Starting phenix.real_space_refine on Tue Mar 3 16:33:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i28_52579/03_2026/9i28_52579.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i28_52579/03_2026/9i28_52579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i28_52579/03_2026/9i28_52579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i28_52579/03_2026/9i28_52579.map" model { file = "/net/cci-nas-00/data/ceres_data/9i28_52579/03_2026/9i28_52579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i28_52579/03_2026/9i28_52579.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.700 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 4354 2.51 5 N 1198 2.21 5 O 1314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6908 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 427} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 427} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.42, per 1000 atoms: 0.21 Number of scatterers: 6908 At special positions: 0 Unit cell: (112.005, 83.185, 65.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 4 15.00 Mg 2 11.99 O 1314 8.00 N 1198 7.00 C 4354 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: 0.68 Conformation dependent library (CDL) restraints added in 281.5 milliseconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 48.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 100 through 110 removed outlier: 3.720A pdb=" N PHE A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 142 through 151 removed outlier: 3.886A pdb=" N LEU A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 Processing helix chain 'A' and resid 203 through 223 Processing helix chain 'A' and resid 236 through 252 Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.632A pdb=" N SER A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 267 through 279 removed outlier: 4.079A pdb=" N ALA A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.719A pdb=" N SER A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 345 removed outlier: 3.697A pdb=" N ALA A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 Processing helix chain 'A' and resid 402 through 419 Processing helix chain 'A' and resid 422 through 430 removed outlier: 3.718A pdb=" N GLU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 440 removed outlier: 3.517A pdb=" N PHE A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 448 Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 37 through 50 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 100 through 110 removed outlier: 3.724A pdb=" N PHE B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 142 through 151 removed outlier: 3.886A pdb=" N LEU B 146 " --> pdb=" O ASN B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 203 through 223 Processing helix chain 'B' and resid 236 through 252 removed outlier: 3.554A pdb=" N GLY B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 256 removed outlier: 4.569A pdb=" N SER B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 267 through 279 removed outlier: 4.053A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 removed outlier: 3.720A pdb=" N SER B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 336 through 345 removed outlier: 3.700A pdb=" N ALA B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 384 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 422 through 430 removed outlier: 3.684A pdb=" N GLU B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 440 removed outlier: 3.517A pdb=" N PHE B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 75 removed outlier: 6.666A pdb=" N LYS A 82 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 74 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 80 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 25 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 126 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA A 27 " --> pdb=" O HIS A 124 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 302 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.966A pdb=" N ILE A 190 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN A 231 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE A 228 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 261 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA A 230 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR A 391 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE A 367 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AA4, first strand: chain 'B' and resid 70 through 75 removed outlier: 6.655A