Starting phenix.real_space_refine on Thu May 1 02:10:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thj_41266/05_2025/8thj_41266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thj_41266/05_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_41266/05_2025/8thj_41266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thj_41266/05_2025/8thj_41266.map" model { file = "/net/cci-nas-00/data/ceres_data/8thj_41266/05_2025/8thj_41266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thj_41266/05_2025/8thj_41266.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 8.04, per 1000 atoms: 0.83 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: 2.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.96 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: 2.83 Time building geometry restraints manager: 2.80 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 615 or resid 701 through 702 or (resid 703 and ( \ name C1 or name C11 or name 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 O1 \ 4 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: 450.990 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.450 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 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:14.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 493.350 ------------------------------------------------------------------------------- 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 : 5.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP B 200 HIS 0.002 0.001 HIS A 285 PHE 0.016 0.001 PHE A 478 TYR 0.024 0.001 TYR A 3 ARG 0.002 0.000 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.14006 ( 701) hydrogen bonds : angle 5.29687 ( 2046) covalent geometry : bond 0.00288 ( 9864) covalent geometry : angle 0.52430 (13384) *********************** 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 : 1.001 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: 1.1537 time to fit residues: 135.7157 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 : 1.125 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.093108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076407 restraints weight = 20218.023| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.51 r_work: 0.3050 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9864 Z= 0.180 Angle : 0.580 7.773 13384 Z= 0.301 Chirality : 0.041 0.143 1612 Planarity : 0.004 0.035 1608 Dihedral : 8.334 59.551 1395 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.83 % Allowed : 11.72 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.24), residues: 1226 helix: 2.17 (0.17), residues: 954 sheet: None (None), residues: 0 loop : 0.01 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 176 HIS 0.005 0.002 HIS B 285 PHE 0.023 0.002 PHE A 478 TYR 0.013 0.002 TYR B 3 ARG 0.003 0.001 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.05687 ( 701) hydrogen bonds : angle 4.36534 ( 2046) covalent geometry : bond 0.00428 ( 9864) covalent geometry : angle 0.58006 (13384) *********************** 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 104 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 1.020 Fit side-chains REVERT: A 518 MET cc_start: 0.8610 (mtt) cc_final: 0.8407 (mtp) REVERT: A 532 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8774 (mtm) outliers start: 29 outliers final: 7 residues processed: 94 average time/residue: 1.2588 time to fit residues: 127.9930 Evaluate side-chains 78 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 A residue 450 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 450 THR 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 14 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 96 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.094539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.077955 restraints weight = 20547.014| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.50 r_work: 0.3075 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9864 Z= 0.128 Angle : 0.516 8.008 13384 Z= 0.263 Chirality : 0.039 0.120 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.940 59.983 1394 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.95 % Allowed : 13.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.25), residues: 1226 helix: 2.51 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.34 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 227 HIS 0.002 0.001 HIS B 285 PHE 0.017 0.001 PHE A 478 TYR 0.009 0.001 TYR B 3 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 701) hydrogen bonds : angle 4.15658 ( 2046) covalent geometry : bond 0.00296 ( 9864) covalent geometry : angle 0.51629 (13384) *********************** 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 96 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.105 Fit side-chains REVERT: A 411 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8316 (mp) REVERT: A 564 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.7437 (tmt) REVERT: A 587 LEU cc_start: 0.8725 (mm) cc_final: 0.8475 (mm) REVERT: B 556 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8888 (mpp) REVERT: B 564 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.7413 (tmt) REVERT: B 587 LEU cc_start: 0.8718 (mm) cc_final: 0.8463 (mm) outliers start: 20 outliers final: 2 residues processed: 91 average time/residue: 1.1809 time to fit residues: 115.9830 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 : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 556 MET 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 102 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 0.0670 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.094966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.078428 restraints weight = 20238.720| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.48 r_work: 0.3088 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9864 Z= 0.121 Angle : 0.512 8.465 13384 Z= 0.257 Chirality : 0.038 0.120 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.903 59.337 1394 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.73 % Allowed : 12.99 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.25), residues: 1226 helix: 2.58 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -0.37 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 227 HIS 0.002 0.001 HIS B 285 PHE 0.016 0.001 PHE A 478 TYR 0.008 0.001 TYR B 3 ARG 0.002 0.000 ARG B 226 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 701) hydrogen bonds : angle 4.04520 ( 2046) covalent geometry : bond 0.00275 ( 9864) covalent geometry : angle 0.51193 (13384) *********************** 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 106 