Starting phenix.real_space_refine on Wed Aug 5 00:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hr5_34958/08_2026/8hr5_34958.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hr5_34958/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8hr5_34958/08_2026/8hr5_34958.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hr5_34958/08_2026/8hr5_34958.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hr5_34958/08_2026/8hr5_34958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hr5_34958/08_2026/8hr5_34958.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hr5_34958/08_2026/8hr5_34958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hr5_34958/08_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-2.2rc3-6140/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: {'RNAv2': 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: 1.76, per 1000 atoms: 0.23 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: 0.51 Conformation dependent library (CDL) restraints added in 382.1 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: 0.92 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: 1.40 Time building geometry restraints manager: 0.72 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 1.20e-02 6.94e+03 2.55e+01 bond pdb=" O3' G C 99 " pdb=" P A C 100 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.20e-02 6.94e+03 1.95e+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: 10622 1.57 - 3.14: 659 3.14 - 4.71: 95 4.71 - 6.28: 20 6.28 - 7.85: 2 Bond angle restraints: 11398 Sorted by residual: angle pdb=" C3' G C 91 " pdb=" O3' G C 91 " pdb=" P U C 92 " ideal model delta sigma weight residual 119.70 125.26 -5.56 1.20e+00 6.94e-01 2.15e+01 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 ... (remaining 11393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 4123 35.63 - 71.25: 326 71.25 - 106.88: 15 106.88 - 142.51: 0 142.51 - 178.13: 2 Dihedral angle restraints: 4466 sinusoidal: 2370 harmonic: 2096 Sorted by residual: dihedral pdb=" C4' A C 216 " pdb=" C3' A C 216 " pdb=" C2' A C 216 " pdb=" C1' A C 216 " ideal model delta sinusoidal sigma weight residual 36.34 -37.47 73.81 1 3.10e+00 1.04e-01 7.20e+02 dihedral pdb=" C4' A C 96 " pdb=" C3' A C 96 " pdb=" C2' A C 96 " pdb=" C1' A C 96 " ideal model delta sinusoidal sigma weight residual 36.34 -37.27 73.62 1 3.10e+00 1.04e-01 7.17e+02 dihedral pdb=" C4' G C 44 " pdb=" C3' G C 44 " pdb=" C2' G C 44 " pdb=" C1' G C 44 " ideal model delta sinusoidal sigma weight residual 36.34 -36.66 73.00 1 3.10e+00 1.04e-01 7.07e+02 ... (remaining 4463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1110 0.062 - 0.125: 153 0.125 - 0.187: 43 0.187 - 0.250: 110 0.250 - 0.312: 18 Chirality restraints: 1434 Sorted by residual: chirality pdb=" C2' A C 216 " pdb=" C3' A C 216 " pdb=" O2' A C 216 " pdb=" C1' A C 216 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" P U C 92 " pdb=" OP1 U C 92 " pdb=" OP2 U C 92 " pdb=" O5' U C 92 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' G C 91 " pdb=" C3' G C 91 " pdb=" O2' G C 91 " pdb=" C1' G C 91 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.25e+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: 6.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.980 ------------------------------------------------------------------------------- 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= 0.321 Angle : 0.824 7.848 11398 Z= 0.485 Chirality : 0.084 0.312 1434 Planarity : 0.003 0.040 1009 Dihedral : 20.851 178.134 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 0.00480 / 0.32 ( 7964) covalent geometry : angle 0.82385 / 0.49 (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 : 0.237 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: 0.0991 time to fit residues: 13.3987 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 : 0.266 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.4293 r_free = 0.4293 target = 0.182477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.147381 restraints weight = 11643.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146825 restraints weight = 15726.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.147791 restraints weight = 13712.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.148000 restraints weight = 10861.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.148286 restraints weight = 10065.195| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7964 Z= 0.236 Angle : 1.113 22.942 11398 Z= 0.477 Chirality : 0.105 2.394 1434 Planarity : 0.004 0.039 1009 Dihedral : 19.812 166.918 2198 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.88 % Allowed : 13.46 % Favored : 83.65 % 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: 0.81 (0.32), residues: 699 helix: 2.11 (0.26), residues: 354 sheet: -0.93 (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 0.019 0.002 TYR A 150 PHE 0.017 0.002 PHE A 370 TRP 0.006 0.001 TRP B 24 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.24 ( 7964) covalent geometry : angle 1.11274 / 0.48 (11398) hydrogen bonds : bond 0.06617 / 4.49 ( 440) hydrogen bonds : angle 4.13941 / 3.10 ( 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 91 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.228 Fit side-chains REVERT: A 356 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6392 (m-10) REVERT: B 63 ASP cc_start: 0.6121 (t0) cc_final: 0.5839 (t0) outliers start: 12 outliers final: 6 residues processed: 82 average time/residue: 0.0593 time to fit residues: 7.5352 Evaluate side-chains 77 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 58 optimal weight: 0.0060 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 0.0070 overall best weight: 0.5416 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.186775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154194 restraints weight = 11364.