pdb=" N LYS B 82 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL B 74 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 80 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B 25 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE B 126 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA B 27 " --> pdb=" O HIS B 124 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 302 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 160 through 164 removed outlier: 6.747A pdb=" N VAL B 161 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N KCX B 191 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR B 163 " --> pdb=" O KCX B 191 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 190 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASN B 231 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE B 228 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU B 261 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 230 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 320 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR B 391 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE B 367 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 349 305 hydrogen bonds defined for protein. 897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1285 1.32 - 1.45: 1860 1.45 - 1.57: 3861 1.57 - 1.69: 4 1.69 - 1.81: 62 Bond restraints: 7072 Sorted by residual: bond pdb=" NZ KCX A 191 " pdb=" CX KCX A 191 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C ILE B 190 " pdb=" N KCX B 191 " ideal model delta sigma weight residual 1.329 1.275 0.054 1.40e-02 5.10e+03 1.48e+01 bond pdb=" CX KCX B 191 " pdb=" OQ2 KCX B 191 " ideal model delta sigma weight residual 1.251 1.325 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" NZ KCX B 191 " pdb=" CX KCX B 191 " ideal model delta sigma weight residual 1.411 1.339 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CX KCX A 191 " pdb=" OQ2 KCX A 191 " ideal model delta sigma weight residual 1.251 1.314 -0.063 2.00e-02 2.50e+03 9.84e+00 ... (remaining 7067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9393 1.78 - 3.57: 163 3.57 - 5.35: 17 5.35 - 7.13: 16 7.13 - 8.92: 5 Bond angle restraints: 9594 Sorted by residual: angle pdb=" CA PRO B 195 " pdb=" C PRO B 195 " pdb=" N GLN B 196 " ideal model delta sigma weight residual 116.45 119.52 -3.07 8.50e-01 1.38e+00 1.30e+01 angle pdb=" CA PRO B 195 " pdb=" C PRO B 195 " pdb=" O PRO B 195 " ideal model delta sigma weight residual 121.38 118.76 2.62 7.70e-01 1.69e+00 1.15e+01 angle pdb=" O1P CAP A 501 " pdb=" P1 CAP A 501 " pdb=" O3P CAP A 501 " ideal model delta sigma weight residual 109.50 118.42 -8.92 3.00e+00 1.11e-01 8.83e+00 angle pdb=" CA ASP A 117 " pdb=" CB ASP A 117 " pdb=" CG ASP A 117 " ideal model delta sigma weight residual 112.60 115.51 -2.91 1.00e+00 1.00e+00 8.47e+00 angle pdb=" O1P CAP B 501 " pdb=" P1 CAP B 501 " pdb=" O3P CAP B 501 " ideal model delta sigma weight residual 109.50 118.12 -8.62 3.00e+00 1.11e-01 8.26e+00 ... (remaining 9589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.51: 4059 31.51 - 63.01: 61 63.01 - 94.52: 6 94.52 - 126.03: 0 126.03 - 157.54: 4 Dihedral angle restraints: 4130 sinusoidal: 1600 harmonic: 2530 Sorted by residual: dihedral pdb=" C5 CAP B 501 " pdb=" O5 CAP B 501 " pdb=" P2 CAP B 501 " pdb=" O4P CAP B 501 " ideal model delta sinusoidal sigma weight residual 160.56 3.02 157.54 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C5 CAP A 501 " pdb=" O5 CAP A 501 " pdb=" P2 CAP A 501 " pdb=" O4P CAP A 501 " ideal model delta sinusoidal sigma weight residual 160.56 6.24 154.32 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C1 CAP A 501 " pdb=" O1 CAP A 501 " pdb=" P1 CAP A 501 " pdb=" O2P CAP A 501 " ideal model delta sinusoidal sigma weight residual 53.66 -157.92 -148.42 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 4127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 570 0.028 - 0.056: 285 0.056 - 0.085: 77 0.085 - 0.113: 57 0.113 - 0.141: 21 Chirality restraints: 1010 Sorted by residual: chirality pdb=" CA LEU A 227 " pdb=" N LEU A 227 " pdb=" C LEU A 227 " pdb=" CB LEU A 227 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA VAL B 24 " pdb=" N VAL B 24 " pdb=" C VAL B 24 " pdb=" CB VAL B 24 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VAL A 24 " pdb=" N VAL A 24 " pdb=" C VAL A 24 " pdb=" CB VAL A 24 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1007 not shown) Planarity restraints: 1270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 364 