Starting phenix.real_space_refine on Sun Apr 7 04:51:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thj_41266/04_2024/8thj_41266_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thj_41266/04_2024/8thj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thj_41266/04_2024/8thj_41266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thj_41266/04_2024/8thj_41266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thj_41266/04_2024/8thj_41266_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thj_41266/04_2024/8thj_41266_updated.pdb" } 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 Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 5.75, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 3.90 Conformation dependent library (CDL) restraints added in 1.7 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... running ksdssp... Secondary structure from input PDB file: 58 helices and 0 sheets defined 79.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 40 through 62 removed outlier: 3.784A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 77 through 108 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 148 removed outlier: 3.829A pdb=" N ALA A 126 " --> pdb=" O TRP A 123 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 127 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 128 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 3.785A pdb=" N ILE A 133 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 172 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.630A pdb=" N LYS A 178 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 189 through 205 removed outlier: 3.953A pdb=" N VAL A 193 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 removed outlier: 3.716A pdb=" N PHE A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 removed outlier: 3.544A pdb=" N ASN A 231 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 235 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 282 through 296 Processing helix chain 'A' and resid 301 through 319 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 323 through 336 removed outlier: 3.840A pdb=" N CYS A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 357 through 386 removed outlier: 3.640A pdb=" N PHE A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix removed outlier: 3.839A pdb=" N THR A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 421 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 427 through 443 Processing helix chain 'A' and resid 451 through 485 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 487 through 494 Processing helix chain 'A' and resid 502 through 518 removed outlier: 3.778A pdb=" N MET A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 539 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 544 through 560 removed outlier: 3.671A pdb=" N GLY A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU A 560 " --> pdb=" O MET A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 579 through 602 Proline residue: A 588 - end of helix removed outlier: 4.493A pdb=" N ILE A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 604 through 614 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 2 through 4 No H-bonds generated for 'chain 'B' and resid 2 through 4' Processing helix chain 'B' and resid 7 through 32 Processing helix chain 'B' and resid 40 through 62 removed outlier: 3.791A pdb=" N TYR B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 77 through 108 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 148 removed outlier: 3.812A pdb=" N ALA B 126 " --> pdb=" O TRP B 123 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 127 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 128 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Proline residue: B 129 - end of helix removed outlier: 3.762A pdb=" N ILE B 133 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 174 through 179 removed outlier: 3.635A pdb=" N LYS B 178 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 189 through 206 removed outlier: 3.966A pdb=" N VAL B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 206 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 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 227 through 239 removed outlier: 3.666A pdb=" N ASN B 231 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 235 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 259 Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 301 through 319 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) Processing helix chain 'B' and resid 323 through 339 removed outlier: 3.839A pdb=" N CYS B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'B' and resid 357 through 386 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 396 through 421 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 427 through 444 Processing helix chain 'B' and resid 451 through 485 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 487 through 494 Processing helix chain 'B' and resid 502 through 518 removed outlier: 3.770A pdb=" N MET B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 539 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 544 through 560 removed outlier: 3.673A pdb=" N GLY B 558 " --> pdb=" O ASN B 554 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU B 560 " --> pdb=" O MET B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 575 Processing helix chain 'B' and resid 579 through 602 Proline residue: B 588 - end of helix removed outlier: 4.504A pdb=" N ILE B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 604 through 614 removed outlier: 4.815A pdb=" N VAL B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) Proline residue: B 611 - end of helix 635 hydrogen bonds defined for protein. 