Starting phenix.real_space_refine on Thu Jul 2 02:16:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1b_61970/07_2026/9k1b_61970.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1b_61970/07_2026/9k1b_61970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k1b_61970/07_2026/9k1b_61970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1b_61970/07_2026/9k1b_61970.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1b_61970/07_2026/9k1b_61970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1b_61970/07_2026/9k1b_61970.cif" } resolution = 3.34 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= -0.004 sd= 0.073 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 S 39 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3704 2.51 5 N 883 2.21 5 O 985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5614 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4036 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 28, 'TRANS': 509} Chain breaks: 1 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'PHE:plan': 7, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 7, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 179 Chain: "H" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "L" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 717 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 7 Ad-hoc single atom residues: {' NA': 2, ' CL': 1} Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Time building chain proxies: 1.48, per 1000 atoms: 0.26 Number of scatterers: 5614 At special positions: 0 Unit cell: (84.315, 88.695, 105.12, 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) Cl 1 17.00 S 39 16.00 Na 2 11.00 O 985 8.00 N 883 7.00 C 3704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 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: 0.32 Conformation dependent library (CDL) restraints added in 137.6 milliseconds 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1386 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 58.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.600A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.931A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 78 removed outlier: 4.277A pdb=" N ALA A 78 " --> pdb=" O GLY A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 78' Processing helix chain 'A' and resid 79 through 105 removed outlier: 5.903A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.940A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.921A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.249A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.863A pdb=" N TRP A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 236 removed outlier: 3.852A pdb=" N CYS A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 removed outlier: 3.782A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 266 Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.586A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.750A pdb=" N ALA A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.801A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 356 removed outlier: 3.804A pdb=" N GLY A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 346 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.510A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 416 removed outlier: 3.953A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 removed outlier: 3.761A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.918A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.884A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.755A pdb=" N LEU A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.777A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 removed outlier: 3.571A pdb=" N ILE A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 removed outlier: 3.533A pdb=" N LYS A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.969A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.658A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.198A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP L 36 " --> pdb=" O TRP L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.822A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 933 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: 0.61 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 845 1.31 - 1.44: 1744 1.44 - 1.57: 3133 1.57 - 1.69: 1 1.69 - 1.82: 55 Bond restraints: 5778 Sorted by residual: bond pdb=" N GLU A 107 " pdb=" CA GLU