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 365 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 190 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C ILE B 190 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE B 190 " -0.013 2.00e-02 2.50e+03 pdb=" N KCX B 191 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CAP A 501 " 0.023 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C2 CAP A 501 " -0.007 2.00e-02 2.50e+03 pdb=" O6 CAP A 501 " -0.008 2.00e-02 2.50e+03 pdb=" O7 CAP A 501 " -0.008 2.00e-02 2.50e+03 ... (remaining 1267 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 38 2.64 - 3.20: 6343 3.20 - 3.77: 11498 3.77 - 4.33: 17148 4.33 - 4.90: 27333 Nonbonded interactions: 62360 Sorted by model distance: nonbonded pdb="MG MG B 500 " pdb=" O6 CAP B 501 " model vdw 2.073 2.170 nonbonded pdb="MG MG A 500 " pdb=" O6 CAP A 501 " model vdw 2.121 2.170 nonbonded pdb=" OQ2 KCX A 191 " pdb="MG MG A 500 " model vdw 2.125 2.170 nonbonded pdb="MG MG A 500 " pdb=" O2 CAP A 501 " model vdw 2.141 2.170 nonbonded pdb="MG MG A 500 " pdb=" O3 CAP A 501 " model vdw 2.160 2.170 ... (remaining 62355 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.720 Find NCS groups from input model: 0.110 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:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 0.082 7072 Z= 0.226 Angle : 0.637 8.916 9594 Z= 0.313 Chirality : 0.043 0.141 1010 Planarity : 0.005 0.054 1270 Dihedral : 13.215 157.535 2530 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.44 % Allowed : 6.03 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.19 (0.27), residues: 888 helix: 0.72 (0.25), residues: 394 sheet: -1.09 (0.44), residues: 138 loop : -0.53 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.013 0.002 TYR A 286 PHE 0.013 0.002 PHE A 45 TRP 0.004 0.001 TRP B 357 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 7072) covalent geometry : angle 0.63726 ( 9594) hydrogen bonds : bond 0.13984 ( 305) hydrogen bonds : angle 6.84494 ( 897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.297 Fit side-chains REVERT: A 107 LEU cc_start: 0.8552 (mt) cc_final: 0.8157 (mp) REVERT: A 206 ASP cc_start: 0.7156 (m-30) cc_final: 0.6946 (m-30) REVERT: A 213 ASP cc_start: 0.8012 (t70) cc_final: 0.7791 (t0) REVERT: A 432 GLU cc_start: 0.8041 (mp0) cc_final: 0.7478 (mt-10) REVERT: B 432 GLU cc_start: 0.8032 (mp0) cc_final: 0.7743 (mm-30) outliers start: 3 outliers final: 2 residues processed: 162 average time/residue: 0.5186 time to fit residues: 88.5006 Evaluate side-chains 111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain B residue 117 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS A 415 GLN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.165465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144095 restraints weight = 8651.234| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.45 r_work: 0.3634 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7072 Z= 0.240 Angle : 0.597 6.857 9594 Z= 0.314 Chirality : 0.044 0.132 1010 Planarity : 0.005 0.050 1270 Dihedral : 10.165 146.420 1012 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.09 % Allowed : 13.82 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.04 (0.27), residues: 888 helix: 0.96 (0.25), residues: 386 sheet: -1.05 (0.44), residues: 138 loop : -0.57 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.024 0.003 TYR A 448 PHE 0.013 0.002 PHE B 45 TRP 0.005 0.001 TRP B 417 HIS 0.005 0.001 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 7072) covalent geometry : angle 0.59675 ( 9594) hydrogen bonds : bond 0.04754 ( 305) hydrogen bonds : angle 5.44154 ( 897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.256 Fit side-chains REVERT: A 107 LEU cc_start: 0.8560 (mt) cc_final: 0.8212 (mp) REVERT: A 375 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7771 (mtt180) REVERT: A 425 ASP cc_start: 0.8285 (m-30) cc_final: 0.7937 (m-30) REVERT: A 432 GLU cc_start: 0.8055 (mp0) cc_final: 0.7714 (mp0) outliers start: 21 outliers final: 11 residues processed: 121 average time/residue: 0.5359 time to fit residues: 68.4625 Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.167187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146489 restraints weight = 8542.349| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.39 r_work: 0.3661 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7072 Z= 0.187 Angle : 0.552 6.459 9594 Z= 0.290 Chirality : 0.043 0.141 1010 Planarity : 0.004 0.047 1270 Dihedral : 9.419 164.036 1008 