Starting phenix.real_space_refine on Thu Jul 2 08:23:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hr5_34958/07_2026/8hr5_34958.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hr5_34958/07_2026/8hr5_34958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hr5_34958/07_2026/8hr5_34958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hr5_34958/07_2026/8hr5_34958.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hr5_34958/07_2026/8hr5_34958.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hr5_34958/07_2026/8hr5_34958.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hr5_34958/07_2026/8hr5_34958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hr5_34958/07_2026/8hr5_34958.map" } resolution = 3.73 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 123 5.49 5 S 17 5.16 5 C 4339 2.51 5 N 1351 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7595 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3327 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 5, 'TRANS': 460} Chain breaks: 2 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 628 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 9, 'GLN:plan1': 9, 'GLU:plan': 25, 'ASP:plan': 11, 'ASN:plan1': 10, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 286 Chain: "B" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1660 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 3, 'TRANS': 241} Chain breaks: 2 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 479 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 13, 'ARG:plan': 5, 'GLN:plan1': 4, 'GLU:plan': 15, 'ASN:plan1': 11, 'TYR:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 200 Chain: "C" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2163 Classifications: {'RNA': 101} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 50, 'rna3p_pyr': 41} Link IDs: {'rna2p': 10, 'rna3p': 90} Chain breaks: 3 Chain: "D" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Time building chain proxies: 1.65, per 1000 atoms: 0.22 Number of scatterers: 7595 At special positions: 0 Unit cell: (80.36, 117.26, 113.16, 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 17 16.00 P 123 15.00 O 1765 8.00 N 1351 7.00 C 4339 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: 0.76 Conformation dependent library (CDL) restraints added in 300.4 milliseconds 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1364 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 5 sheets defined 55.3% alpha, 12.2% beta 42 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 14 through 53 removed outlier: 3.616A pdb=" N ARG A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 81 removed outlier: 3.974A pdb=" N GLU A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 131 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 162 through 182 removed outlier: 4.218A pdb=" N LEU A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.672A pdb=" N ASP A 205 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 206 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 206' Processing helix chain 'A' and resid 237 through 249 removed outlier: 3.620A pdb=" N ARG A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 340 removed outlier: 3.517A pdb=" N PHE A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 removed outlier: 4.045A pdb=" N LYS A 344 " --> pdb=" O LYS A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 345 through 382 removed outlier: 3.618A pdb=" N ASN A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 422 removed outlier: 3.646A pdb=" N LEU A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'B' and resid 14 through 52 removed outlier: 3.546A pdb=" N TYR B 50 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 79 removed outlier: 3.944A pdb=" N ILE B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 148 removed outlier: 4.314A pdb=" N VAL B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 181 removed outlier: 4.384A pdb=" N SER B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.792A pdb=" N LEU B 206 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.855A pdb=" N HIS B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.617A pdb=" N THR A 201 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 257 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 258 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU A 267 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE A 216 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 207 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.617A pdb=" N THR A 201 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 257 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 258 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 