Starting phenix.real_space_refine on Thu Jul 2 11:03:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvc_42615/07_2026/8uvc_42615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvc_42615/07_2026/8uvc_42615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uvc_42615/07_2026/8uvc_42615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvc_42615/07_2026/8uvc_42615.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvc_42615/07_2026/8uvc_42615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvc_42615/07_2026/8uvc_42615.cif" } resolution = 2.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.050 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 S 52 5.16 5 Na 2 4.78 5 C 5838 2.51 5 N 1272 2.21 5 O 1390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 8558 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4011 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 34, 'TRANS': 478} Chain breaks: 2 Chain: "B" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4011 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 34, 'TRANS': 478} Chain breaks: 2 Chain: "A" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 12, 271 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'3PE': 2, 'AKG': 1, 'C14': 4, 'CLR': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Conformer: "B" Number of residues, atoms: 12, 271 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'3PE': 2, 'AKG': 1, 'C14': 4, 'CLR': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 bond proxies already assigned to first conformer: 267 Chain: "B" Number of atoms: 254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 10, 243 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'3PE': 2, 'AKG': 1, 'C14': 2, 'CLR': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Conformer: "B" Number of residues, atoms: 10, 243 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'3PE': 2, 'AKG': 1, 'C14': 2, 'CLR': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 bond proxies already assigned to first conformer: 241 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 AAKG A 702 " occ=0.50 ... (18 atoms not shown) pdb=" O5 BAKG A 702 " occ=0.50 residue: pdb=" C1 AAKG B 702 " occ=0.50 ... (18 atoms not shown) pdb=" O5 BAKG B 702 " occ=0.50 Time building chain proxies: 1.88, per 1000 atoms: 0.22 Number of scatterers: 8558 At special positions: 0 Unit cell: (85.8, 106.425, 82.5, 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 52 16.00 P 4 15.00 Na 2 11.00 O 1390 8.00 N 1272 7.00 C 5838 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: 0.53 Conformation dependent library (CDL) restraints added in 313.0 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 removed outlier: 3.831A pdb=" N ALA A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 34 Proline residue: A 24 - end of helix Proline residue: A 29 - end of helix removed outlier: 3.692A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.805A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.794A pdb=" N PHE A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.566A pdb=" N GLY A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 143 through 164 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 220 through 247 removed outlier: 3.782A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.869A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 7.059A pdb=" N THR A 251 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.924A pdb=" N LEU A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 301 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'A' and resid 339 through 358 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 389 removed outlier: 3.897A pdb=" N ILE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.816A pdb=" N PHE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 426 through 446 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 457 through 462 removed outlier: 4.257A pdb=" N ASN A 461 " --> pdb=" O PRO A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 483 through 502 Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 505 through 517 removed outlier: 3.916A pdb=" N LEU A 509 " --> pdb=" O HIS A 505 " (cutoff:3.500A) Proline residue: A 512 - end of helix Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 540 through 566 removed outlier: 4.149A pdb=" N LEU A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 14 through 34 Proline residue: B 24 - end of helix Proline residue: B 29 - end of helix removed outlier: 3.693A pdb=" N PHE B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.805A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 87 through 106 removed outlier: 3.794A pdb=" N PHE B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.567A pdb=" N GLY B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 143 