Starting phenix.real_space_refine on Sat Aug 23 05:59:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thj_41266/08_2025/8thj_41266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thj_41266/08_2025/8thj_41266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thj_41266/08_2025/8thj_41266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thj_41266/08_2025/8thj_41266.map" model { file = "/net/cci-nas-00/data/ceres_data/8thj_41266/08_2025/8thj_41266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thj_41266/08_2025/8thj_41266.cif" } resolution = 2.99 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= 0.006 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 68 5.16 5 Na 4 4.78 5 C 6476 2.51 5 N 1474 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9642 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4756 Classifications: {'peptide': 615} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 588} Chain: "B" Number of atoms: 4756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4756 Classifications: {'peptide': 615} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 588} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 66 Unusual residues: {' NA': 2, 'PGT': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' NA': 2, 'PGT': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Time building chain proxies: 2.44, per 1000 atoms: 0.25 Number of scatterers: 9642 At special positions: 0 Unit cell: (131.571, 83.0625, 90.372, 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 68 16.00 P 4 15.00 Na 4 11.00 O 1616 8.00 N 1474 7.00 C 6476 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: 0.80 Conformation dependent library (CDL) restraints added in 305.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2276 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 1 through 5 Processing helix chain 'A' and resid 6 through 34 Processing helix chain 'A' and resid 39 through 63 removed outlier: 3.784A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 76 through 109 removed outlier: 4.043A pdb=" N PHE A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 126 through 149 removed outlier: 3.697A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 removed outlier: 4.036A pdb=" N PHE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.630A pdb=" N LYS A 178 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 191 through 206 removed outlier: 3.530A pdb=" N ILE A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 3.716A pdb=" N PHE A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.766A pdb=" N ALA A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 260 removed outlier: 4.401A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 277 Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.699A pdb=" N GLY A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 320 removed outlier: 4.096A pdb=" N ASP A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 334 through 337 removed outlier: 3.555A pdb=" N GLY A 337 " --> pdb=" O CYS A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 337' Processing helix chain 'A' and resid 343 through 354 Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 364 through 387 removed outlier: 3.695A pdb=" N GLY A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 422 removed outlier: 3.571A pdb=" N LEU A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ALA A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR A 412 " --> pdb=" O TRP A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 426 through 444 Processing helix chain 'A' and resid 450 through 486 removed outlier: 3.842A pdb=" N VAL A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.623A pdb=" N VAL A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.699A pdb=" N PHE A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Proline residue: A 531 - end of helix Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 543 through 557 Processing helix chain 'A' and resid 558 through 561 Processing helix chain 'A' and resid 565 through 576 Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 589 through 603 removed outlier: 4.370A pdb=" N VAL A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 4.300A pdb=" N ILE A 607 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Proline residue: A 611 - end of helix Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.542A pdb=" N ASN B 5 " --> pdb=" O LYS B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 34 Processing helix chain 'B' and resid 39 through 63 removed outlier: 3.791A pdb=" N TYR B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 76 through 109 removed outlier: 3.935A pdb=" N PHE B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 126 through 149 removed outlier: 3.717A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 173 removed outlier: 3.982A pdb=" N PHE B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 removed outlier: 3.635A pdb=" N LYS B 178 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 191 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 3.721A pdb=" N PHE B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 removed outlier: 3.769A pdb=" N ALA B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 260 removed outlier: 4.397A pdb=" N PHE B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 277 Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.714A pdb=" N GLY B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 320 removed outlier: 4.133A pdb=" N ASP B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLN B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 320 " --> pdb=" O MET B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 335 through 340 removed outlier: 4.030A pdb=" N LEU