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.68 % Allowed : 15.29 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.01 (0.27), residues: 888 helix: 1.02 (0.25), residues: 386 sheet: -1.01 (0.43), residues: 138 loop : -0.61 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.026 0.002 TYR B 448 PHE 0.011 0.002 PHE B 45 TRP 0.005 0.001 TRP B 417 HIS 0.005 0.002 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 7072) covalent geometry : angle 0.55202 ( 9594) hydrogen bonds : bond 0.04218 ( 305) hydrogen bonds : angle 5.14362 ( 897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.249 Fit side-chains REVERT: A 13 LYS cc_start: 0.8558 (mtmm) cc_final: 0.8332 (ptpt) REVERT: A 107 LEU cc_start: 0.8546 (mt) cc_final: 0.8180 (mp) REVERT: A 375 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7698 (mtt180) REVERT: A 432 GLU cc_start: 0.7990 (mp0) cc_final: 0.7667 (mp0) REVERT: B 375 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7759 (mtt180) outliers start: 25 outliers final: 10 residues processed: 126 average time/residue: 0.5364 time to fit residues: 71.3074 Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 7 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.167235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145947 restraints weight = 8752.755| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.47 r_work: 0.3652 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7072 Z= 0.132 Angle : 0.520 5.682 9594 Z= 0.272 Chirality : 0.041 0.142 1010 Planarity : 0.004 0.044 1270 Dihedral : 9.343 172.990 1008 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.71 % Allowed : 16.76 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.18 (0.27), residues: 888 helix: 1.41 (0.26), residues: 374 sheet: -1.00 (0.43), residues: 140 loop : -0.70 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 276 TYR 0.024 0.002 TYR B 448 PHE 0.011 0.001 PHE B 327 TRP 0.005 0.001 TRP B 417 HIS 0.004 0.001 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7072) covalent geometry : angle 0.51972 ( 9594) hydrogen bonds : bond 0.03712 ( 305) hydrogen bonds : angle 4.92056 ( 897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.303 Fit side-chains REVERT: A 107 LEU cc_start: 0.8598 (mt) cc_final: 0.8219 (mp) REVERT: A 375 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7619 (mtt180) REVERT: A 432 GLU cc_start: 0.7960 (mp0) cc_final: 0.7677 (mp0) REVERT: B 400 ILE cc_start: 0.8526 (tt) cc_final: 0.7855 (pt) REVERT: B 432 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7999 (mm-30) outliers start: 32 outliers final: 10 residues processed: 136 average time/residue: 0.5054 time to fit residues: 72.7609 Evaluate side-chains 115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 87 optimal weight: 0.0970 chunk 65 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.169209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.147661 restraints weight = 8749.574| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.49 r_work: 0.3677 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7072 Z= 0.115 Angle : 0.513 5.299 9594 Z= 0.268 Chirality : 0.041 0.145 1010 Planarity : 0.004 0.043 1270 Dihedral : 9.315 175.905 1008 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.26 % Allowed : 19.26 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.34 (0.27), residues: 888 helix: 1.60 (0.26), residues: 372 sheet: -0.95 (0.42), residues: 140 loop : -0.64 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 276 TYR 0.023 0.002 TYR B 448 PHE 0.010 0.001 PHE B 45 TRP 0.005 0.001 TRP B 417 HIS 0.009 0.001 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7072) covalent geometry : angle 0.51269 ( 9594) hydrogen bonds : bond 0.03458 ( 305) hydrogen bonds : angle 4.74140 ( 897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.240 Fit side-chains REVERT: A 13 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8360 (ptpt) REVERT: A 107 LEU cc_start: 0.8573 (mt) cc_final: 0.8200 (mp) REVERT: A 400 ILE cc_start: 0.8505 (tt) cc_final: 0.7899 (pt) REVERT: B 72 TYR cc_start: 0.8002 (p90) cc_final: 0.7615 (p90) REVERT: B 107 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8154 (mp) REVERT: B 115 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7190 (mtt) REVERT: B 375 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7659 (mtt180) REVERT: B 400 ILE cc_start: 0.8356 (tt) cc_final: 0.7919 (pt) REVERT: B 432 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7922 (mm-30) outliers start: 29 outliers final: 8 residues processed: 131 average