through 164 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 220 through 247 removed outlier: 3.782A pdb=" N ILE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.869A pdb=" N THR B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 7.059A pdb=" N THR B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.924A pdb=" N LEU B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 301 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 320 through 334 Processing helix chain 'B' and resid 339 through 358 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 377 through 389 removed outlier: 3.897A pdb=" N ILE B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.815A pdb=" N PHE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 426 through 446 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 457 through 462 removed outlier: 4.257A pdb=" N ASN B 461 " --> pdb=" O PRO B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 483 through 502 Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 505 through 517 removed outlier: 3.916A pdb=" N LEU B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Proline residue: B 512 - end of helix Processing helix chain 'B' and resid 527 through 535 Processing helix chain 'B' and resid 540 through 566 removed outlier: 4.149A pdb=" N LEU B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 572 550 hydrogen bonds defined for protein. 1608 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: 1.17 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1228 1.30 - 1.43: 2188 1.43 - 1.55: 5266 1.55 - 1.68: 26 1.68 - 1.81: 90 Bond restraints: 8798 Sorted by residual: bond pdb=" C ARG B 126 " pdb=" O ARG B 126 " ideal model delta sigma weight residual 1.236 1.173 0.064 1.25e-02 6.40e+03 2.60e+01 bond pdb=" C ARG A 126 " pdb=" O ARG A 126 " ideal model delta sigma weight residual 1.236 1.173 0.064 1.25e-02 6.40e+03 2.59e+01 bond pdb=" C LEU B 129 " pdb=" O LEU B 129 " ideal model delta sigma weight residual 1.236 1.194 0.043 1.15e-02 7.56e+03 1.39e+01 bond pdb=" C LEU A 129 " pdb=" O LEU A 129 " ideal model delta sigma weight residual 1.236 1.194 0.043 1.15e-02 7.56e+03 1.39e+01 bond pdb=" C GLN A 84 " pdb=" O GLN A 84 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.28e-02 6.10e+03 1.11e+01 ... (remaining 8793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11503 1.71 - 3.43: 370 3.43 - 5.14: 65 5.14 - 6.85: 18 6.85 - 8.57: 8 Bond angle restraints: 11964 Sorted by residual: angle pdb=" C LEU B 87 " pdb=" N ASP B 88 " pdb=" CA ASP B 88 " ideal model delta sigma weight residual 120.60 129.17 -8.57 1.60e+00 3.91e-01 2.87e+01 angle pdb=" C LEU A 87 " pdb=" N ASP A 88 " pdb=" CA ASP A 88 " ideal model delta sigma weight residual 120.60 129.16 -8.56 1.60e+00 3.91e-01 2.86e+01 angle pdb=" CA LEU B 87 " pdb=" C LEU B 87 " pdb=" O LEU B 87 " ideal model delta sigma weight residual 121.87 116.15 5.72 1.10e+00 8.26e-01 2.70e+01 angle pdb=" CA LEU A 87 " pdb=" C LEU A 87 " pdb=" O LEU A 87 " ideal model delta sigma weight residual 121.87 116.17 5.70 1.10e+00 8.26e-01 2.69e+01 angle pdb=" CA LEU B 87 " pdb=" C LEU B 87 " pdb=" N ASP B 88 " ideal model delta sigma weight residual 115.30 121.61 -6.31 1.33e+00 5.65e-01 2.25e+01 ... (remaining 11959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.25: 5330 24.25 - 48.50: 202 48.50 - 72.75: 48 72.75 - 96.99: 6 96.99 - 121.24: 12 Dihedral angle restraints: 5598 sinusoidal: 2640 harmonic: 2958 Sorted by residual: dihedral pdb=" C PHE B 86 " pdb=" N PHE B 86 " pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " ideal model delta harmonic sigma weight residual -122.60 -135.30 12.70 0 2.50e+00 1.60e-01 2.58e+01 dihedral pdb=" C PHE A 86 " pdb=" N PHE A 86 " pdb=" CA PHE A 86 " pdb=" CB PHE A 86 " ideal model delta harmonic sigma weight residual -122.60 -135.28 12.68 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" N PHE B 86 " pdb=" C PHE B 86 " pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " ideal model delta harmonic sigma weight residual 122.80 134.02 -11.22 0 2.50e+00 1.60e-01 2.01e+01 ... (remaining 5595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1321 0.093 - 0.187: 64 0.187 - 0.280: 3 0.280 - 0.374: 0 0.374 - 0.467: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA PHE B 86 " pdb=" N PHE B 86 " pdb=" C PHE B 86 " pdb=" CB PHE B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA PHE A 86 " pdb=" N PHE A 86 " pdb=" C PHE A 86 " pdb=" CB PHE A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA LEU B 87 " pdb=" N LEU B 87 " pdb=" C LEU B 87 " pdb=" CB LEU B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1387 not shown) Planarity restraints: 1396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 133 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C VAL B 133 