Starting phenix.real_space_refine on Fri Feb 14 11:17:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thj_41266/02_2025/8thj_41266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thj_41266/02_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_41266/02_2025/8thj_41266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thj_41266/02_2025/8thj_41266.map" model { file = "/net/cci-nas-00/data/ceres_data/8thj_41266/02_2025/8thj_41266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thj_41266/02_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-5592/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: 7.96, 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: 2.48 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: 0.94 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: 2.68 Time building geometry restraints manager: 2.83 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: 11.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.320 Process input model: 27.530 Find NCS groups from input model: 0.480 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.890 ------------------------------------------------------------------------------- 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= 0.189 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 *********************** 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 : 1.044 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: 1.2413 time to fit residues: 145.4395 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 : 1.014 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076447 restraints weight = 20218.026| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.50 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= 0.278 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 *********************** 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 : 1.070 Fit side-chains REVERT: A 518 MET cc_start: 0.8610 (mtt) cc_final: 0.8408 (mtp) REVERT: A 532 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8771 (mtm) outliers start: 29 outliers final: 7 residues processed: 94 average time/residue: 1.2656 time to fit residues: 128.2750 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 : 1.019 ------------------------------------------------------------------------------- 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: 0.9990 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 111 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 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 = 0.3473 r_free = 0.3473 target = 0.094666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.078131 restraints weight = 20518.120| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.51 r_work: 0.3075 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9864 Z= 0.189 Angle : 0.517 8.681 13384 Z= 0.262 Chirality : 0.039 0.120 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.955 59.959 1394 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.15 % Allowed : 12.79 % 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 (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: 2.81 (0.25), residues: 1226 helix: 2.50 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.35 (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 0.002 0.000 ARG A 181 *********************** 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 98 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 1.012 Fit side-chains REVERT: A 78 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7671 (tmmm) REVERT: A 411 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8317 (mp) REVERT: A 564 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.7508 (tmt) REVERT: A 587 LEU cc_start: 0.8724 (mm) cc_final: 0.8459 (mm) REVERT: B 556 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8877 (mpp) REVERT: B 564 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.7453 (tmt) REVERT: B 587 LEU cc_start: 0.8736 (mm) cc_final: 0.8459 (mm) outliers start: 22 outliers final: 2 residues processed: 92 average time/residue: 1.2783 time to fit residues: 126.2798 Evaluate side-chains 79 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS 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: 1.9990 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.093230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.076471 restraints weight = 20357.914| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.51 r_work: 0.3058 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9864 Z= 0.237 Angle : 0.534 8.904 13384 Z= 0.271 Chirality : 0.039 0.119 1612 Planarity : 0.004 0.036 1608 Dihedral : 8.026 59.850 1394 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.83 % Allowed : 12.79 % Favored : 84.38 % 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: 2.72 (0.24), residues: 1226 helix: 2.49 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -0.46 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 227 HIS 0.004 0.001 HIS B 285 PHE 0.018 0.001 PHE A 478 TYR 0.010 0.001 TYR A 3 ARG 0.002 0.000 ARG A 181 *********************** 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 105 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 1.128 Fit side-chains REVERT: A 175 ASP cc_start: 0.7824 (p0) cc_final: 0.7507 (t0) REVERT: A 411 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8283 (mp) REVERT: A 556 MET cc_start: 0.9080 (mpp) cc_final: 0.8858 (mpm) REVERT: A 587 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8519 (mm) REVERT: B 411 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8313 (mp) REVERT: B 556 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8895 (mpp) REVERT: B 564 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.7139 (tmt) REVERT: B 587 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8524 (mm) outliers start: 29 outliers final: 10 residues processed: 93 average time/residue: 1.2260 time to fit residues: 123.3588 Evaluate side-chains 92 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 411 LEU 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 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 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: 0.9980 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.093719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.076989 restraints weight = 20407.511| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.50 r_work: 0.3068 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2297 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= 0.203 Angle : 0.514 8.420 13384 Z= 0.261 Chirality : 0.039 0.119 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.961 59.189 1394 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.54 % Allowed : 12.79 % 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 (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: 2.81 (0.24), residues: 1226 helix: 2.54 (0.17), residues: 930 sheet: None (None), residues: 0 loop : -0.41 (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 0.009 0.001 TYR A 3 ARG 0.002 0.000 ARG A 181 *********************** 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: 26 poor density : 80 time to evaluate : 1.152 Fit side-chains REVERT: A 78 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7658 (tmmm) REVERT: A 175 ASP cc_start: 0.7772 (p0) cc_final: 0.7469 (t0) REVERT: A 587 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8549 (mm) REVERT: B 175 ASP cc_start: 0.7748 (p0) cc_final: 0.7479 (t0) REVERT: B 411 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8287 (mp) REVERT: B 556 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8919 (mpp) REVERT: B 587 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8562 (mm) outliers start: 26 outliers final: 7 residues processed: 98 average time/residue: 1.2048 time to fit residues: 127.6935 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 : 1.120 ------------------------------------------------------------------------------- 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 450 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain B residue 98 PHE 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 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: 1.9990 chunk 23 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 0.0270 chunk 93 optimal weight: 3.