1533 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: 2.72 Time building geometry restraints manager: 4.23 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: 92.72 - 100.98: 34 100.98 - 109.23: 496 109.23 - 117.49: 6850 117.49 - 125.74: 5877 125.74 - 134.00: 127 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: 8402 3.15 - 3.73: 14636 3.73 - 4.32: 19741 4.32 - 4.90: 34225 Nonbonded interactions: 77088 Sorted by model distance: nonbonded pdb=" OG1 THR B 395 " pdb=" OE1 GLN B 398 " model vdw 1.983 2.440 nonbonded pdb=" OG1 THR A 395 " pdb=" OE1 GLN A 398 " model vdw 2.001 2.440 nonbonded pdb=" O4P PGT A 704 " pdb=" O6 PGT A 704 " model vdw 2.077 2.440 nonbonded pdb=" OE1 GLN B 26 " pdb=" OG SER B 40 " model vdw 2.121 2.440 nonbonded pdb=" O GLY B 558 " pdb="NA NA B 702 " model vdw 2.133 2.470 ... (remaining 77083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 5.600 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: 22.610 Check model and map are aligned: 0.190 Set scattering table: 0.090 Process input model: 29.210 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.190 ------------------------------------------------------------------------------- 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= 0.187 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 fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.078 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: 1.2513 time to fit residues: 146.9948 Evaluate side-chains 79 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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: 0.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9864 Z= 0.277 Angle : 0.575 7.406 13384 Z= 0.300 Chirality : 0.041 0.127 1612 Planarity : 0.005 0.036 1608 Dihedral : 8.150 59.126 1395 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.93 % Allowed : 12.30 % Favored : 84.77 % 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: 1.98 (0.25), residues: 1226 helix: 1.82 (0.17), residues: 932 sheet: None (None), residues: 0 loop : -0.27 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 200 HIS 0.005 0.001 HIS B 285 PHE 0.025 0.002 PHE A 478 TYR 0.011 0.002 TYR A 153 ARG 0.003 0.000 ARG A 381 *********************** 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 108 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 1.131 Fit side-chains outliers start: 30 outliers final: 8 residues processed: 97 average time/residue: 1.2059 time to fit residues: 126.5813 Evaluate side-chains 79 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 391 THR 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 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 119 optimal weight: 0.1980 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9864 Z= 0.168 Angle : 0.503 8.452 13384 Z= 0.256 Chirality : 0.038 0.122 1612 Planarity : 0.005 0.033 1608 Dihedral : 7.763 59.457 1395 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: 2.02 (0.25), residues: 1226 helix: 1.82 (0.18), residues: 940 sheet: None (None), residues: 0 loop : -0.17 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 200 HIS 0.002 0.001 HIS B 285 PHE 0.018 0.001 PHE A 478 TYR 0.009 0.001 TYR A 3 ARG 0.002 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 1.018 Fit side-chains REVERT: A 411 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8624 (mp) REVERT: A 489 MET cc_start: 0.8179 (ttp) cc_final: 0.7698 (tmt) REVERT: A 532 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8358 (mtm) outliers start: 25 outliers final: 6 residues processed: 91 average time/residue: 1.2833 time to fit residues: 126.1448 Evaluate side-chains 79 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 529 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 111 optimal weight: 0.4980 chunk 117 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9864 Z= 0.155 Angle : 0.505 9.107 13384 Z= 0.252 Chirality : 0.038 0.230 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.620 59.878 1394 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.05 % Allowed : 15.23 % Favored : 82.71 % 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: 2.02 (0.25), residues: 1226 helix: 1.87 (0.18), residues: 928 sheet: None (None), residues: 0 loop : -0.29 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 200 HIS 0.003 0.001 HIS B 285 PHE 0.017 0.001 PHE A 478 TYR 0.007 0.001 TYR B 3 ARG 0.002 0.000 ARG B 226 *********************** 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 94 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 1.112 Fit side-chains REVERT: A 411 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 564 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.7395 (tmt) REVERT: B 411 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8607 (mp) REVERT: B 556 MET cc_start: 0.9187 (mpp) cc_final: 0.8983 (mpm) REVERT: B 564 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7376 (tmt) outliers start: 21 outliers final: 6 residues processed: 88 average time/residue: 1.3417 time to fit residues: 127.1611 Evaluate side-chains 82 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 564 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2307 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= 0.200 Angle : 0.524 9.646 13384 Z= 0.260 Chirality : 0.040 0.307 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.576 58.673 1394 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.12 % Allowed : 14.45 % Favored : 82.42 % 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: 1.94 (0.25), residues: 1226 helix: 1.82 (0.18), residues: 928 sheet: None (None), residues: 0 loop : -0.34 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.003 0.001 HIS B 285 PHE 0.016 0.001 PHE A 478 TYR 0.010 0.001 TYR B 3 ARG 0.001 0.000 ARG B 226 *********************** 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 105 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 73 time to evaluate : 1.674 Fit side-chains REVERT: A 411 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8577 (mp) REVERT: A 564 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7125 (tmt) REVERT: B 329 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8851 (mt) REVERT: B 411 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8595 (mp) REVERT: B 424 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9157 (tp) REVERT: B 564 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7077 (tmt) outliers start: 32 outliers final: 11 residues processed: 95 average time/residue: 1.3522 time to fit residues: 138.4241 Evaluate side-chains 90 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 564 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9864 Z= 0.195 Angle : 0.526 13.320 13384 Z= 0.260 Chirality : 0.039 0.324 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.549 59.273 1394 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.03 % Allowed : 14.84 % Favored : 82.13 % 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: 1.94 (0.25), residues: 1226 helix: 1.81 (0.18), residues: 930 sheet: None (None), residues: 0 loop : -0.31 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.003 0.001 HIS B 285 PHE 0.015 0.001 PHE A 478 TYR 0.009 0.001 TYR B 3 ARG 0.001 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 107 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 76 time to evaluate : 