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.153803 restraints weight = 16665.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154341 restraints weight = 14558.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.154609 restraints weight = 12334.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.155066 restraints weight = 10738.843| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7964 Z= 0.156 Angle : 0.858 11.970 11398 Z= 0.380 Chirality : 0.077 1.722 1434 Planarity : 0.003 0.035 1009 Dihedral : 19.843 170.066 2197 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.40 % Allowed : 15.62 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.32), residues: 699 helix: 2.70 (0.26), residues: 358 sheet: -0.84 (0.54), residues: 95 loop : -1.15 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.011 0.001 TYR B 30 PHE 0.011 0.001 PHE A 370 TRP 0.006 0.001 TRP A 220 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 ( 7964) covalent geometry : angle 0.85815 / 0.38 (11398) hydrogen bonds : bond 0.05444 / 3.62 ( 440) hydrogen bonds : angle 3.76856 / 2.81 ( 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 88 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.275 Fit side-chains REVERT: B 63 ASP cc_start: 0.6200 (t0) cc_final: 0.5919 (t0) REVERT: B 192 ASN cc_start: 0.7876 (t0) cc_final: 0.7608 (t0) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 0.0631 time to fit residues: 7.6410 Evaluate side-chains 72 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain B residue 4 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: 0.1980 chunk 80 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 0.0670 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.185931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.151816 restraints weight = 11564.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.151089 restraints weight = 14679.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.151791 restraints weight = 14294.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.152225 restraints weight = 11100.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.152348 restraints weight = 10168.879| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2281 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= 0.147 Angle : 0.811 12.164 11398 Z= 0.359 Chirality : 0.071 1.668 1434 Planarity : 0.003 0.034 1009 Dihedral : 19.461 170.078 2197 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.61 % Allowed : 18.51 % Favored : 77.88 % 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: 1.61 (0.32), residues: 699 helix: 3.00 (0.26), residues: 357 sheet: -0.90 (0.52), residues: 102 loop : -1.08 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 241 TYR 0.012 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 0.00286 / 0.15 ( 7964) covalent geometry : angle 0.81097 / 0.36 (11398) hydrogen bonds : bond 0.04886 / 3.30 ( 440) hydrogen bonds : angle 3.53568 / 2.65 ( 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 87 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.229 Fit side-chains REVERT: B 63 ASP cc_start: 0.6191 (t0) cc_final: 0.5920 (t0) outliers start: 15 outliers final: 8 residues processed: 79 average time/residue: 0.0675 time to fit residues: 8.1966 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 : 0.256 ------------------------------------------------------------------------------- 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 220 TRP Chi-restraints excluded: chain A residue 326 MET 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 256 ASP 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: 5.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.0070 chunk 59 optimal weight: 0.6980 chunk 28 optimal weight: 0.0270 chunk 72 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 overall best weight: 0.3234 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.188203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154494 restraints weight = 11474.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.153956 restraints weight = 14439.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.155375 restraints weight = 14352.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.155388 restraints weight = 10721.