253 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 302 removed outlier: 5.400A pdb=" N VAL A 289 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLU A 390 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL A 291 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 201 removed outlier: 3.521A pdb=" N THR B 201 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B 257 " --> pdb=" O THR B 201 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.89 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: 1314 1.33 - 1.45: 2528 1.45 - 1.57: 3856 1.57 - 1.69: 239 1.69 - 1.81: 27 Bond restraints: 7964 Sorted by residual: bond pdb=" O3' A C 79 " pdb=" P U C 80 " ideal model delta sigma weight residual 1.607 1.546 0.061 1.50e-02 4.44e+03 1.63e+01 bond pdb=" O3' G C 99 " pdb=" P A C 100 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.25e+01 bond pdb=" C3' DT E 6 " pdb=" C2' DT E 6 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DG D 25 " pdb=" C2' DG D 25 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.40e+00 bond pdb=" N VAL A 4 " pdb=" CA VAL A 4 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 8.11e+00 ... (remaining 7959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 10865 1.57 - 3.14: 478 3.14 - 4.71: 43 4.71 - 6.28: 10 6.28 - 7.85: 2 Bond angle restraints: 11398 Sorted by residual: angle pdb=" N GLY A 55 " pdb=" CA GLY A 55 " pdb=" C GLY A 55 " ideal model delta sigma weight residual 113.24 107.38 5.86 1.31e+00 5.83e-01 2.00e+01 angle pdb=" N3 DT D 17 " pdb=" C4 DT D 17 " pdb=" O4 DT D 17 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" O4 DT D 17 " pdb=" C4 DT D 17 " pdb=" C5 DT D 17 " ideal model delta sigma weight residual 124.90 121.94 2.96 7.00e-01 2.04e+00 1.78e+01 angle pdb=" N3 DT D 22 " pdb=" C4 DT D 22 " pdb=" O4 DT D 22 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT D 27 " pdb=" C4 DT D 27 " pdb=" O4 DT D 27 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 11393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 4218 35.63 - 71.25: 229 71.25 - 106.88: 12 106.88 - 142.51: 2 142.51 - 178.13: 5 Dihedral angle restraints: 4466 sinusoidal: 2370 harmonic: 2096 Sorted by residual: dihedral pdb=" O4' U C 94 " pdb=" C1' U C 94 " pdb=" N1 U C 94 " pdb=" C2 U C 94 " ideal model delta sinusoidal sigma weight residual 200.00 29.81 170.19 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U C 77 " pdb=" C1' U C 77 " pdb=" N1 U C 77 " pdb=" C2 U C 77 " ideal model delta sinusoidal sigma weight residual 200.00 41.62 158.38 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' U C 76 " pdb=" C1' U C 76 " pdb=" N1 U C 76 " pdb=" C2 U C 76 " ideal model delta sinusoidal sigma weight residual 232.00 61.11 170.89 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 4463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1130 0.048 - 0.097: 205 0.097 - 0.145: 53 0.145 - 0.193: 41 0.193 - 0.241: 5 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA MET A 221 " pdb=" N MET A 221 " pdb=" C MET A 221 " pdb=" CB MET A 221 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C3' G C 91 " pdb=" C4' G C 91 " pdb=" O3' G C 91 " pdb=" C2' G C 91 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' A C 207 " pdb=" C4' A C 207 " pdb=" O3' A C 207 " pdb=" C2' A C 207 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1431 not shown) Planarity restraints: 1009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 27 " -0.027 2.00e-02 2.50e+03 1.21e-02 4.41e+00 pdb=" N9 G C 27 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G C 27 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G C 27 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G C 27 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G C 27 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G C 27 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G C 27 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G C 27 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G C 27 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G C 27 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G C 27 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 40 " 0.022 2.00e-02 2.50e+03 1.18e-02 3.13e+00 pdb=" N1 C C 40 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C C 40 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C C 40 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C C 40 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C C 40 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C C 40 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C C 40 " -0.005 2.00e-02 2.50e+03 pdb=" C6 C C 40 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 90 " -0.011 2.00e-02 2.50e+03 1.06e-02 2.52e+00 