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- 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 = 0.094490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.077715 restraints weight = 20555.200| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.51 r_work: 0.3076 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2482 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= 0.185 Angle : 0.503 8.621 13384 Z= 0.254 Chirality : 0.038 0.120 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.857 59.275 1394 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.34 % Allowed : 13.67 % Favored : 83.98 % 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 (0.24), residues: 1226 helix: 2.61 (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 0.008 0.001 TYR A 153 ARG 0.002 0.000 ARG B 226 *********************** 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 99 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 1.087 Fit side-chains REVERT: A 78 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7573 (tmmm) REVERT: A 175 ASP cc_start: 0.7730 (p0) cc_final: 0.7450 (t0) REVERT: A 587 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8532 (mm) REVERT: B 175 ASP cc_start: 0.7736 (p0) cc_final: 0.7491 (t0) REVERT: B 329 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8564 (mt) REVERT: B 587 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8543 (mm) outliers start: 24 outliers final: 6 residues processed: 91 average time/residue: 1.3046 time to fit residues: 127.7468 Evaluate side-chains 84 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 99 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- 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 = 0.094848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078062 restraints weight = 20663.069| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.53 r_work: 0.3084 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9864 Z= 0.175 Angle : 0.504 9.122 13384 Z= 0.252 Chirality : 0.038 0.119 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.783 59.378 1394 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.15 % Allowed : 13.87 % Favored : 83.98 % 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: 3.02 (0.25), residues: 1226 helix: 2.65 (0.17), residues: 934 sheet: None (None), residues: 0 loop : -0.23 (0.37), residues: 292 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 0.014 0.001 PHE A 478 TYR 0.008 0.001 TYR B 3 ARG 0.002 0.000 ARG A 181 *********************** 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 96 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 1.119 Fit side-chains REVERT: A 78 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7516 (tmmm) REVERT: A 175 ASP cc_start: 0.7728 (p0) cc_final: 0.7442 (t0) REVERT: A 587 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8540 (mm) REVERT: B 175 ASP cc_start: 0.7742 (p0) cc_final: 0.7498 (t0) REVERT: B 587 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8562 (mm) outliers start: 22 outliers final: 10 residues processed: 91 average time/residue: 1.3111 time to fit residues: 128.3778 Evaluate side-chains 87 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 366 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.0170 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.095637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.078895 restraints weight = 20720.527| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.53 r_work: 0.3107 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9864 Z= 0.162 Angle : 0.497 9.994 13384 Z= 0.246 Chirality : 0.038 0.120 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.672 59.642 1394 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.76 % Allowed : 14.65 % Favored : 83.59 % 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: 3.08 (0.25), residues: 1226 helix: 2.70 (0.17), residues: 932 sheet: None (None), residues: 0 loop : -0.21 (0.37), residues: 294 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 0.007 0.001 TYR B 3 ARG 0.002 0.000 ARG A 181 *********************** 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 94 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 1.042 Fit side-chains REVERT: A 78 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7492 (tmmm) REVERT: A 175 ASP cc_start: 0.7671 (p0) cc_final: 0.7432 (t0) REVERT: B 175 ASP cc_start: 0.7690 (p0) cc_final: 0.7464 (t0) REVERT: B 329 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8566 (mt) REVERT: B 587 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8580 (mm) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 1.2481 time to fit residues: 122.5415 Evaluate side-chains 87 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.0050 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.095009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.078250 restraints weight = 20645.090| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.54 r_work: 0.3066 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2751 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= 0.182 Angle : 0.506 9.761 13384 Z= 0.250 Chirality : 0.038 0.218 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.671 59.756 1394 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.95 % Allowed : 14.65 % 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: 3.05 (0.25), residues: 1226 helix: 2.67 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.23 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 227 HIS 0.002 0.001 HIS B 285 PHE 0.014 0.001 PHE A 478 TYR 0.008 0.001 TYR B 3 ARG 0.001 0.000 ARG A 181 *********************** 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: 20 poor density : 72 time to evaluate : 1.125 Fit side-chains REVERT: A 78 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7543 (tmmm) REVERT: A 175 ASP cc_start: 0.7700 (p0) cc_final: 0.7465 (t0) REVERT: B 175 ASP cc_start: 0.7734 (p0) cc_final: 0.7500 (t0) REVERT: B 329 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8595 (mt) outliers start: 20 outliers final: 12 residues processed: 88 average time/residue: 1.2740 time to fit residues: 120.8349 Evaluate side-chains 85 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 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 586 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: 0.9990 chunk 25 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 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 = 0.3460 r_free = 0.3460 target = 0.093611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.076804 restraints weight = 20718.831| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.53 r_work: 0.3070 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2772 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= 0.227 Angle : 0.528 10.923 13384 Z= 0.264 Chirality : 0.039 0.127 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.747 58.637 1394 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.37 % Allowed : 14.94 % Favored : 83.69 % 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 : -0.30 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 200 HIS 0.003 0.001 HIS A 285 PHE 0.015 0.001 PHE A 478 TYR 0.010 0.001 TYR B 3 ARG 0.002 0.000 ARG A 80 ********************** 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 86 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 1.096 Fit side-chains REVERT: A 78 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7592 (tmmm) REVERT: A 175 ASP cc_start: 0.7694 (p0) cc_final: 0.7435 (t0) REVERT: B 175 ASP cc_start: 0.7717 (p0) cc_final: 0.7476 (t0) REVERT: B 329 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8587 (mt) outliers start: 14 outliers final: 11 residues processed: 85 average time/residue: 1.3194 time to fit residues: 120.4558 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 : 1.161 ------------------------------------------------------------------------------- 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 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 586 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 60 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 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 = 0.3474 r_free = 0.3474 target = 0.094550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.077855 restraints weight = 20647.507| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.53 r_work: 0.3089 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9864 Z= 0.185 Angle : 0.516 11.496 13384 Z= 0.254 Chirality : 0.038 0.126 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.705 58.249 1394 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.56 % Allowed : 15.04 % 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: 2.98 (0.25), residues: 1226 helix: 2.61 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.25 (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 A 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4920.12 seconds wall clock time: 89 minutes 12.39 seconds (5352.39 seconds total)