A 107 " ideal model delta sigma weight residual 1.456 1.398 0.059 1.16e-02 7.43e+03 2.55e+01 bond pdb=" C GLU A 107 " pdb=" O GLU A 107 " ideal model delta sigma weight residual 1.233 1.185 0.048 1.17e-02 7.31e+03 1.68e+01 bond pdb=" C ASP A 416 " pdb=" O ASP A 416 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.28e-02 6.10e+03 8.72e+00 bond pdb=" O3 TAU A 701 " pdb=" S TAU A 701 " ideal model delta sigma weight residual 1.478 1.429 0.049 2.00e-02 2.50e+03 5.92e+00 bond pdb=" O2 TAU A 701 " pdb=" S TAU A 701 " ideal model delta sigma weight residual 1.477 1.525 -0.048 2.00e-02 2.50e+03 5.77e+00 ... (remaining 5773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 7785 2.19 - 4.38: 124 4.38 - 6.57: 11 6.57 - 8.77: 3 8.77 - 10.96: 1 Bond angle restraints: 7924 Sorted by residual: angle pdb=" CG1 VAL A 562 " pdb=" CB VAL A 562 " pdb=" CG2 VAL A 562 " ideal model delta sigma weight residual 110.80 121.76 -10.96 2.20e+00 2.07e-01 2.48e+01 angle pdb=" N GLU A 107 " pdb=" CA GLU A 107 " pdb=" CB GLU A 107 " ideal model delta sigma weight residual 111.46 104.28 7.18 1.54e+00 4.22e-01 2.17e+01 angle pdb=" CA VAL A 562 " pdb=" CB VAL A 562 " pdb=" CG2 VAL A 562 " ideal model delta sigma weight residual 110.40 118.23 -7.83 1.70e+00 3.46e-01 2.12e+01 angle pdb=" CA VAL A 562 " pdb=" CB VAL A 562 " pdb=" CG1 VAL A 562 " ideal model delta sigma weight residual 110.40 116.17 -5.77 1.70e+00 3.46e-01 1.15e+01 angle pdb=" N CYS A 305 " pdb=" CA CYS A 305 " pdb=" C CYS A 305 " ideal model delta sigma weight residual 112.93 109.56 3.37 1.12e+00 7.97e-01 9.04e+00 ... (remaining 7919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.89: 2898 12.89 - 25.78: 240 25.78 - 38.67: 79 38.67 - 51.55: 20 51.55 - 64.44: 10 Dihedral angle restraints: 3247 sinusoidal: 1061 harmonic: 2186 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual -86.00 -127.10 41.10 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CA SER A 205 " pdb=" C SER A 205 " pdb=" N LEU A 206 " pdb=" CA LEU A 206 " ideal model delta harmonic sigma weight residual 180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE A 58 " pdb=" C PHE A 58 " pdb=" N VAL A 59 " pdb=" CA VAL A 59 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 3244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.308: 908 0.308 - 0.617: 0 0.617 - 0.925: 0 0.925 - 1.233: 0 1.233 - 1.542: 1 Chirality restraints: 909 Sorted by residual: chirality pdb=" CB VAL A 562 " pdb=" CA VAL A 562 " pdb=" CG1 VAL A 562 " pdb=" CG2 VAL A 562 " both_signs ideal model delta sigma weight residual False -2.63 -1.09 -1.54 2.00e-01 2.50e+01 5.94e+01 chirality pdb=" CB VAL L 59 " pdb=" CA VAL L 59 " pdb=" CG1 VAL L 59 " pdb=" CG2 VAL L 59 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 906 not shown) Planarity restraints: 980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 199 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C TRP A 199 " -0.039 2.00e-02 2.50e+03 pdb=" O TRP A 199 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU A 200 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO L 60 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 87 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C LEU A 87 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU A 87 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 88 " -0.013 2.00e-02 2.50e+03 ... (remaining 977 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 13 2.43 - 3.04: 3624 3.04 - 3.66: 8108 3.66 - 4.28: 12075 4.28 - 4.90: 20678 Nonbonded interactions: 44498 Sorted by model distance: nonbonded pdb=" OD1 ASP A 401 " pdb="NA NA A 702 " model vdw 1.807 3.210 nonbonded pdb=" OG SER A 402 " pdb="NA NA A 702 " model vdw 1.937 3.210 nonbonded pdb=" OG SER A 301 " pdb="NA NA A 703 " model vdw 2.012 3.210 nonbonded pdb=" O PHE A 58 " pdb=" O1 TAU A 701 " model vdw 2.020 3.040 nonbonded pdb=" O VAL A 59 " pdb="NA NA A 702 " model vdw 2.060 3.210 ... (remaining 44493 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 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: 1.210 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 5.690 Find NCS groups from input model: 0.010 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 : 0.004 0.084 5781 Z= 0.201 Angle : 0.701 10.957 7930 Z= 0.391 Chirality : 0.066 1.542 909 Planarity : 0.005 0.063 980 Dihedral : 12.018 64.441 1852 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.37 % Allowed : 9.61 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.12 (0.31), residues: 755 helix: 0.08 (0.27), residues: 366 sheet: 0.54 (0.50), residues: 118 loop : -0.38 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG H 104 TYR 0.017 0.001 TYR A 69 PHE 0.023 0.002 PHE L 63 TRP 0.020 0.002 TRP A 541 HIS 0.005 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.20 ( 5778) covalent geometry : angle 0.70075 / 0.39 ( 7924) SS BOND : bond 0.00346 / 0.23 ( 3) SS BOND : angle 0.90513 / 0.66 ( 6) hydrogen bonds : bond 0.15770 / 10.25 ( 327) hydrogen bonds : angle 6.30764 / 4.37 ( 933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.123 Fit side-chains REVERT: A 107 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7195 (mt-10) REVERT: A 416 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6959 (m-30) REVERT: A 487 ARG cc_start: 0.8318 (ttp-110) cc_final: 0.7925 (mtp85) REVERT: L 95 TYR cc_start: 0.8325 (m-80) cc_final: 0.8084 (m-80) outliers start: 2 outliers final: 0 residues processed: 105 average time/residue: 0.0586 time to fit residues: 8.1513 Evaluate side-chains 88 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 416 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.143820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125029 restraints weight = 8057.738| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.06 r_work: 0.3442 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5781 Z= 0.124 Angle : 0.571 7.929 7930 Z= 0.298 Chirality : 0.041 0.138 909 Planarity : 0.005 0.043 980 Dihedral : 5.891 55.127 824 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.40 % Allowed : 10.17 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.77 (0.32), residues: 755 helix: 1.15 (0.28), residues: 368 sheet: 0.69 (0.51), residues: 112 loop : -0.34 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 104 TYR 0.008 0.001 TYR H 60 PHE 0.013 0.001 PHE A 79 TRP 0.020 0.002 TRP A 470 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5778) covalent geometry : angle 0.57024 / 0.30 ( 7924) SS BOND : bond 0.00606 / 0.37 ( 3) SS BOND : angle 0.89614 / 0.58 ( 6) hydrogen bonds : bond 0.04095 / 2.76 ( 327) hydrogen bonds : angle 4.67786 / 3.28 ( 933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.209 Fit side-chains REVERT: A 107 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: A 353 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8236 (tp40) REVERT: A 459 ASP cc_start: 0.8929 (t70) cc_final: 0.8725 (t0) REVERT: A 487 ARG cc_start: 0.8130 (ttp-110) cc_final: 0.7751 (mtp85) REVERT: L 95 TYR cc_start: 0.8483 (m-80) cc_final: 0.8277 (m-80) outliers start: 13 outliers final: 8 residues processed: 97 average time/residue: 0.0594 time to fit residues: 7.8971 Evaluate side-chains 89 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121487 restraints weight = 7946.967| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.10 r_work: 0.3361 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5781 Z= 0.118 Angle : 0.549 6.821 7930 Z= 0.280 Chirality : 0.041 0.158 909 Planarity : 0.004 0.041 980 Dihedral : 5.057 48.632 822 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.96 % Allowed : 10.72 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.03 (0.32), residues: 755 helix: 1.49 (0.28), residues: 369 sheet: 0.57 (0.50), residues: 115 loop : -0.31 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 104 TYR 0.009 0.001 TYR A 315 PHE 0.015 0.001 PHE A 79 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 5778) covalent geometry : angle 0.54864 / 0.28 ( 7924) SS BOND : bond 0.00576 / 0.36 ( 3) SS BOND : angle 0.93540 / 0.59 ( 6) hydrogen bonds : bond 0.03888 / 2.63 ( 327) hydrogen bonds : angle 4.40346 / 3.09 ( 933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.137 Fit side-chains REVERT: A 107 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: A 353 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8129 (tp40) REVERT: A 459 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8764 (t0) REVERT: L 95 TYR cc_start: 0.8584 (m-80) cc_final: 0.8282 (m-80) outliers start: 16 outliers final: 6 residues processed: 103 average time/residue: 0.0444 time to fit residues: 6.3794 Evaluate side-chains 92 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 71 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 0.0060 chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.140910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.121866 restraints weight = 8026.238| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.11 