pdb=" N1 U C 90 " -0.003 2.00e-02 2.50e+03 pdb=" C2 U C 90 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U C 90 " 0.007 2.00e-02 2.50e+03 pdb=" N3 U C 90 " -0.007 2.00e-02 2.50e+03 pdb=" C4 U C 90 " -0.010 2.00e-02 2.50e+03 pdb=" O4 U C 90 " 0.007 2.00e-02 2.50e+03 pdb=" C5 U C 90 " -0.011 2.00e-02 2.50e+03 pdb=" C6 U C 90 " 0.023 2.00e-02 2.50e+03 ... (remaining 1006 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 687 2.73 - 3.27: 7314 3.27 - 3.82: 13145 3.82 - 4.36: 14335 4.36 - 4.90: 22495 Nonbonded interactions: 57976 Sorted by model distance: nonbonded pdb=" O2' G C 74 " pdb=" O4' G C 75 " model vdw 2.191 3.040 nonbonded pdb=" O2' A C 71 " pdb=" O4' A C 72 " model vdw 2.195 3.040 nonbonded pdb=" O LEU A 320 " pdb=" OG1 THR A 324 " model vdw 2.244 3.040 nonbonded pdb=" O2 U C 87 " pdb=" O6 G C 99 " model vdw 2.246 2.432 nonbonded pdb=" O4 U C 47 " pdb=" O6 G C 68 " model vdw 2.246 2.432 ... (remaining 57971 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.410 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 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 : 0.005 0.061 7964 Z= 0.318 Angle : 0.696 7.848 11398 Z= 0.478 Chirality : 0.049 0.241 1434 Planarity : 0.003 0.040 1009 Dihedral : 19.453 178.134 3102 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.37 % Allowed : 2.16 % Favored : 94.47 % 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 are not related in a simple way. whole: 0.07 (0.32), residues: 699 helix: 1.21 (0.27), residues: 352 sheet: -1.12 (0.55), residues: 90 loop : -1.10 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 404 TYR 0.018 0.002 TYR A 150 PHE 0.013 0.002 PHE A 370 TRP 0.021 0.002 TRP A 24 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.32 ( 7964) covalent geometry : angle 0.69639 / 0.48 (11398) hydrogen bonds : bond 0.18117 / 12.28 ( 440) hydrogen bonds : angle 6.44768 / 4.66 ( 1183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.200 Fit side-chains REVERT: B 52 ASN cc_start: 0.8797 (t0) cc_final: 0.8536 (t0) REVERT: B 63 ASP cc_start: 0.5379 (t0) cc_final: 0.5051 (t0) REVERT: B 147 ASP cc_start: 0.8139 (t70) cc_final: 0.7926 (t0) outliers start: 14 outliers final: 1 residues processed: 102 average time/residue: 0.0965 time to fit residues: 13.0083 Evaluate side-chains 71 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.183308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.149204 restraints weight = 11611.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.148715 restraints weight = 15946.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.149251 restraints weight = 14052.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.149661 restraints weight = 11403.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.149886 restraints weight = 10208.639| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7964 Z= 0.196 Angle : 0.656 7.821 11398 Z= 0.349 Chirality : 0.037 0.162 1434 Planarity : 0.004 0.039 1009 Dihedral : 19.607 173.191 2198 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.64 % Allowed : 13.46 % Favored : 83.89 % 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 are not related in a simple way. whole: 0.83 (0.32), residues: 699 helix: 2.14 (0.26), residues: 354 sheet: -0.96 (0.51), residues: 103 loop : -1.18 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 134 TYR 0.020 0.002 TYR A 150 PHE 0.017 0.002 PHE A 370 TRP 0.006 0.001 TRP A 24 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 ( 7964) covalent geometry : angle 0.65614 / 0.35 (11398) hydrogen bonds : bond 0.06436 / 4.30 ( 440) hydrogen bonds : angle 4.09342 / 3.07 ( 1183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.226 Fit side-chains REVERT: A 356 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.6327 (m-10) REVERT: B 63 ASP cc_start: 0.6099 (t0) cc_final: 0.5836 (t0) outliers start: 11 outliers final: 6 residues processed: 81 average time/residue: 0.0584 time to fit residues: 7.3206 Evaluate side-chains 78 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.183318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.150057 restraints weight = 11361.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.149594 restraints weight = 16490.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.150233 restraints weight = 14920.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.150577 restraints weight = 12006.