B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 354 Processing helix chain 'B' and resid 356 through 387 removed outlier: 4.378A pdb=" N ILE B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 395 through 422 removed outlier: 3.562A pdb=" N LEU B 399 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TRP B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR B 412 " --> pdb=" O TRP B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 426 through 445 Processing helix chain 'B' and resid 450 through 486 removed outlier: 3.833A pdb=" N VAL B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET B 471 " --> pdb=" O VAL B 467 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.523A pdb=" N ARG B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 518 removed outlier: 3.639A pdb=" N VAL B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 540 removed outlier: 3.693A pdb=" N PHE B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Proline residue: B 531 - end of helix Proline residue: B 535 - end of helix Processing helix chain 'B' and resid 543 through 557 Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 565 through 576 Processing helix chain 'B' and resid 578 through 587 Processing helix chain 'B' and resid 589 through 603 removed outlier: 4.369A pdb=" N VAL B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 615 removed outlier: 4.267A pdb=" N ILE B 607 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) Proline residue: B 611 - end of helix 701 hydrogen bonds defined for protein. 2046 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: 1.74 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1484 1.32 - 1.45: 2566 1.45 - 1.57: 5680 1.57 - 1.69: 8 1.69 - 1.81: 126 Bond restraints: 9864 Sorted by residual: bond pdb=" C PRO B 562 " pdb=" O PRO B 562 " ideal model delta sigma weight residual 1.243 1.215 0.028 8.50e-03 1.38e+04 1.11e+01 bond pdb=" C PRO A 562 " pdb=" O PRO A 562 " ideal model delta sigma weight residual 1.243 1.215 0.028 8.50e-03 1.38e+04 1.11e+01 bond pdb=" CA PRO B 562 " pdb=" C PRO B 562 " ideal model delta sigma weight residual 1.517 1.536 -0.019 6.70e-03 2.23e+04 8.20e+00 bond pdb=" CA PRO A 562 " pdb=" C PRO A 562 " ideal model delta sigma weight residual 1.517 1.536 -0.019 6.70e-03 2.23e+04 7.67e+00 bond pdb=" N TYR B 3 " pdb=" CA TYR B 3 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.32e-02 5.74e+03 3.62e+00 ... (remaining 9859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 12950 1.19 - 2.39: 321 2.39 - 3.58: 74 3.58 - 4.78: 34 4.78 - 5.97: 5 Bond angle restraints: 13384 Sorted by residual: angle pdb=" CA PRO A 562 " pdb=" C PRO A 562 " pdb=" O PRO A 562 " ideal model delta sigma weight residual 120.73 117.58 3.15 7.90e-01 1.60e+00 1.59e+01 angle pdb=" CA PRO B 562 " pdb=" C PRO B 562 " pdb=" O PRO B 562 " ideal model delta sigma weight residual 120.73 117.78 2.95 7.90e-01 1.60e+00 1.39e+01 angle pdb=" C THR B 561 " pdb=" CA THR B 561 " pdb=" CB THR B 561 " ideal model delta sigma weight residual 109.85 114.00 -4.15 1.14e+00 7.69e-01 1.33e+01 angle pdb=" CA PRO A 562 " pdb=" C PRO A 562 " pdb=" N PRO A 563 " ideal model delta sigma weight residual 118.06 121.04 -2.98 8.30e-01 1.45e+00 1.29e+01 angle pdb=" C THR A 561 " pdb=" CA THR A 561 " pdb=" CB THR A 561 " ideal model delta sigma weight residual 109.85 113.70 -3.85 1.14e+00 7.69e-01 1.14e+01 ... (remaining 13379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 5118 17.28 - 34.55: 525 34.55 - 51.83: 131 51.83 - 69.11: 17 69.11 - 86.38: 5 Dihedral angle restraints: 5796 sinusoidal: 2262 harmonic: 3534 Sorted by residual: dihedral pdb=" CA PRO A 563 " pdb=" C PRO A 563 " pdb=" N MET A 564 " pdb=" CA MET A 564 " ideal model delta harmonic sigma weight residual 180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA PRO B 563 " pdb=" C PRO B 563 " pdb=" N MET B 564 " pdb=" CA MET B 564 " ideal model delta harmonic sigma weight residual -180.00 -156.67 -23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ILE B 607 " pdb=" C ILE B 607 " pdb=" N THR B 608 " pdb=" CA THR B 608 " ideal model delta harmonic sigma weight residual -180.00 -162.69 -17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1220 0.039 - 0.078: 300 0.078 - 0.118: 85 0.118 - 0.157: 5 0.157 - 0.196: 2 Chirality restraints: 1612 Sorted by residual: chirality pdb=" CA TYR A 3 " pdb=" N TYR A 3 " pdb=" C TYR A 3 " pdb=" CB TYR A 3 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CA TYR B 3 " pdb=" N TYR B 3 " pdb=" C TYR B 3 " pdb=" CB TYR B 3 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA VAL B 340 " pdb=" N VAL B 340 " pdb=" C VAL B 340 " pdb=" CB VAL B 340 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1609 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 564 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C MET B 564 " -0.043 2.00e-02 2.50e+03 pdb=" O MET B 564 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY B 565 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 564 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C MET A 564 " 0.042 2.00e-02 2.50e+03 pdb=" O MET A 564 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 565 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 3 " 0.016 2.00e-02 2.50e+03 1.04e-02 2.15e+00 pdb=" CG TYR A 3 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 3 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 3 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 3 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 3 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 3 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 3 " 0.005 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 84 2.57 - 3.15: 8277 3.15 - 3.73: 14698 3.73 - 4.32: 