r_work: 0.3370 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5781 Z= 0.108 Angle : 0.531 7.384 7930 Z= 0.268 Chirality : 0.040 0.156 909 Planarity : 0.004 0.046 980 Dihedral : 4.820 47.058 822 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.59 % Allowed : 12.20 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.32), residues: 755 helix: 1.64 (0.28), residues: 375 sheet: 0.51 (0.51), residues: 115 loop : -0.36 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 104 TYR 0.013 0.001 TYR A 578 PHE 0.013 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 5778) covalent geometry : angle 0.53109 / 0.27 ( 7924) SS BOND : bond 0.00543 / 0.35 ( 3) SS BOND : angle 0.89483 / 0.57 ( 6) hydrogen bonds : bond 0.03577 / 2.44 ( 327) hydrogen bonds : angle 4.28835 / 3.00 ( 933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.130 Fit side-chains REVERT: A 53 SER cc_start: 0.8780 (m) cc_final: 0.8545 (m) REVERT: A 107 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: A 353 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8061 (tp40) REVERT: A 459 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8789 (t0) REVERT: A 581 THR cc_start: 0.8428 (m) cc_final: 0.7911 (p) REVERT: H 100 GLU cc_start: 0.8867 (tp30) cc_final: 0.8553 (tp30) outliers start: 14 outliers final: 8 residues processed: 98 average time/residue: 0.0542 time to fit residues: 7.5465 Evaluate side-chains 95 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.137466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118212 restraints weight = 8201.557| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.15 r_work: 0.3331 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5781 Z= 0.145 Angle : 0.568 6.955 7930 Z= 0.288 Chirality : 0.041 0.149 909 Planarity : 0.004 0.046 980 Dihedral : 4.972 51.137 822 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.77 % Allowed : 13.31 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.01 (0.32), residues: 755 helix: 1.55 (0.28), residues: 375 sheet: 0.44 (0.51), residues: 115 loop : -0.41 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.014 0.001 TYR L 50 PHE 0.017 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 5778) covalent geometry : angle 0.56701 / 0.29 ( 7924) SS BOND : bond 0.00643 / 0.40 ( 3) SS BOND : angle 1.03497 / 0.67 ( 6) hydrogen bonds : bond 0.04072 / 2.77 ( 327) hydrogen bonds : angle 4.39575 / 3.06 ( 933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.198 Fit side-chains REVERT: A 53 SER cc_start: 0.8685 (m) cc_final: 0.8466 (m) REVERT: A 107 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: A 353 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8165 (tp40) REVERT: A 581 THR cc_start: 0.8700 (m) cc_final: 0.8275 (p) REVERT: H 60 TYR cc_start: 0.9035 (m-80) cc_final: 0.8753 (m-80) REVERT: H 100 GLU cc_start: 0.9041 (tp30) cc_final: 0.8592 (tp30) REVERT: L 95 TYR cc_start: 0.8598 (m-80) cc_final: 0.8252 (m-80) outliers start: 15 outliers final: 9 residues processed: 96 average time/residue: 0.0657 time to fit residues: 8.6772 Evaluate side-chains 96 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.140770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.122201 restraints weight = 8111.769| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.08 r_work: 0.3384 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5781 Z= 0.128 Angle : 0.546 7.478 7930 Z= 0.276 Chirality : 0.040 0.150 909 Planarity : 0.004 0.045 980 Dihedral : 4.930 53.337 822 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.40 % Allowed : 14.23 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.00 (0.32), residues: 755 helix: 1.59 (0.28), residues: 375 sheet: 0.37 (0.51), residues: 115 loop : -0.48 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 56 TYR 0.014 0.001 TYR A 578 PHE 0.014 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 5778) covalent geometry : angle 0.54514 / 0.28 ( 7924) SS BOND : bond 0.00585 / 0.37 ( 3) SS BOND : angle 0.93729 / 0.60 ( 6) hydrogen bonds : bond 0.03817 / 2.60 ( 327) hydrogen bonds : angle 4.33426 / 3.02 ( 933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.263 Fit side-chains REVERT: A 53 SER cc_start: 0.8703 (m) cc_final: 0.8488 (m) REVERT: A 107 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: A 353 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8194 (tp40) REVERT: A 581 THR cc_start: 0.8723 (m) cc_final: 0.8299 (p) REVERT: H 60 TYR cc_start: 0.9014 (m-80) cc_final: 