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.150872 restraints weight = 10779.384| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7964 Z= 0.172 Angle : 0.600 8.404 11398 Z= 0.319 Chirality : 0.036 0.162 1434 Planarity : 0.004 0.039 1009 Dihedral : 19.466 172.628 2197 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.88 % Allowed : 17.31 % Favored : 79.81 % 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 are not related in a simple way. whole: 1.25 (0.32), residues: 699 helix: 2.58 (0.26), residues: 359 sheet: -1.04 (0.53), residues: 97 loop : -1.10 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.018 0.002 TYR A 150 PHE 0.016 0.002 PHE A 370 TRP 0.006 0.001 TRP A 220 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 7964) covalent geometry : angle 0.59971 / 0.32 (11398) hydrogen bonds : bond 0.05814 / 3.85 ( 440) hydrogen bonds : angle 3.84779 / 2.88 ( 1183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.230 Fit side-chains REVERT: B 51 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7252 (ttm) REVERT: B 63 ASP cc_start: 0.6203 (t0) cc_final: 0.5932 (t0) outliers start: 12 outliers final: 7 residues processed: 78 average time/residue: 0.0735 time to fit residues: 8.3387 Evaluate side-chains 76 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 39 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 0.0170 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.184320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.149634 restraints weight = 11541.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.149447 restraints weight = 15138.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150112 restraints weight = 13370.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.150554 restraints weight = 10784.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.150876 restraints weight = 9571.991| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7964 Z= 0.135 Angle : 0.560 9.140 11398 Z= 0.294 Chirality : 0.035 0.189 1434 Planarity : 0.003 0.041 1009 Dihedral : 19.342 173.598 2197 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.85 % Allowed : 18.99 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.32), residues: 699 helix: 2.96 (0.26), residues: 357 sheet: -0.98 (0.52), residues: 102 loop : -1.13 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 241 TYR 0.011 0.001 TYR A 150 PHE 0.020 0.002 PHE A 319 TRP 0.005 0.001 TRP A 220 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 ( 7964) covalent geometry : angle 0.55953 / 0.29 (11398) hydrogen bonds : bond 0.05093 / 3.39 ( 440) hydrogen bonds : angle 3.60340 / 2.69 ( 1183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.247 Fit side-chains REVERT: B 63 ASP cc_start: 0.6133 (t0) cc_final: 0.5853 (t0) outliers start: 16 outliers final: 8 residues processed: 83 average time/residue: 0.0684 time to fit residues: 8.3820 Evaluate side-chains 73 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 10 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 69 optimal weight: 0.0470 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 72 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.183614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.148741 restraints weight = 11504.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.148092 restraints weight = 14838.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148882 restraints weight = 13364.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149156 restraints weight = 10603.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.149319 restraints weight = 9884.710| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7964 Z= 0.128 Angle : 0.544 9.000 11398 Z= 0.288 Chirality : 0.035 0.197 1434 Planarity : 0.003 0.033 1009 Dihedral : 19.217 173.865 2197 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.61 % Allowed : 20.67 % Favored : 75.72 % 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 are not related in a simple way. whole: 1.67 (0.32), residues: 699 helix: 3.11 (0.26), residues: 358 sheet: -0.95 (0.52), residues: 102 loop : -1.17 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 404 TYR 0.012 0.001 TYR A 150 PHE 0.012 0.001 PHE A 370 TRP 0.006 0.001 TRP A 220 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 ( 7964) covalent geometry : angle 0.54378 / 0.29 (11398) hydrogen bonds : bond 0.04795 / 3.18 ( 440) hydrogen bonds : angle 3.45516 / 2.58 ( 1183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.198 Fit side-chains REVERT: B 63 ASP cc_start: 0.6200 (t0) cc_final: 0.5936 (t0) outliers start: 15 outliers final: 11 residues processed: 79 average time/residue: 0.0504 time to fit residues: 6.4514 Evaluate side-chains 77 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 0.0370 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.179286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146824 restraints weight = 11647.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146373 restraints weight = 17211.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.146941 restraints weight = 15659.