19576 4.32 - 4.90: 34189 Nonbonded interactions: 76824 Sorted by model distance: nonbonded pdb=" OG1 THR B 395 " pdb=" OE1 GLN B 398 " model vdw 1.983 3.040 nonbonded pdb=" OG1 THR A 395 " pdb=" OE1 GLN A 398 " model vdw 2.001 3.040 nonbonded pdb=" O4P PGT A 704 " pdb=" O6 PGT A 704 " model vdw 2.077 3.040 nonbonded pdb=" OE1 GLN B 26 " pdb=" OG SER B 40 " model vdw 2.121 3.040 nonbonded pdb=" O GLY B 558 " pdb="NA NA B 702 " model vdw 2.133 2.470 ... (remaining 76819 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 702 or (resid 703 and (name C1 or name C11 or na \ me C12 or name C13 or name C2 or name C3 or name C30 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C5 or name C6 or name C8 or name N1 or \ name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 \ or name O7 or name P1 )) or resid 704)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.740 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: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.890 Find NCS groups from input model: 0.160 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:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.003 0.030 9864 Z= 0.158 Angle : 0.524 5.973 13384 Z= 0.303 Chirality : 0.038 0.196 1612 Planarity : 0.003 0.035 1608 Dihedral : 14.891 86.383 3520 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.88 % Allowed : 11.43 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.86 (0.25), residues: 1226 helix: 2.45 (0.17), residues: 940 sheet: None (None), residues: 0 loop : 0.01 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.024 0.001 TYR A 3 PHE 0.016 0.001 PHE A 478 TRP 0.006 0.001 TRP B 200 HIS 0.002 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9864) covalent geometry : angle 0.52430 (13384) hydrogen bonds : bond 0.14006 ( 701) hydrogen bonds : angle 5.29687 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.374 Fit side-chains REVERT: A 489 MET cc_start: 0.7944 (ttp) cc_final: 0.7735 (tmt) outliers start: 9 outliers final: 1 residues processed: 109 average time/residue: 0.5031 time to fit residues: 59.0210 Evaluate side-chains 79 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.1980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.079140 restraints weight = 20368.762| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.52 r_work: 0.3096 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9864 Z= 0.134 Angle : 0.544 7.507 13384 Z= 0.280 Chirality : 0.040 0.158 1612 Planarity : 0.004 0.033 1608 Dihedral : 8.127 59.188 1395 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.83 % Allowed : 11.13 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.79 (0.25), residues: 1226 helix: 2.35 (0.17), residues: 954 sheet: None (None), residues: 0 loop : 0.06 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.009 0.001 TYR B 3 PHE 0.020 0.001 PHE A 478 TRP 0.010 0.001 TRP B 227 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9864) covalent geometry : angle 0.54391 (13384) hydrogen bonds : bond 0.05071 ( 701) hydrogen bonds : angle 4.22929 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.411 Fit side-chains outliers start: 29 outliers final: 5 residues processed: 94 average time/residue: 0.5355 time to fit residues: 54.3847 Evaluate side-chains 75 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 68 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.077587 restraints weight = 20520.620| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.50 r_work: 0.3073 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9864 Z= 0.144 Angle : 0.515 9.134 13384 Z= 0.267 Chirality : 0.039 0.121 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.965 59.435 1394 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.25 % Allowed : 12.70 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.76 (0.25), residues: 1226 helix: 2.46 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.33 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 226 TYR 0.010 0.001 TYR B 3 PHE 0.018 0.001 PHE A 478 TRP 0.007 0.001 TRP B 227 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9864) covalent geometry : angle 0.51463 (13384) hydrogen bonds : bond 0.05087 ( 701) hydrogen bonds : angle 4.17411 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.326 Fit side-chains REVERT: B 564 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.7366 (tmt) REVERT: B 587 LEU cc_start: 0.8767 (mm) cc_final: 0.8561 (mt) outliers start: 23 outliers final: 5 residues processed: 97 average time/residue: 0.5091 time to fit residues: 53.3010 Evaluate side-chains 78 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 564 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 100 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.095930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079480 restraints weight = 20567.039| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.51 r_work: 0.3098 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9864 Z= 0.114 Angle : 0.517 12.352 13384 Z= 0.255 Chirality : 0.038 0.121 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.876 59.815 1394 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.34 % Allowed : 12.70 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.91 (0.25), residues: 1226 helix: 2.60 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -0.33 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.007 0.001 TYR B 3 PHE 0.015 0.001 PHE A 478 TRP 0.010 0.001 TRP B 227 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9864) covalent geometry : angle 0.51740 (13384) hydrogen bonds : bond 0.04376 ( 701) hydrogen bonds : angle 3.99386 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.338 Fit side-chains REVERT: A 78 