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL B 133 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 134 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 133 " -0.014 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C VAL A 133 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL A 133 " -0.019 2.00e-02 2.50e+03 pdb=" N THR A 134 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 132 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C MET B 132 " -0.050 2.00e-02 2.50e+03 pdb=" O MET B 132 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL B 133 " 0.017 2.00e-02 2.50e+03 ... (remaining 1393 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1943 2.79 - 3.32: 8603 3.32 - 3.84: 14966 3.84 - 4.37: 17900 4.37 - 4.90: 30108 Nonbonded interactions: 73520 Sorted by model distance: nonbonded pdb=" OG SER B 139 " pdb=" OD1 ASN B 144 " model vdw 2.262 3.040 nonbonded pdb=" OG SER A 139 " pdb=" OD1 ASN A 144 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A 561 " pdb=" OG1 THR A 565 " model vdw 2.269 3.040 nonbonded pdb=" O LEU B 561 " pdb=" OG1 THR B 565 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR B 240 " pdb=" O PHE B 521 " model vdw 2.339 3.040 ... (remaining 73515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 701 or resid 703 or resid 706 through 707)) selection = (chain 'B' and (resid 1 through 701 or resid 703 or resid 706 through 707)) } 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=0.50 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.810 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 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 0.064 8798 Z= 0.298 Angle : 0.732 8.567 11964 Z= 0.414 Chirality : 0.047 0.467 1390 Planarity : 0.005 0.037 1396 Dihedral : 14.953 121.241 3674 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.47 % Allowed : 1.40 % Favored : 98.14 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.27), residues: 1014 helix: 1.95 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 0.79 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 228 TYR 0.021 0.003 TYR A 301 PHE 0.023 0.002 PHE B 72 TRP 0.017 0.002 TRP A 418 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.30 ( 8798) covalent geometry : angle 0.73168 / 0.41 (11964) hydrogen bonds : bond 0.11590 / 7.58 ( 550) hydrogen bonds : angle 4.47670 / 3.30 ( 1608) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.263 Fit side-chains REVERT: A 123 GLN cc_start: 0.6894 (mp10) cc_final: 0.6486 (mp10) REVERT: A 223 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7265 (tp30) REVERT: B 223 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7303 (tp30) outliers start: 4 outliers final: 2 residues processed: 138 average time/residue: 0.4139 time to fit residues: 61.4071 Evaluate side-chains 113 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 86 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077643 restraints weight = 14560.313| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.05 r_work: 0.2815 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8798 Z= 0.127 Angle : 0.559 7.010 11964 Z= 0.270 Chirality : 0.040 0.135 1390 Planarity : 0.005 0.040 1396 Dihedral : 11.077 88.965 1852 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.40 % Allowed : 5.35 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.27), residues: 1014 helix: 2.04 (0.19), residues: 784 sheet: None (None), residues: 0 loop : 0.82 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 227 TYR 0.015 0.001 TYR A 226 PHE 0.019 0.001 PHE B 363 TRP 0.016 0.002 TRP B 418 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8798) covalent geometry : angle 0.55889 / 0.27 (11964) hydrogen bonds : bond 0.03863 / 2.57 ( 550) hydrogen bonds : angle 3.86317 / 2.85 ( 1608) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.288 Fit side-chains REVERT: A 223 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7288 (tp30) REVERT: B 1 MET cc_start: 0.5972 (OUTLIER) cc_final: 0.4781 (mmt) REVERT: B 223 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7325 (tp30) REVERT: B 272 VAL cc_start: 0.9008 (m) cc_final: 0.8770 (p) REVERT: B 404 ASP cc_start: 0.7737 (t0) cc_final: 0.7531 (t0) REVERT: B 525 VAL cc_start: 0.9145 (m) cc_final: 0.8920 (p) outliers start: 12 outliers final: 5 residues processed: 118 average time/residue: 0.3526 time to fit residues: 45.3030 Evaluate side-chains 113 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 0.0870 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.075859 restraints weight = 16911.947| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.20 r_work: 0.2782 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8798 Z= 0.121 Angle : 0.519 5.465 11964 Z= 0.256 Chirality : 0.040 0.152 1390 Planarity : 0.005 0.041 1396 Dihedral : 10.694 89.745 1852 