time/residue: 0.5141 time to fit residues: 71.0895 Evaluate side-chains 115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 0.0470 chunk 49 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 69 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 76 optimal weight: 0.0170 chunk 54 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.170906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150276 restraints weight = 8680.512| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.40 r_work: 0.3711 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7072 Z= 0.102 Angle : 0.508 5.324 9594 Z= 0.265 Chirality : 0.041 0.159 1010 Planarity : 0.004 0.039 1270 Dihedral : 9.005 173.516 1008 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.94 % Allowed : 20.88 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.39 (0.28), residues: 888 helix: 1.37 (0.26), residues: 396 sheet: -0.86 (0.43), residues: 136 loop : -0.44 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 276 TYR 0.025 0.001 TYR B 448 PHE 0.010 0.001 PHE B 45 TRP 0.006 0.001 TRP B 417 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7072) covalent geometry : angle 0.50836 ( 9594) hydrogen bonds : bond 0.03303 ( 305) hydrogen bonds : angle 4.60095 ( 897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.283 Fit side-chains REVERT: A 400 ILE cc_start: 0.8316 (tt) cc_final: 0.8051 (pt) REVERT: B 72 TYR cc_start: 0.7912 (p90) cc_final: 0.7540 (p90) REVERT: B 115 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7289 (mtt) REVERT: B 400 ILE cc_start: 0.8389 (tt) cc_final: 0.8028 (pt) REVERT: B 432 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7836 (mm-30) outliers start: 20 outliers final: 8 residues processed: 129 average time/residue: 0.5200 time to fit residues: 70.9161 Evaluate side-chains 119 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 81 optimal weight: 0.0770 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 78 optimal weight: 0.0670 chunk 75 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.172038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.150753 restraints weight = 8623.025| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.49 r_work: 0.3705 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7072 Z= 0.105 Angle : 0.514 5.143 9594 Z= 0.268 Chirality : 0.041 0.150 1010 Planarity : 0.004 0.039 1270 Dihedral : 8.897 179.684 1008 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.94 % Allowed : 22.35 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.34 (0.28), residues: 888 helix: 1.41 (0.26), residues: 396 sheet: -1.08 (0.43), residues: 146 loop : -0.45 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 78 TYR 0.025 0.001 TYR A 448 PHE 0.010 0.001 PHE B 45 TRP 0.011 0.001 TRP B 184 HIS 0.010 0.001 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7072) covalent geometry : angle 0.51395 ( 9594) hydrogen bonds : bond 0.03244 ( 305) hydrogen bonds : angle 4.59371 ( 897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.250 Fit side-chains REVERT: A 400 ILE cc_start: 0.8436 (tt) cc_final: 0.8026 (pt) REVERT: A 432 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7760 (mm-30) REVERT: B 72 TYR cc_start: 0.7894 (p90) cc_final: 0.7527 (p90) REVERT: B 78 ARG cc_start: 0.8331 (mtp85) cc_final: 0.8125 (mtp180) REVERT: B 301 ARG cc_start: 0.8168 (ptm160) cc_final: 0.7951 (pmm-80) REVERT: B 400 ILE cc_start: 0.8293 (tt) cc_final: 0.7963 (pt) REVERT: B 432 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7811 (mm-30) outliers start: 20 outliers final: 9 residues processed: 129 average time/residue: 0.5445 time to fit residues: 74.1955 Evaluate side-chains 115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.166571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.144836 restraints weight = 8753.623| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.47 r_work: 0.3634 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7072 Z= 0.186 Angle : 0.602 6.050 9594 Z= 0.314 Chirality : 0.044 0.137 1010 Planarity : 0.004 0.040 1270 Dihedral : 8.975 177.103 1008 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.65 % Allowed : 23.53 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.17 (0.27), residues: 888 helix: 1.20 (0.26), residues: 380 sheet: -1.10 (0.43), residues: 146 loop : -0.41 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 78 TYR 0.028 0.002 TYR B 448 PHE 0.012 0.002 PHE B 45 TRP 0.016 0.001 TRP B 184 HIS 0.009 0.002 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 7072) covalent geometry : angle 0.60181 ( 9594) hydrogen bonds : bond 0.03948 ( 305) hydrogen bonds : angle 4.84810 ( 897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.332 Fit side-chains REVERT: A 400 ILE cc_start: 0.8565 (tt) cc_final: 0.7755 (pt) REVERT: B 72 TYR cc_start: 0.7929 (p90) cc_final: 0.7548 (p90) REVERT: B 103 SER cc_start: 0.8883 (t) cc_final: 0.8316 (m) REVERT: B 400 ILE cc_start: 0.8545 (tt) cc_final: 0.7988 (pt) outliers start: 18 outliers final: 10 residues processed: 120 average time/residue: 0.5079 time to fit residues: 64.7464 Evaluate side-chains 118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 HIS B 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146681 restraints weight = 8695.388| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.49 r_work: 0.3650 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7072 Z= 0.149 Angle : 0.572 6.186 9594 Z= 0.297 Chirality : 0.043 0.142 1010 Planarity : 0.004 0.039 1270 Dihedral : 8.498 173.775 1008 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.91 % Allowed : 23.82 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.06 (0.28), residues: 888 helix: 0.99 (0.25), residues: 392 sheet: -1.14 (0.43), residues: 146 loop : -0.36 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.025 0.002 TYR A 448 PHE 0.011 0.002 PHE B 45 TRP 0.015 0.001 TRP B 184 HIS 0.011 0.001 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7072) covalent geometry : angle 0.57245 ( 9594) hydrogen bonds : bond 0.03723 ( 305) hydrogen bonds : angle 4.82982 ( 897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.229 Fit side-chains REVERT: A 400 ILE cc_start: 0.8399 (tt) cc_final: 0.7668 (pt) REVERT: A 432 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7787 (mm-30) REVERT: B 72 TYR cc_start: 0.7921 (p90) cc_final: 0.7605 (p90) REVERT: B 400 ILE cc_start: 0.8515 (tt) cc_final: 0.7933 (pt) outliers start: 13 outliers final: 10 residues processed: 115 average time/residue: 0.5046 time to fit residues: 61.6614 Evaluate side-chains 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.146345 restraints weight = 8591.026| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.51 r_work: 0.3651 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7072 Z= 0.148 Angle : 0.588 7.496 9594 Z= 0.302 Chirality : 0.043 0.143 1010 Planarity : 0.004 0.038 1270 Dihedral : 7.500 141.719 1008 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.06 % Allowed : 23.38 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.08 (0.28), residues: 888 helix: 0.92 (0.25), residues: 402 sheet: -1.15 (0.43), residues: 146 loop : -0.26 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.020 0.002 TYR B 448 PHE 0.011 0.002 PHE B 45 TRP 0.019 0.001 TRP A 184 HIS 0.012 0.002 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7072) covalent geometry : angle 0.58789 ( 9594) hydrogen bonds : bond 0.03711 ( 305) hydrogen bonds : angle 4.83854 ( 897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.182 Fit side-chains REVERT: A 400 ILE cc_start: 0.8414 (tt) cc_final: 0.7658 (pt) REVERT: A 432 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7799 (mm-30) REVERT: B 72 TYR cc_start: 0.7926 (p90) cc_final: 0.7596 (p90) REVERT: B 400 ILE cc_start: 0.8531 (tt) cc_final: 0.7880 (pt) REVERT: B 432 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7853 (mm-30) outliers start: 14 outliers final: 10 residues processed: 113 average time/residue: 0.5025 time to fit residues: 60.0900 Evaluate side-chains 117 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.169332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.147002 restraints weight = 8631.685| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.51 r_work: 0.3661 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7072 Z= 0.137 Angle : 0.590 10.110 9594 Z= 0.300 Chirality : 0.043 0.144 1010 Planarity : 0.004 0.037 1270 Dihedral : 6.993 123.259 1008 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.76 % Allowed : 23.68 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.08 (0.28), residues: 888 helix: 0.92 (0.25), residues: 402 sheet: -1.13 (0.43), residues: 146 loop : -0.27 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.020 0.002 TYR B 265 PHE 0.011 0.001 PHE B 45 TRP 0.030 0.002 TRP A 184 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7072) covalent geometry : angle 0.58984 ( 9594) hydrogen bonds : bond 0.03647 ( 305) hydrogen bonds : angle 4.83210 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2462.95 seconds wall clock time: 42 minutes 41.03 seconds (2561.03 seconds total)