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.155788 restraints weight = 11055.217| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7964 Z= 0.127 Angle : 0.771 11.311 11398 Z= 0.342 Chirality : 0.067 1.494 1434 Planarity : 0.003 0.029 1009 Dihedral : 19.302 171.520 2197 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.92 % Allowed : 21.39 % Favored : 76.68 % 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 are not related in a simple way. whole: 1.83 (0.32), residues: 699 helix: 3.30 (0.26), residues: 353 sheet: -0.83 (0.52), residues: 102 loop : -1.11 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 404 TYR 0.009 0.001 TYR A 150 PHE 0.010 0.001 PHE A 370 TRP 0.005 0.001 TRP A 24 HIS 0.002 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 ( 7964) covalent geometry : angle 0.77117 / 0.34 (11398) hydrogen bonds : bond 0.04499 / 2.99 ( 440) hydrogen bonds : angle 3.37720 / 2.52 ( 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 80 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.231 Fit side-chains REVERT: B 63 ASP cc_start: 0.6162 (t0) cc_final: 0.5891 (t0) outliers start: 8 outliers final: 5 residues processed: 77 average time/residue: 0.0616 time to fit residues: 7.3426 Evaluate side-chains 72 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 156 ILE 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: 0.0070 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.187788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154554 restraints weight = 11535.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.154389 restraints weight = 15027.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.154368 restraints weight = 14827.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.154623 restraints weight = 13008.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.154868 restraints weight = 10981.254| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2694 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= 0.131 Angle : 0.770 11.068 11398 Z= 0.340 Chirality : 0.066 1.415 1434 Planarity : 0.003 0.031 1009 Dihedral : 19.107 172.643 2197 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.12 % Allowed : 20.43 % Favored : 76.44 % 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: 1.89 (0.32), residues: 699 helix: 3.37 (0.26), residues: 354 sheet: -0.87 (0.52), residues: 102 loop : -1.12 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 241 TYR 0.011 0.001 TYR A 367 PHE 0.013 0.001 PHE A 370 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 0.00252 / 0.13 ( 7964) covalent geometry : angle 0.77013 / 0.34 (11398) hydrogen bonds : bond 0.04501 / 3.01 ( 440) hydrogen bonds : angle 3.28210 / 2.45 ( 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 86 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.200 Fit side-chains REVERT: B 63 ASP cc_start: 0.6215 (t0) cc_final: 0.5951 (t0) outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.0592 time to fit residues: 7.5139 Evaluate side-chains 72 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 220 TRP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.0470 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 43 optimal weight: 0.0370 chunk 58 optimal weight: 0.0470 chunk 73 optimal weight: 5.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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 = 0.4340 r_free = 0.4340 target = 0.186525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.151774 restraints weight = 11683.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.151947 restraints weight = 12938.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152379 restraints weight = 11411.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.152764 restraints weight = 10026.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152976 restraints weight = 8894.851| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7964 Z= 0.121 Angle : 0.754 10.783 11398 Z= 0.332 Chirality : 0.065 1.337 1434 Planarity : 0.003 0.027 1009 Dihedral : 19.021 172.014 2197 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.40 % Allowed : 21.88 % 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: 1.95 (0.32), residues: 699 helix: 3.43 (0.26), residues: 354 sheet: -0.83 (0.51), residues: 103 loop : -1.11 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 404 TYR 0.011 0.001 TYR A 367 PHE 0.010 0.001 PHE A 370 TRP 0.005 0.001 TRP A 24 HIS 0.002 0.001 HIS A 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 ( 7964) covalent geometry : angle 0.75404 / 0.33 (11398) hydrogen bonds : bond 0.04294 / 2.85 ( 440) hydrogen bonds : angle 3.22134 / 2.39 ( 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 79 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.226 Fit side-chains REVERT: B 63 ASP cc_start: 0.6114 (t0) cc_final: 0.5841 (t0) outliers start: 10 outliers final: 8 residues processed: 75 average time/residue: 0.0518 time to fit residues: 6.4758 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 : 0.236 ------------------------------------------------------------------------------- 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 156 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.184264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.151284 restraints weight = 11508.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151112 restraints weight = 16141.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151556 restraints weight = 14691.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.151959 restraints weight = 12155.