS cc_start: 0.9080 (mtmt) cc_final: 0.8806 (mttp) REVERT: H 86 ARG cc_start: 0.8802 (mmt90) cc_final: 0.8428 (mmt90) REVERT: H 116 LYS cc_start: 0.9037 (tttt) cc_final: 0.8707 (ttmt) REVERT: H 121 TYR cc_start: 0.9248 (t80) cc_final: 0.8853 (t80) REVERT: F 31 LYS cc_start: 0.9060 (tttt) cc_final: 0.8809 (tttm) outliers start: 21 outliers final: 19 residues processed: 169 average time/residue: 0.1324 time to fit residues: 31.2265 Evaluate side-chains 175 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 73 THR 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 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 118 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain K residue 320 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.0270 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 100 optimal weight: 40.0000 chunk 58 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.093125 restraints weight = 21094.894| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.98 r_work: 0.2940 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14152 Z= 0.141 Angle : 0.629 27.099 20339 Z= 0.344 Chirality : 0.054 2.024 2297 Planarity : 0.004 0.045 1578 Dihedral : 30.199 165.209 4211 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.68 % Allowed : 20.16 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.28), residues: 911 helix: 2.60 (0.21), residues: 589 sheet: -2.44 (0.75), residues: 44 loop : -0.80 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 52 TYR 0.032 0.001 TYR B 88 PHE 0.009 0.001 PHE A 67 TRP 0.002 0.001 TRP K 349 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00297 (14152) covalent geometry : angle 0.62894 (20339) hydrogen bonds : bond 0.03460 ( 814) hydrogen bonds : angle 2.91654 ( 2059) ********************** 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 174 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7539 (ptp-110) REVERT: C 36 LYS cc_start: 0.9081 (mtmt) cc_final: 0.8796 (mttp) REVERT: H 37 TYR cc_start: 0.9406 (m-80) cc_final: 0.9025 (m-80) REVERT: H 86 ARG cc_start: 0.8767 (mmt90) cc_final: 0.8398 (mmt90) REVERT: H 116 LYS cc_start: 0.8995 (tttt) cc_final: 0.8660 (ttmt) REVERT: H 121 TYR cc_start: 0.9243 (t80) cc_final: 0.8861 (t80) REVERT: F 31 LYS cc_start: 0.9019 (tttt) cc_final: 0.8802 (tttm) outliers start: 13 outliers final: 11 residues processed: 167 average time/residue: 0.1446 time to fit residues: 33.5644 Evaluate side-chains 177 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain K residue 272 MET Chi-restraints excluded: chain K residue 320 LEU Chi-restraints excluded: chain F residue 22 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 113 optimal weight: 2.9990 chunk 95 optimal weight: 50.0000 chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.149210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.089727 restraints weight = 20953.823| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.90 r_work: 0.2876 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14152 Z= 0.246 Angle : 0.669 27.190 20339 Z= 0.363 Chirality : 0.056 2.013 2297 Planarity : 0.004 0.041 1578 Dihedral : 30.415 164.762 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 : 2.07 % Allowed : 19.12 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.28), residues: 911 helix: 2.44 (0.21), residues: 585 sheet: -2.66 (0.72), residues: 43 loop : -0.95 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 52 TYR 0.035 0.002 TYR B 88 PHE 0.011 0.002 PHE C 25 TRP 0.003 0.001 TRP K 349 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00565 (14152) covalent geometry : angle 0.66940 (20339) hydrogen bonds : bond 0.04063 ( 814) hydrogen bonds : angle 3.11035 ( 2059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.07 seconds wall clock time: 61 minutes 58.07 seconds (3718.07 seconds total)