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7604 (tmmm) REVERT: A 175 ASP cc_start: 0.7745 (p0) cc_final: 0.7435 (t0) REVERT: A 532 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8672 (mtm) REVERT: A 564 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.7225 (tmt) REVERT: A 587 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8395 (mm) REVERT: B 175 ASP cc_start: 0.7716 (p0) cc_final: 0.7478 (t0) REVERT: B 587 LEU cc_start: 0.8750 (mm) cc_final: 0.8511 (mm) outliers start: 24 outliers final: 4 residues processed: 93 average time/residue: 0.5694 time to fit residues: 57.0619 Evaluate side-chains 84 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.093037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076168 restraints weight = 20723.240| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.54 r_work: 0.3051 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9864 Z= 0.162 Angle : 0.550 13.826 13384 Z= 0.274 Chirality : 0.040 0.120 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.993 59.038 1394 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.64 % Allowed : 12.70 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.80 (0.24), residues: 1226 helix: 2.53 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -0.39 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.011 0.001 TYR A 3 PHE 0.018 0.001 PHE A 478 TRP 0.008 0.001 TRP B 200 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9864) covalent geometry : angle 0.54993 (13384) hydrogen bonds : bond 0.05220 ( 701) hydrogen bonds : angle 4.13504 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.455 Fit side-chains REVERT: A 78 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7709 (tmmm) REVERT: A 411 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8214 (mp) REVERT: A 556 MET cc_start: 0.9055 (mpp) cc_final: 0.8832 (mpm) REVERT: A 587 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8425 (mm) REVERT: B 175 ASP cc_start: 0.7785 (p0) cc_final: 0.7510 (t0) REVERT: B 411 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 556 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8882 (mpp) REVERT: B 587 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8535 (mm) outliers start: 27 outliers final: 7 residues processed: 94 average time/residue: 0.5781 time to fit residues: 58.6663 Evaluate side-chains 84 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 587 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 0.0040 chunk 40 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.078854 restraints weight = 20497.127| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.50 r_work: 0.3097 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9864 Z= 0.110 Angle : 0.516 12.936 13384 Z= 0.253 Chirality : 0.038 0.121 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.839 59.277 1394 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.95 % Allowed : 13.87 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.97 (0.25), residues: 1226 helix: 2.63 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -0.27 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.007 0.001 TYR B 3 PHE 0.013 0.001 PHE A 478 TRP 0.009 0.001 TRP B 227 HIS 0.002 0.000 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9864) covalent geometry : angle 0.51576 (13384) hydrogen bonds : bond 0.04230 ( 701) hydrogen bonds : angle 3.92407 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.448 Fit side-chains REVERT: A 78 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7577 (tmmm) REVERT: A 587 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8392 (mm) REVERT: B 175 ASP cc_start: 0.7727 (p0) cc_final: 0.7485 (t0) REVERT: B 587 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8523 (mm) outliers start: 20 outliers final: 5 residues processed: 86 average time/residue: 0.6377 time to fit residues: 58.8393 Evaluate side-chains 81 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 587 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 97 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.094529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077839 restraints weight = 20433.213| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.49 r_work: 0.3081 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9864 Z= 0.124 Angle : 0.523 13.776 13384 Z= 0.257 Chirality : 0.038 0.120 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.782 59.166 1394 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.66 % Allowed : 14.16 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.02 (0.25), residues: 1226 helix: 2.67 (0.17), residues: 932 sheet: None (None), residues: 0 loop : -0.26 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 181 TYR 0.008 0.001 TYR B 3 PHE 0.015 0.001 PHE A 478 TRP 0.007 0.001 TRP B 227 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9864) covalent geometry : angle 0.52306 (13384) hydrogen bonds : bond 0.04483 ( 701) hydrogen bonds : angle 3.98676 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.439 Fit side-chains REVERT: A 78 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7535 (tmmm) REVERT: A 587 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8431 (mm) REVERT: B 175 ASP cc_start: 0.7727 (p0) cc_final: 0.7489 (t0) REVERT: B 329 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8571 (mt) REVERT: B 587 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8533 (mm) outliers start: 17 outliers final: 6 residues processed: 86 average time/residue: 0.6469 time to fit residues: 59.7531 Evaluate side-chains 82 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 587 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.076587 restraints weight = 20648.429| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.53 