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.152044 restraints weight = 11264.562| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7964 Z= 0.195 Angle : 0.831 10.764 11398 Z= 0.367 Chirality : 0.066 1.247 1434 Planarity : 0.003 0.033 1009 Dihedral : 19.025 171.648 2197 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.37 % Allowed : 21.63 % 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: 1.73 (0.33), residues: 699 helix: 3.18 (0.26), residues: 356 sheet: -0.84 (0.51), residues: 108 loop : -1.18 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 241 TYR 0.023 0.002 TYR A 150 PHE 0.020 0.002 PHE A 370 TRP 0.006 0.001 TRP A 220 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 ( 7964) covalent geometry : angle 0.83125 / 0.37 (11398) hydrogen bonds : bond 0.05224 / 3.57 ( 440) hydrogen bonds : angle 3.38516 / 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: 14 poor density : 67 time to evaluate : 0.194 Fit side-chains REVERT: B 63 ASP cc_start: 0.6277 (t0) cc_final: 0.6048 (t0) outliers start: 14 outliers final: 12 residues processed: 76 average time/residue: 0.0609 time to fit residues: 7.1567 Evaluate side-chains 76 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 393 SER 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 228 VAL Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.171929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135286 restraints weight = 11931.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135974 restraints weight = 12256.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136384 restraints weight = 9912.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136788 restraints weight = 8843.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136891 restraints weight = 8053.722| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7964 Z= 0.251 Angle : 0.939 12.213 11398 Z= 0.418 Chirality : 0.068 1.110 1434 Planarity : 0.004 0.035 1009 Dihedral : 19.232 168.155 2197 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.12 % Allowed : 23.32 % 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: 1.13 (0.33), residues: 699 helix: 2.57 (0.26), residues: 361 sheet: -0.97 (0.50), residues: 116 loop : -1.41 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 134 TYR 0.028 0.003 TYR A 150 PHE 0.025 0.003 PHE A 370 TRP 0.009 0.002 TRP A 24 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.25 ( 7964) covalent geometry : angle 0.93864 / 0.42 (11398) hydrogen bonds : bond 0.06547 / 4.48 ( 440) hydrogen bonds : angle 3.75043 / 2.83 ( 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 81 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.222 Fit side-chains REVERT: B 47 ASP cc_start: 0.7326 (t0) cc_final: 0.7121 (t0) outliers start: 13 outliers final: 9 residues processed: 76 average time/residue: 0.0573 time to fit residues: 6.9038 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 : 0.223 ------------------------------------------------------------------------------- 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 393 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.175241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137888 restraints weight = 11959.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137976 restraints weight = 8757.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138822 restraints weight = 7798.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.138993 restraints weight = 6748.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139065 restraints weight = 6202.779| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7964 Z= 0.155 Angle : 0.827 10.102 11398 Z= 0.365 Chirality : 0.064 1.155 1434 Planarity : 0.003 0.032 1009 Dihedral : 19.083 166.685 2197 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.16 % Allowed : 25.00 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.53 (0.33), residues: 699 helix: 3.13 (0.27), residues: 355 sheet: -1.05 (0.51), residues: 108 loop : -1.40 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.023 0.002 TYR A 150 PHE 0.012 0.002 PHE A 370 TRP 0.009 0.001 TRP A 220 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 ( 7964) covalent geometry : angle 0.82668 / 0.37 (11398) hydrogen bonds : bond 0.05399 / 3.65 ( 440) hydrogen bonds : angle 3.47894 / 2.61 ( 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 73 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.165 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 70 average time/residue: 0.0577 time to fit residues: 6.1868 Evaluate side-chains 71 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 393 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.174778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136560 restraints weight = 11960.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138837 restraints weight = 10022.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.139338 restraints weight = 7359.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139358 restraints weight = 6205.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139494 restraints weight = 5926.505| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3199 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= 0.163 Angle : 0.832 9.912 11398 Z= 0.366 Chirality : 0.064 1.119 1434 Planarity : 0.003 0.033 1009 Dihedral : 19.040 166.966 2197 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.40 % Allowed : 25.00 % Favored : 72.60 % 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: 3.14 (0.27), residues: 357 sheet: -0.82 (0.52), residues: 110 loop : -1.39 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 202 TYR 0.019 0.002 TYR A 150 PHE 0.016 0.002 PHE A 370 TRP 0.008 0.001 TRP A 220 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 7964) covalent geometry : angle 0.83216 / 0.37 (11398) hydrogen bonds : bond 0.05363 / 3.61 ( 440) hydrogen bonds : angle 3.47016 / 2.59 ( 1183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1211.01 seconds wall clock time: 21 minutes 38.93 seconds (1298.93 seconds total)