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.40 % Allowed : 7.33 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.27), residues: 1014 helix: 2.19 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 1.18 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.015 0.001 TYR B 226 PHE 0.015 0.001 PHE B 363 TRP 0.020 0.002 TRP B 418 HIS 0.003 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 8798) covalent geometry : angle 0.51924 / 0.26 (11964) hydrogen bonds : bond 0.03711 / 2.49 ( 550) hydrogen bonds : angle 3.83091 / 2.82 ( 1608) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.237 Fit side-chains REVERT: A 1 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.3980 (mmt) REVERT: A 223 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7371 (tp30) REVERT: B 1 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.4838 (mmt) REVERT: B 223 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7328 (tp30) REVERT: B 272 VAL cc_start: 0.9033 (m) cc_final: 0.8809 (p) REVERT: B 330 GLU cc_start: 0.7884 (tp30) cc_final: 0.7341 (tm-30) REVERT: B 404 ASP cc_start: 0.7719 (t0) cc_final: 0.7424 (t0) REVERT: B 525 VAL cc_start: 0.9145 (m) cc_final: 0.8935 (p) outliers start: 12 outliers final: 5 residues processed: 115 average time/residue: 0.3572 time to fit residues: 44.7694 Evaluate side-chains 115 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 42 optimal weight: 0.0020 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN A 552 ASN B 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.075783 restraints weight = 18066.441| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.23 r_work: 0.2777 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8798 Z= 0.117 Angle : 0.512 5.507 11964 Z= 0.252 Chirality : 0.040 0.162 1390 Planarity : 0.005 0.041 1396 Dihedral : 10.736 89.940 1852 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.63 % Allowed : 7.44 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.27), residues: 1014 helix: 2.18 (0.19), residues: 780 sheet: None (None), residues: 0 loop : 1.26 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 503 TYR 0.017 0.001 TYR B 226 PHE 0.015 0.001 PHE A 352 TRP 0.019 0.001 TRP B 418 HIS 0.003 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8798) covalent geometry : angle 0.51169 / 0.25 (11964) hydrogen bonds : bond 0.03562 / 2.40 ( 550) hydrogen bonds : angle 3.81378 / 2.81 ( 1608) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.307 Fit side-chains REVERT: A 86 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.7503 (t80) REVERT: A 223 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7336 (tp30) REVERT: A 225 GLU cc_start: 0.8029 (tp30) cc_final: 0.7825 (tp30) REVERT: A 478 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7858 (t80) REVERT: B 1 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.4708 (mmt) REVERT: B 223 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7321 (tp30) REVERT: B 272 VAL cc_start: 0.9025 (m) cc_final: 0.8791 (p) REVERT: B 330 GLU cc_start: 0.7878 (tp30) cc_final: 0.7384 (tm-30) REVERT: B 404 ASP cc_start: 0.7710 (t0) cc_final: 0.7380 (t0) outliers start: 14 outliers final: 6 residues processed: 120 average time/residue: 0.3585 time to fit residues: 46.8862 Evaluate side-chains 120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN B 144 ASN B 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.075461 restraints weight = 12831.986| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.84 r_work: 0.2750 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8798 Z= 0.141 Angle : 0.537 5.590 11964 Z= 0.265 Chirality : 0.042 0.166 1390 Planarity : 0.005 0.040 1396 Dihedral : 10.937 89.820 1852 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.21 % Allowed : 7.44 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.27), residues: 1014 helix: 2.18 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 1.10 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 503 TYR 0.018 0.001 TYR B 226 PHE 0.015 0.001 PHE A 352 TRP 0.022 0.002 TRP B 418 HIS 0.008 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 8798) covalent geometry : angle 0.53734 / 0.26 (11964) hydrogen bonds : bond 0.03838 / 2.58 ( 550) hydrogen bonds : angle 3.86847 / 2.84 ( 1608) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.210 Fit side-chains REVERT: A 223 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7385 (tp30) REVERT: A 478 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7822 (t80) REVERT: B 1 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.4765 (mmt) REVERT: B 223 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7323 (tp30) REVERT: B 272 VAL cc_start: 0.9092 (m) cc_final: 0.8855 (p) REVERT: B 330 GLU cc_start: 0.7867 (tp30) cc_final: 0.7451 (tm-30) REVERT: B 404 ASP cc_start: 0.7820 (t0) cc_final: 0.7482 (t0) outliers start: 19 outliers final: 9 residues processed: 118 average time/residue: 0.3678 time to fit residues: 47.1349 Evaluate side-chains 119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 63 optimal weight: 0.0040 chunk 41 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.075633 restraints weight = 17910.850| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.13 r_work: 0.2749 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8798 Z= 0.115 Angle : 0.519 7.176 11964 Z= 0.253 Chirality : 0.040 0.190 1390 Planarity : 0.005 0.041 1396 Dihedral : 10.833 88.675 1852 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.63 % Allowed : 8.37 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.27), residues: 1014 helix: 2.18 (0.19), residues: 780 sheet: None (None), residues: 0 loop : 1.23 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 503 TYR 0.018 0.001 TYR A 226 PHE 0.014 0.001 PHE A 352 TRP 0.020 0.001 TRP B 418 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 8798) covalent geometry : angle 0.51909 / 0.25 (11964) hydrogen bonds : bond 0.03491 / 2.35 ( 550) hydrogen bonds : angle 3.79204 / 2.79 ( 1608) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.300 Fit side-chains REVERT: A 1 MET cc_start: 0.5425 (OUTLIER) cc_final: 0.3957 (mmm) REVERT: A 223 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7374 (tp30) REVERT: A 478 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7829 (t80) REVERT: B 1 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.4686 (mmt) REVERT: B 150 MET cc_start: 0.9321 (tmm) cc_final: 0.9088 (ttp) REVERT: B 223 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7365 (tp30) REVERT: B 272 VAL cc_start: 0.9074 (m) cc_final: 0.8829 (p) REVERT: B 330 GLU cc_start: 0.7976 (tp30) cc_final: 0.7367 (mm-30) REVERT: B 404 ASP cc_start: 0.7844 (t0) cc_final: 0.7499 (t0) outliers start: 14 outliers final: 7 residues processed: 116 average time/residue: 0.3960 time to fit residues: 49.7146 Evaluate side-chains 119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.075830 restraints weight = 12616.897| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.85 r_work: 0.2754 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8798 Z= 0.134 Angle : 0.537 5.916 11964 Z= 0.262 Chirality : 0.041 0.179 1390 Planarity : 0.005 0.040 1396 Dihedral : 10.925 88.820 1852 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.28 % Allowed : 9.07 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.27), residues: 1014 helix: 2.20 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 1.09 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 503 TYR 0.018 0.001 TYR B 226 PHE 0.015 0.001 PHE A 352 TRP 0.021 0.002 TRP B 418 HIS 0.004 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 8798) covalent geometry : angle 0.53701 / 0.26 (11964) hydrogen bonds : bond 0.03713 / 2.50 ( 550) hydrogen bonds : angle 3.83733 / 2.82 ( 1608) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.263 Fit side-chains REVERT: A 1 MET cc_start: 0.5496 (OUTLIER) cc_final: 0.3952 (mmm) REVERT: A 223 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7404 (tp30) REVERT: A 478 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.7952 (t80) REVERT: B 1 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.4695 (mmt) REVERT: B 150 MET cc_start: 0.9360 (tmm) cc_final: 0.9140 (ttp) REVERT: B 272 VAL cc_start: 0.9131 (m) cc_final: 0.8859 (p) REVERT: B 330 GLU cc_start: 0.7974 (tp30) cc_final: 0.7383 (mm-30) REVERT: B 404 ASP cc_start: 0.7893 (t0) cc_final: 0.7543 (t0) outliers start: 11 outliers final: 7 residues processed: 116 average time/residue: 0.3574 time to fit residues: 45.2417 Evaluate side-chains 116 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.074912 restraints weight = 14382.629| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.97 r_work: 0.2736 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8798 Z= 0.135 Angle : 0.541 6.279 11964 Z= 0.265 Chirality : 0.041 0.184 1390 Planarity : 0.005 0.041 1396 Dihedral : 10.980 88.833 1852 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.51 % Allowed : 9.07 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.27), residues: 1014 helix: 2.20 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 1.07 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.018 0.001 TYR A 226 PHE 0.015 0.001 PHE A 352 TRP 0.021 0.002 TRP B 418 HIS 0.004 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8798) covalent geometry : angle 0.54074 / 0.26 (11964) hydrogen bonds : bond 0.03718 / 2.50 ( 550) hydrogen bonds : angle 3.83614 / 2.82 ( 1608) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.295 Fit side-chains REVERT: A 1 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.3902 (mmm) REVERT: A 478 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7981 (t80) REVERT: B 1 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.4681 (mmt) REVERT: B 225 GLU cc_start: 0.8268 (tp30) cc_final: 0.8007 (tp30) REVERT: B 272 VAL cc_start: 0.9136 (m) cc_final: 0.8848 (p) REVERT: B 330 GLU cc_start: 0.8031 (tp30) cc_final: 0.7415 (mm-30) REVERT: B 404 ASP cc_start: 0.7940 (t0) cc_final: 0.7601 (t0) outliers start: 13 outliers final: 7 residues processed: 114 average time/residue: 0.3656 time to fit residues: 45.4103 Evaluate side-chains 122 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.107003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.076136 restraints weight = 12701.470| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.86 r_work: 0.2761 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8798 Z= 0.125 Angle : 0.534 6.665 11964 Z= 0.261 Chirality : 0.041 0.189 1390 Planarity : 0.005 0.041 1396 Dihedral : 10.937 88.324 1852 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.28 % Allowed : 9.42 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.27), residues: 1014 helix: 2.22 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 1.05 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.019 0.001 TYR A 226 PHE 0.018 0.001 PHE A 477 TRP 0.021 0.002 TRP B 418 HIS 0.009 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 8798) covalent geometry : angle 0.53381 / 0.26 (11964) hydrogen bonds : bond 0.03584 / 2.41 ( 550) hydrogen bonds : angle 3.81191 / 2.80 ( 1608) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.302 Fit side-chains REVERT: A 1 MET cc_start: 0.5617 (OUTLIER) cc_final: 0.3992 (mmm) REVERT: A 478 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.7959 (t80) REVERT: B 1 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.4674 (mmt) REVERT: B 225 GLU cc_start: 0.8264 (tp30) cc_final: 0.7992 (tp30) REVERT: B 272 VAL cc_start: 0.9135 (m) cc_final: 0.8854 (p) REVERT: B 330 GLU cc_start: 0.8009 (tp30) cc_final: 0.7403 (mm-30) REVERT: B 404 ASP cc_start: 0.7959 (t0) cc_final: 0.7622 (t0) outliers start: 11 outliers final: 7 residues processed: 119 average time/residue: 0.3654 time to fit residues: 47.5585 Evaluate side-chains 120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.075474 restraints weight = 16701.755| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.09 r_work: 0.2748 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8798 Z= 0.121 Angle : 0.535 6.916 11964 Z= 0.261 Chirality : 0.040 0.189 1390 Planarity : 0.005 0.041 1396 Dihedral : 10.877 87.955 1852 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.28 % Allowed : 9.65 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.27), residues: 1014 helix: 2.22 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 1.06 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.019 0.001 TYR B 226 PHE 0.018 0.001 PHE A 477 TRP 0.020 0.002 TRP B 418 HIS 0.007 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8798) covalent geometry : angle 0.53458 / 0.26 (11964) hydrogen bonds : bond 0.03531 / 2.37 ( 550) hydrogen bonds : angle 3.80887 / 2.80 ( 1608) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.242 Fit side-chains REVERT: A 1 MET cc_start: 0.5613 (OUTLIER) cc_final: 0.3948 (mmm) REVERT: A 478 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.7976 (t80) REVERT: B 1 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.4600 (mmt) REVERT: B 225 GLU cc_start: 0.8281 (tp30) cc_final: 0.8005 (tp30) REVERT: B 272 VAL cc_start: 0.9102 (m) cc_final: 0.8815 (p) REVERT: B 330 GLU cc_start: 0.8039 (tp30) cc_final: 0.7448 (mm-30) REVERT: B 404 ASP cc_start: 0.7944 (t0) cc_final: 0.7608 (t0) outliers start: 11 outliers final: 7 residues processed: 118 average time/residue: 0.3610 time to fit residues: 46.4407 Evaluate side-chains 121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.075845 restraints weight = 15149.340| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.00 r_work: 0.2755 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8798 Z= 0.122 Angle : 0.540 7.794 11964 Z= 0.263 Chirality : 0.041 0.190 1390 Planarity : 0.005 0.041 1396 Dihedral : 10.854 88.187 1852 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.16 % Allowed : 10.00 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.27), residues: 1014 helix: 2.21 (0.19), residues: 774 sheet: None (None), residues: 0 loop : 1.07 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.019 0.001 TYR A 226 PHE 0.019 0.001 PHE A 477 TRP 0.020 0.002 TRP B 418 HIS 0.007 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 8798) covalent geometry : angle 0.53984 / 0.26 (11964) hydrogen bonds : bond 0.03549 / 2.38 ( 550) hydrogen bonds : angle 3.81217 / 2.80 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3689.39 seconds wall clock time: 63 minutes 22.44 seconds (3802.44 seconds total)