0.991 Fit side-chains REVERT: A 411 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 329 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8853 (mt) REVERT: B 411 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8586 (mp) outliers start: 31 outliers final: 15 residues processed: 100 average time/residue: 1.1647 time to fit residues: 126.1462 Evaluate side-chains 92 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 411 LEU 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 494 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 411 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9864 Z= 0.162 Angle : 0.525 11.568 13384 Z= 0.258 Chirality : 0.039 0.312 1612 Planarity : 0.004 0.036 1608 Dihedral : 7.440 59.509 1394 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.05 % Allowed : 15.92 % Favored : 82.03 % 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: 2.02 (0.25), residues: 1226 helix: 1.87 (0.18), residues: 916 sheet: None (None), residues: 0 loop : -0.21 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 200 HIS 0.002 0.000 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 B 226 *********************** 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 97 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 1.104 Fit side-chains REVERT: B 329 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8829 (mt) REVERT: B 424 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9057 (tp) outliers start: 21 outliers final: 13 residues processed: 94 average time/residue: 1.2524 time to fit residues: 126.9976 Evaluate side-chains 88 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 THR 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 494 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9864 Z= 0.205 Angle : 0.531 10.410 13384 Z= 0.263 Chirality : 0.039 0.306 1612 Planarity : 0.004 0.036 1608 Dihedral : 7.436 59.532 1394 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.54 % Allowed : 15.82 % Favored : 81.64 % 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: 1.93 (0.25), residues: 1226 helix: 1.82 (0.18), residues: 916 sheet: None (None), residues: 0 loop : -0.28 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.003 0.001 HIS B 285 PHE 0.015 0.001 PHE A 478 TYR 0.009 0.001 TYR B 3 ARG 0.001 0.000 ARG A 80 *********************** 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 99 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 73 time to evaluate : 1.051 Fit side-chains REVERT: B 329 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8836 (mt) REVERT: B 424 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9058 (tp) outliers start: 26 outliers final: 14 residues processed: 96 average time/residue: 1.2084 time to fit residues: 125.4140 Evaluate side-chains 89 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 391 THR 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 494 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 424 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 2.9990 chunk 102 optimal weight: 0.0170 chunk 109 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2767 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= 0.166 Angle : 0.516 9.841 13384 Z= 0.255 Chirality : 0.038 0.282 1612 Planarity : 0.004 0.036 1608 Dihedral : 7.349 59.272 1394 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.05 % Allowed : 15.92 % Favored : 82.03 % 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: 2.01 (0.25), residues: 1226 helix: 1.87 (0.18), residues: 916 sheet: None (None), residues: 0 loop : -0.23 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.002 0.000 HIS B 285 PHE 0.014 0.001 PHE A 478 TYR 0.007 0.001 TYR A 3 ARG 0.001 0.000 ARG B 226 *********************** 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 96 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.989 Fit side-chains REVERT: B 329 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8811 (mt) REVERT: B 424 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9061 (tp) outliers start: 21 outliers final: 13 residues processed: 94 average time/residue: 1.1805 time to fit residues: 119.8497 Evaluate side-chains 89 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 391 THR 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 424 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2815 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= 0.187 Angle : 0.535 12.359 13384 Z= 0.262 Chirality : 0.039 0.284 1612 Planarity : 0.004 0.035 1608 Dihedral : 7.317 58.260 1394 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.66 % Allowed : 16.60 % Favored : 81.74 % 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: 2.00 (0.25), residues: 1226 helix: 1.84 (0.18), residues: 918 sheet: None (None), residues: 0 loop : -0.15 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.003 0.001 HIS B 285 PHE 0.014 0.001 PHE A 478 TYR 0.009 0.001 TYR A 3 ARG 0.001 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 88 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 1.148 Fit side-chains REVERT: B 329 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8826 (mt) REVERT: B 424 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9051 (tp) outliers start: 17 outliers final: 13 residues processed: 87 average time/residue: 1.2879 time to fit residues: 120.7409 Evaluate side-chains 84 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 391 THR 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 199 VAL 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 424 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.094623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.077936 restraints weight = 20538.140| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.52 r_work: 0.3096 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2906 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= 0.149 Angle : 0.530 12.513 13384 Z= 0.256 Chirality : 0.038 0.272 1612 Planarity : 0.004 0.034 1608 Dihedral : 7.207 58.956 1394 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.37 % Allowed : 16.80 % Favored : 81.84 % 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: 2.12 (0.25), residues: 1226 helix: 1.93 (0.18), residues: 916 sheet: None (None), residues: 0 loop : -0.09 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 200 HIS 0.002 0.000 HIS B 285 PHE 0.013 0.001 PHE A 478 TYR 0.007 0.001 TYR A 3 ARG 0.001 0.000 ARG B 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3065.97 seconds wall clock time: 56 minutes 23.82 seconds (3383.82 seconds total)