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.147114 restraints weight = 11988.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.147457 restraints weight = 10885.636| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7964 Z= 0.231 Angle : 0.658 8.336 11398 Z= 0.343 Chirality : 0.038 0.187 1434 Planarity : 0.004 0.040 1009 Dihedral : 19.185 175.423 2197 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.61 % Allowed : 21.63 % Favored : 74.76 % 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 are not related in a simple way. whole: 1.29 (0.33), residues: 699 helix: 2.74 (0.27), residues: 361 sheet: -0.99 (0.50), residues: 116 loop : -1.36 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 241 TYR 0.029 0.003 TYR A 150 PHE 0.025 0.003 PHE A 370 TRP 0.007 0.002 TRP A 220 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 ( 7964) covalent geometry : angle 0.65759 / 0.34 (11398) hydrogen bonds : bond 0.06157 / 4.17 ( 440) hydrogen bonds : angle 3.69483 / 2.78 ( 1183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.252 Fit side-chains REVERT: B 63 ASP cc_start: 0.6332 (t0) cc_final: 0.6090 (t0) outliers start: 15 outliers final: 9 residues processed: 74 average time/residue: 0.0530 time to fit residues: 6.3541 Evaluate side-chains 73 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.0370 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 58 optimal weight: 0.0060 chunk 73 optimal weight: 6.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.184172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.149139 restraints weight = 11382.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.149217 restraints weight = 13155.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.150604 restraints weight = 12750.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.150376 restraints weight = 10107.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.150616 restraints weight = 10169.660| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7964 Z= 0.121 Angle : 0.541 8.904 11398 Z= 0.287 Chirality : 0.035 0.208 1434 Planarity : 0.003 0.032 1009 Dihedral : 19.112 174.626 2197 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 21.88 % Favored : 75.00 % 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 are not related in a simple way. whole: 1.63 (0.33), residues: 699 helix: 3.16 (0.26), residues: 360 sheet: -1.11 (0.49), residues: 108 loop : -1.29 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 241 TYR 0.009 0.001 TYR A 367 PHE 0.010 0.001 PHE A 356 TRP 0.008 0.001 TRP A 24 HIS 0.002 0.001 HIS A 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.12 ( 7964) covalent geometry : angle 0.54120 / 0.29 (11398) hydrogen bonds : bond 0.04810 / 3.19 ( 440) hydrogen bonds : angle 3.37464 / 2.52 ( 1183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.221 Fit side-chains REVERT: B 63 ASP cc_start: 0.6026 (t0) cc_final: 0.5807 (t0) outliers start: 13 outliers final: 8 residues processed: 79 average time/residue: 0.0538 time to fit residues: 6.6571 Evaluate side-chains 74 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.0270 chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.182253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147449 restraints weight = 11525.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.147196 restraints weight = 14467.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.148479 restraints weight = 14395.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148333 restraints weight = 11750.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.148953 restraints weight = 11775.603| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7964 Z= 0.151 Angle : 0.561 8.413 11398 Z= 0.295 Chirality : 0.035 0.206 1434 Planarity : 0.003 0.035 1009 Dihedral : 19.032 175.449 2197 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.61 % Allowed : 22.36 % Favored : 74.04 % 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 are not related in a simple way. whole: 1.59 (0.33), residues: 699 helix: 3.20 (0.26), residues: 356 sheet: -1.16 (0.50), residues: 108 loop : -1.35 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 241 TYR 0.015 0.002 TYR A 150 PHE 0.015 0.002 PHE A 370 TRP 0.007 0.001 TRP A 220 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 7964) covalent geometry : angle 0.56100 / 0.30 (11398) hydrogen bonds : bond 0.05031 / 3.36 ( 440) hydrogen bonds : angle 3.38327 / 2.53 ( 1183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.216 Fit side-chains REVERT: B 63 ASP cc_start: 0.6093 (t0) cc_final: 0.5877 (t0) outliers start: 15 outliers final: 9 residues processed: 77 average time/residue: 0.0502 time to fit residues: 6.2444 Evaluate side-chains 74 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 66 optimal weight: 5.