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 1.081 Fit side-chains REVERT: A 78 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7605 (tmmm) REVERT: A 175 ASP cc_start: 0.7736 (p0) cc_final: 0.7434 (t0) REVERT: A 556 MET cc_start: 0.9087 (mpp) cc_final: 0.8864 (mpm) REVERT: A 587 LEU cc_start: 0.8719 (mm) cc_final: 0.8503 (mm) REVERT: B 175 ASP cc_start: 0.7708 (p0) cc_final: 0.7465 (t0) REVERT: B 411 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8281 (mp) REVERT: B 556 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8915 (mpp) REVERT: B 564 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.7238 (tmt) REVERT: B 587 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8518 (mm) outliers start: 28 outliers final: 9 residues processed: 96 average time/residue: 1.2394 time to fit residues: 128.5027 Evaluate side-chains 91 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 450 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain B residue 98 PHE 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 564 MET Chi-restraints excluded: chain B residue 587 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 4 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 0.0870 chunk 91 optimal weight: 10.0000 overall best weight: 0.7162 ------------------------------------------------------------------------------- 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 = 0.094932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078409 restraints weight = 20377.658| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.44 r_work: 0.3095 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9864 Z= 0.120 Angle : 0.504 8.493 13384 Z= 0.254 Chirality : 0.038 0.120 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.844 58.950 1394 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.73 % Allowed : 12.99 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.24), residues: 1226 helix: 2.62 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -0.32 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 227 HIS 0.002 0.001 HIS B 285 PHE 0.015 0.001 PHE A 478 TYR 0.007 0.001 TYR A 3 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 701) hydrogen bonds : angle 4.00094 ( 2046) covalent geometry : bond 0.00277 ( 9864) covalent geometry : angle 0.50420 (13384) *********************** 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 106 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 1.134 Fit side-chains REVERT: A 78 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7569 (tmmm) REVERT: A 175 ASP cc_start: 0.7739 (p0) cc_final: 0.7463 (t0) REVERT: A 587 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8522 (mm) REVERT: B 175 ASP cc_start: 0.7772 (p0) cc_final: 0.7521 (t0) REVERT: B 411 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8299 (mp) REVERT: B 556 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8914 (mpp) REVERT: B 587 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8551 (mm) outliers start: 28 outliers final: 9 residues processed: 96 average time/residue: 1.2560 time to fit residues: 130.4892 Evaluate side-chains 89 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 529 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 304 ASP 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 116 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078063 restraints weight = 20540.760| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.51 r_work: 0.3087 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9864 Z= 0.121 Angle : 0.501 9.146 13384 Z= 0.251 Chirality : 0.038 0.120 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.822 58.728 1394 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.34 % Allowed : 13.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.25), residues: 1226 helix: 2.63 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -0.30 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 227 HIS 0.002 0.001 HIS B 285 PHE 0.015 0.001 PHE A 478 TYR 0.008 0.001 TYR B 3 ARG 0.001 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04428 ( 701) hydrogen bonds : angle 3.99932 ( 2046) covalent geometry : bond 0.00279 ( 9864) covalent geometry : angle 0.50097 (13384) *********************** 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 100 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.986 Fit side-chains REVERT: A 78 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7568 (tmmm) REVERT: A 175 ASP cc_start: 0.7743 (p0) cc_final: 0.7454 (t0) REVERT: A 587 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8519 (mm) REVERT: B 175 ASP cc_start: 0.7737 (p0) cc_final: 0.7498 (t0) REVERT: B 556 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8904 (mpp) REVERT: B 587 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8546 (mm) outliers start: 24 outliers final: 8 residues processed: 92 average time/residue: 1.5705 time to fit residues: 155.2384 Evaluate side-chains 87 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 2.120 ------------------------------------------------------------------------------- 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 450 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 450 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.094467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077625 restraints weight = 20713.812| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.53 r_work: 0.3076 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9864 Z= 0.128 Angle : 0.506 9.253 13384 Z= 0.255 Chirality : 0.038 0.118 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.802 59.097 1394 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.44 % Allowed : 13.28 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.24), residues: 1226 helix: 2.66 (0.17), residues: 932 sheet: None (None), residues: 0 loop : -0.30 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 227 HIS 0.002 0.001 HIS B 285 PHE 0.015 0.001 PHE A 478 TYR 0.009 0.001 TYR A 3 ARG 0.001 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 701) hydrogen bonds : angle 4.01525 ( 2046) covalent geometry : bond 0.00304 ( 9864) covalent geometry : angle 0.50629 (13384) *********************** 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 99 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 1.298 Fit side-chains REVERT: A 78 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7531 (tmmm) REVERT: A 175 ASP cc_start: 0.7738 (p0) cc_final: 0.7446 (t0) REVERT: A 587 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8516 (mm) REVERT: B 175 ASP cc_start: 0.7737 (p0) cc_final: 0.7501 (t0) REVERT: B 329 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8581 (mt) REVERT: B 411 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8263 (mp) REVERT: B 587 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8552 (mm) outliers start: 25 outliers final: 9 residues processed: 93 average time/residue: 1.6872 time to fit residues: 170.0986 Evaluate side-chains 88 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 561 THR 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 366 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 450 THR 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 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.093055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.076165 restraints weight = 20740.846| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.53 r_work: 0.3051 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9864 Z= 0.152 Angle : 0.535 10.238 13384 Z= 0.268 Chirality : 0.039 0.118 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.893 59.727 1394 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.15 % Allowed : 14.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.25), residues: 1226 helix: 2.56 (0.17), residues: 934 sheet: None (None), residues: 0 loop : -0.40 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 200 HIS 0.003 0.001 HIS A 285 PHE 0.016 0.001 PHE A 478 TYR 0.011 0.001 TYR B 3 ARG 0.002 0.000 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 701) hydrogen bonds : angle 4.06964 ( 2046) covalent geometry : bond 0.00365 ( 9864) covalent geometry : angle 0.53461 (13384) *********************** 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 97 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.147 Fit side-chains REVERT: A 78 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7630 (tmmm) REVERT: B 329 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8602 (mt) REVERT: B 587 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8566 (mm) outliers start: 22 outliers final: 10 residues processed: 94 average time/residue: 1.6787 time to fit residues: 170.5626 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 : 2.336 ------------------------------------------------------------------------------- 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 529 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 329 ILE 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 529 VAL Chi-restraints excluded: chain B residue 561 THR 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 31 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.094187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.077425 restraints weight = 20581.846| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.52 r_work: 0.3061 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9864 Z= 0.125 Angle : 0.517 10.946 13384 Z= 0.256 Chirality : 0.038 0.118 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.823 59.639 1394 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.76 % Allowed : 14.84 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.25), residues: 1226 helix: 2.59 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.36 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 227 HIS 0.002 0.001 HIS A 285 PHE 0.014 0.001 PHE A 478 TYR 0.010 0.001 TYR B 3 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 701) hydrogen bonds : angle 3.98577 ( 2046) covalent geometry : bond 0.00295 ( 9864) covalent geometry : angle 0.51674 (13384) *********************** 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 : 0.991 Fit side-chains REVERT: A 78 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7587 (tmmm) REVERT: B 329 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8577 (mt) outliers start: 18 outliers final: 10 residues processed: 88 average time/residue: 1.1892 time to fit residues: 112.9469 Evaluate side-chains 83 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 561 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 329 ILE 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 48 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.094551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.077814 restraints weight = 20633.043| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.53 r_work: 0.3083 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9864 Z= 0.121 Angle : 0.526 12.302 13384 Z= 0.259 Chirality : 0.038 0.119 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.770 59.530 1394 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.07 % Allowed : 15.62 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.25), residues: 1226 helix: 2.59 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.31 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 227 HIS 0.002 0.000 HIS B 285 PHE 0.014 0.001 PHE A 478 TYR 0.009 0.001 TYR B 3 ARG 0.001 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 701) hydrogen bonds : angle 4.00608 ( 2046) covalent geometry : bond 0.00287 ( 9864) covalent geometry : angle 0.52609 (13384) ********************** 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 83 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.004 Fit side-chains REVERT: A 78 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7571 (tmmm) REVERT: B 329 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8577 (mt) outliers start: 11 outliers final: 9 residues processed: 83 average time/residue: 1.2734 time to fit residues: 113.6393 Evaluate side-chains 83 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 B residue 72 THR Chi-restraints excluded: chain B residue 329 ILE 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 60 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.094339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.077540 restraints weight = 20665.556| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.54 r_work: 0.3087 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9864 Z= 0.124 Angle : 0.529 13.897 13384 Z= 0.257 Chirality : 0.038 0.118 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.751 58.962 1394 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.46 % Allowed : 15.23 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.25), residues: 1226 helix: 2.59 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.33 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 227 HIS 0.002 0.001 HIS A 285 PHE 0.014 0.001 PHE A 478 TYR 0.008 0.001 TYR A 3 ARG 0.001 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 701) hydrogen bonds : angle 3.97073 ( 2046) covalent geometry : bond 0.00295 ( 9864) covalent geometry : angle 0.52911 (13384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5753.43 seconds wall clock time: 103 minutes 13.72 seconds (6193.72 seconds total)