0.8735 (m-80) REVERT: L 95 TYR cc_start: 0.8579 (m-80) cc_final: 0.8332 (m-80) outliers start: 13 outliers final: 7 residues processed: 95 average time/residue: 0.0646 time to fit residues: 8.6103 Evaluate side-chains 92 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.0270 chunk 64 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 0.0040 overall best weight: 0.4250 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.143917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125332 restraints weight = 8160.449| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.10 r_work: 0.3411 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5781 Z= 0.100 Angle : 0.514 7.480 7930 Z= 0.256 Chirality : 0.039 0.148 909 Planarity : 0.004 0.045 980 Dihedral : 4.688 49.994 822 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.40 % Allowed : 15.53 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.98 (0.32), residues: 755 helix: 1.61 (0.28), residues: 383 sheet: 0.34 (0.51), residues: 115 loop : -0.60 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 56 TYR 0.016 0.001 TYR A 578 PHE 0.011 0.001 PHE A 79 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 5778) covalent geometry : angle 0.51340 / 0.26 ( 7924) SS BOND : bond 0.00491 / 0.31 ( 3) SS BOND : angle 0.90377 / 0.57 ( 6) hydrogen bonds : bond 0.03292 / 2.24 ( 327) hydrogen bonds : angle 4.18734 / 2.93 ( 933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.205 Fit side-chains REVERT: A 107 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: A 315 TYR cc_start: 0.9046 (m-80) cc_final: 0.8836 (m-80) REVERT: A 491 ASP cc_start: 0.8501 (m-30) cc_final: 0.8268 (m-30) REVERT: A 549 LEU cc_start: 0.8208 (tp) cc_final: 0.7912 (mt) REVERT: A 581 THR cc_start: 0.8730 (m) cc_final: 0.8289 (p) REVERT: H 60 TYR cc_start: 0.8954 (m-80) cc_final: 0.8710 (m-80) REVERT: L 90 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8083 (tt0) REVERT: L 95 TYR cc_start: 0.8569 (m-80) cc_final: 0.8359 (m-80) outliers start: 13 outliers final: 8 residues processed: 97 average time/residue: 0.0583 time to fit residues: 8.1177 Evaluate side-chains 97 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.136421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117809 restraints weight = 8148.379| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.13 r_work: 0.3324 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5781 Z= 0.140 Angle : 0.560 8.221 7930 Z= 0.281 Chirality : 0.041 0.147 909 Planarity : 0.004 0.044 980 Dihedral : 4.882 53.789 822 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.59 % Allowed : 14.97 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.94 (0.32), residues: 755 helix: 1.61 (0.28), residues: 375 sheet: 0.29 (0.51), residues: 115 loop : -0.60 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 56 TYR 0.014 0.001 TYR L 50 PHE 0.016 0.001 PHE A 79 TRP 0.013 0.001 TRP A 199 HIS 0.001 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5778) covalent geometry : angle 0.55978 / 0.28 ( 7924) SS BOND : bond 0.00595 / 0.37 ( 3) SS BOND : angle 0.95242 / 0.59 ( 6) hydrogen bonds : bond 0.03921 / 2.67 ( 327) hydrogen bonds : angle 4.30393 / 3.00 ( 933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.210 Fit side-chains REVERT: A 107 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8036 (mt-10) REVERT: A 315 TYR cc_start: 0.9011 (m-80) cc_final: 0.8753 (m-80) REVERT: A 353 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8099 (tp40) REVERT: A 491 ASP cc_start: 0.8512 (m-30) cc_final: 0.8089 (m-30) REVERT: A 578 TYR cc_start: 0.8022 (t80) cc_final: 0.7809 (t80) REVERT: A 581 THR cc_start: 0.8813 (m) cc_final: 0.8395 (p) REVERT: H 60 TYR cc_start: 0.9028 (m-80) cc_final: 0.8735 (m-80) REVERT: L 95 TYR cc_start: 0.8569 (m-80) cc_final: 0.8363 (m-80) outliers start: 14 outliers final: 10 residues processed: 96 average time/residue: 0.0545 time to fit residues: 7.6431 Evaluate side-chains 97 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 56 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.138630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119826 restraints weight = 8323.028| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.17 r_work: 0.3319 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5781 Z= 0.135 Angle : 0.559 8.970 7930 Z= 0.279 Chirality : 0.041 0.148 909 Planarity : 0.004 0.045 980 Dihedral : 4.595 57.315 819 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.59 % Allowed : 14.97 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.87 (0.32), residues: 755 helix: 1.57 (0.28), residues: 375 sheet: 0.23 (0.51), residues: 115 loop : -0.66 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 56 TYR 0.013 0.001 TYR L 50 PHE 0.015 0.001 PHE A 79 TRP 0.013 0.001 TRP A 199 HIS 0.001 0.001 HIS L 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 5778) covalent geometry : angle 0.55881 / 0.28 ( 7924) SS BOND : bond 0.00568 / 0.36 ( 3) SS BOND : angle 0.93085 / 0.59 ( 6) hydrogen bonds : bond 0.03871 / 2.63 ( 327) hydrogen bonds : angle 4.32484 / 3.01 ( 933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.218 Fit side-chains REVERT: A 107 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: A 315 TYR cc_start: 0.9001 (m-80) cc_final: 0.8741 (m-80) REVERT: A 353 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7966 (tp40) REVERT: A 491 ASP cc_start: 0.8501 (m-30) cc_final: 0.8098 (m-30) REVERT: A 581 THR cc_start: 0.8854 (m) cc_final: 0.8414 (p) REVERT: H 60 TYR cc_start: 0.9034 (m-80) cc_final: 0.8749 (m-80) REVERT: L 95 TYR cc_start: 0.8570 (m-80) cc_final: 0.8359 (m-80) outliers start: 14 outliers final: 12 residues processed: 96 average time/residue: 0.0551 time to fit residues: 7.7291 Evaluate side-chains 99 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.0470 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 0.0570 chunk 69 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.138624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120018 restraints weight = 8284.003| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.14 r_work: 0.3349 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5781 Z= 0.107 Angle : 0.534 9.545 7930 Z= 0.263 Chirality : 0.040 0.145 909 Planarity : 0.004 0.046 980 Dihedral : 4.412 54.985 819 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.40 % Allowed : 15.16 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.98 (0.32), residues: 755 helix: 1.68 (0.28), residues: 376 sheet: 0.29 (0.51), residues: 115 loop : -0.64 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 56 TYR 0.018 0.001 TYR A 578 PHE 0.012 0.001 PHE A 79 TRP 0.012 0.001 TRP A 199 HIS 0.001 0.000 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 5778) covalent geometry : angle 0.53411 / 0.26 ( 7924) SS BOND : bond 0.00476 / 0.31 ( 3) SS BOND : angle 0.84642 / 0.54 ( 6) hydrogen bonds : bond 0.03441 / 2.34 ( 327) hydrogen bonds : angle 4.19463 / 2.93 ( 933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.216 Fit side-chains REVERT: A 107 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: A 315 TYR cc_start: 0.9004 (m-80) cc_final: 0.8752 (m-80) REVERT: A 353 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7890 (tp40) REVERT: A 491 ASP cc_start: 0.8385 (m-30) cc_final: 0.8058 (m-30) REVERT: A 578 TYR cc_start: 0.8115 (t80) cc_final: 0.7820 (t80) REVERT: A 581 THR cc_start: 0.8859 (m) cc_final: 0.8403 (p) REVERT: H 60 TYR cc_start: 0.8992 (m-80) cc_final: 0.8738 (m-80) REVERT: L 90 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8101 (tt0) REVERT: L 95 TYR cc_start: 0.8552 (m-80) cc_final: 0.8332 (m-80) outliers start: 13 outliers final: 11 residues processed: 99 average time/residue: 0.0551 time to fit residues: 7.9516 Evaluate side-chains 102 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.140065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121378 restraints weight = 8296.646| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.17 r_work: 0.3339 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5781 Z= 0.117 Angle : 0.545 9.592 7930 Z= 0.270 Chirality : 0.040 0.147 909 Planarity : 0.004 0.046 980 Dihedral : 4.415 54.979 819 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.77 % Allowed : 14.97 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.97 (0.32), residues: 755 helix: 1.66 (0.28), residues: 376 sheet: 0.28 (0.52), residues: 110 loop : -0.61 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 56 TYR 0.018 0.001 TYR A 578 PHE 0.013 0.001 PHE A 79 TRP 0.013 0.001 TRP A 199 HIS 0.001 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 5778) covalent geometry : angle 0.54478 / 0.27 ( 7924) SS BOND : bond 0.00515 / 0.33 ( 3) SS BOND : angle 0.90366 / 0.56 ( 6) hydrogen bonds : bond 0.03600 / 2.45 ( 327) hydrogen bonds : angle 4.22397 / 2.94 ( 933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1374.38 seconds wall clock time: 24 minutes 18.32 seconds (1458.32 seconds total)