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.172111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.136632 restraints weight = 11944.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136989 restraints weight = 12680.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138480 restraints weight = 11120.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138082 restraints weight = 9155.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138645 restraints weight = 9237.484| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7964 Z= 0.198 Angle : 0.626 7.828 11398 Z= 0.328 Chirality : 0.037 0.203 1434 Planarity : 0.004 0.037 1009 Dihedral : 19.058 176.413 2197 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.33 % Allowed : 22.12 % Favored : 73.56 % 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 are not related in a simple way. whole: 1.37 (0.33), residues: 699 helix: 2.91 (0.26), residues: 361 sheet: -1.15 (0.49), residues: 116 loop : -1.41 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.026 0.002 TYR A 150 PHE 0.020 0.002 PHE A 370 TRP 0.006 0.001 TRP A 220 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 ( 7964) covalent geometry : angle 0.62566 / 0.33 (11398) hydrogen bonds : bond 0.05879 / 3.98 ( 440) hydrogen bonds : angle 3.55230 / 2.67 ( 1183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.217 Fit side-chains REVERT: B 63 ASP cc_start: 0.6181 (t0) cc_final: 0.5963 (t0) outliers start: 18 outliers final: 13 residues processed: 80 average time/residue: 0.0522 time to fit residues: 6.7518 Evaluate side-chains 80 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 67 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.174699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139204 restraints weight = 11921.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140205 restraints weight = 12528.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141220 restraints weight = 10636.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140989 restraints weight = 9040.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141206 restraints weight = 8034.929| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7964 Z= 0.136 Angle : 0.558 7.899 11398 Z= 0.295 Chirality : 0.035 0.211 1434 Planarity : 0.003 0.034 1009 Dihedral : 19.022 175.969 2197 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.37 % Allowed : 23.08 % Favored : 73.56 % 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 are not related in a simple way. whole: 1.62 (0.33), residues: 699 helix: 3.22 (0.27), residues: 356 sheet: -1.13 (0.50), residues: 109 loop : -1.33 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 241 TYR 0.013 0.001 TYR A 367 PHE 0.011 0.001 PHE A 370 TRP 0.007 0.001 TRP A 24 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 ( 7964) covalent geometry : angle 0.55848 / 0.29 (11398) hydrogen bonds : bond 0.05072 / 3.39 ( 440) hydrogen bonds : angle 3.36515 / 2.52 ( 1183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.220 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.0450 time to fit residues: 5.5314 Evaluate side-chains 76 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 256 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.174094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135513 restraints weight = 11920.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137382 restraints weight = 10938.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138022 restraints weight = 8036.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138159 restraints weight = 6913.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138373 restraints weight = 6412.321| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7964 Z= 0.150 Angle : 0.582 9.673 11398 Z= 0.303 Chirality : 0.036 0.213 1434 Planarity : 0.003 0.036 1009 Dihedral : 18.985 176.392 2197 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.88 % Allowed : 23.80 % Favored : 73.32 % 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 are not related in a simple way. whole: 1.51 (0.33), residues: 699 helix: 3.08 (0.27), residues: 360 sheet: -1.18 (0.49), residues: 115 loop : -1.36 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 241 TYR 0.016 0.002 TYR A 150 PHE 0.014 0.002 PHE A 370 TRP 0.006 0.001 TRP A 24 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 7964) covalent geometry : angle 0.58202 / 0.30 (11398) hydrogen bonds : bond 0.05132 / 3.43 ( 440) hydrogen bonds : angle 3.42789 / 2.55 ( 1183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1148.56 seconds wall clock time: 20 minutes 37.20 seconds (1237.20 seconds total)