r_work: 0.3054 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9864 Z= 0.145 Angle : 0.538 13.284 13384 Z= 0.266 Chirality : 0.039 0.118 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.861 59.740 1394 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.15 % Allowed : 13.96 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 2.92 (0.25), residues: 1226 helix: 2.58 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.31 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.010 0.001 TYR B 3 PHE 0.015 0.001 PHE A 478 TRP 0.007 0.001 TRP B 200 HIS 0.003 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9864) covalent geometry : angle 0.53791 (13384) hydrogen bonds : bond 0.04847 ( 701) hydrogen bonds : angle 4.02351 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.371 Fit side-chains REVERT: A 78 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7611 (tmmm) REVERT: A 587 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8478 (mm) REVERT: B 175 ASP cc_start: 0.7744 (p0) cc_final: 0.7498 (t0) REVERT: B 329 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8611 (mt) REVERT: B 587 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8603 (mp) outliers start: 22 outliers final: 13 residues processed: 93 average time/residue: 0.6050 time to fit residues: 60.6389 Evaluate side-chains 90 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 587 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 67 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 0.0010 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.095402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.078716 restraints weight = 20496.652| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.52 r_work: 0.3096 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9864 Z= 0.108 Angle : 0.507 12.864 13384 Z= 0.248 Chirality : 0.038 0.120 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.725 59.978 1394 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.76 % Allowed : 14.45 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.02 (0.25), residues: 1226 helix: 2.65 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.28 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.007 0.001 TYR B 3 PHE 0.013 0.001 PHE A 478 TRP 0.008 0.001 TRP B 227 HIS 0.002 0.000 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9864) covalent geometry : angle 0.50705 (13384) hydrogen bonds : bond 0.04099 ( 701) hydrogen bonds : angle 3.88546 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.462 Fit side-chains REVERT: A 78 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7541 (tmmm) REVERT: A 587 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8448 (mm) REVERT: B 175 ASP cc_start: 0.7714 (p0) cc_final: 0.7469 (t0) REVERT: B 329 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8569 (mt) REVERT: B 587 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8548 (mm) outliers start: 18 outliers final: 11 residues processed: 88 average time/residue: 0.6362 time to fit residues: 60.1779 Evaluate side-chains 88 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.078144 restraints weight = 20544.258| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.52 r_work: 0.3083 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9864 Z= 0.121 Angle : 0.528 14.527 13384 Z= 0.258 Chirality : 0.038 0.119 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.705 59.601 1394 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.56 % Allowed : 14.65 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.01 (0.25), residues: 1226 helix: 2.64 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.30 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 181 TYR 0.008 0.001 TYR B 3 PHE 0.014 0.001 PHE A 478 TRP 0.006 0.001 TRP B 227 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9864) covalent geometry : angle 0.52845 (13384) hydrogen bonds : bond 0.04301 ( 701) hydrogen bonds : angle 3.95484 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.301 Fit side-chains REVERT: A 78 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7560 (tmmm) REVERT: A 587 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8461 (mm) REVERT: B 175 ASP cc_start: 0.7698 (p0) cc_final: 0.7454 (t0) REVERT: B 329 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8581 (mt) outliers start: 16 outliers final: 10 residues processed: 88 average time/residue: 0.6300 time to fit residues: 59.4960 Evaluate side-chains 85 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 529 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 90 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 0.0170 chunk 88 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.094893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078093 restraints weight = 20389.153| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.52 r_work: 0.3084 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9864 Z= 0.120 Angle : 0.531 14.304 13384 Z= 0.256 Chirality : 0.038 0.119 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.695 59.064 1394 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.66 % Allowed : 14.45 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 3.01 (0.25), residues: 1226 helix: 2.64 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.26 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 181 TYR 0.009 0.001 TYR B 3 PHE 0.014 0.001 PHE A 478 TRP 0.006 0.001 TRP B 227 HIS 0.002 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9864) covalent geometry : angle 0.53081 (13384) hydrogen bonds : bond 0.04323 ( 701) hydrogen bonds : angle 3.93229 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.02 seconds wall clock time: 44 minutes 35.04 seconds (2675.04 seconds total)