Starting phenix.real_space_refine on Thu Mar 5 21:59:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tdf_25827/03_2026/7tdf_25827.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tdf_25827/03_2026/7tdf_25827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tdf_25827/03_2026/7tdf_25827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tdf_25827/03_2026/7tdf_25827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tdf_25827/03_2026/7tdf_25827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tdf_25827/03_2026/7tdf_25827.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7502 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 6520 2.51 5 N 1502 2.21 5 O 1708 1.98 5 H 9792 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19566 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 9783 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 577} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 9783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 9783 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 577} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 3.57, per 1000 atoms: 0.18 Number of scatterers: 19566 At special positions: 0 Unit cell: (111.055, 86.005, 106.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1708 8.00 N 1502 7.00 C 6520 6.00 H 9792 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.04 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 101 " distance=2.04 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: 1.49 Conformation dependent library (CDL) restraints added in 665.3 milliseconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 1 sheets defined 83.8% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 58 through 70 removed outlier: 3.826A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 85 through 88 removed outlier: 3.752A pdb=" N GLU A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.688A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 141 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 150 through 172 removed outlier: 3.891A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.567A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 3.579A pdb=" N GLY A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.535A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.365A pdb=" N PHE A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 removed outlier: 3.671A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 385 through 399 removed outlier: 4.000A pdb=" N LEU A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 452 removed outlier: 4.200A pdb=" N TYR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 487 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.795A pdb=" N PHE A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.687A pdb=" N LEU A 533 " --> pdb=" O TRP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 548 through 565 removed outlier: 4.743A pdb=" N ALA A 553 " --> pdb=" O GLN A 549 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 565 through 588 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 615 through 628 Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.676A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 660 removed outlier: 4.211A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 686 Processing helix chain 'B' and resid 21 through 28 Processing helix chain 'B' and resid 29 through 43 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 57 through 70 removed outlier: 3.667A pdb=" N ARG B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 85 through 88 removed outlier: 3.798A pdb=" N GLU B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.589A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 116 through 137 Processing helix chain 'B' and resid 138 through 141 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 150 through 172 removed outlier: 3.937A pdb=" N ASP B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.540A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 238 removed outlier: 3.532A pdb=" N MET B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLY B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 250 through 263 removed outlier: 3.540A pdb=" N THR B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.721A pdb=" N PHE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 335 Processing helix chain 'B' and resid 343 through 356 Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.669A pdb=" N ILE B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 452 removed outlier: 4.089A pdb=" N TYR B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 487 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.697A pdb=" N PHE B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 removed outlier: 3.503A pdb=" N LEU B 533 " --> pdb=" O TRP B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 548 through 565 removed outlier: 4.639A pdb=" N ALA B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE B 554 " --> pdb=" O ARG B 550 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 565 through 588 Processing helix chain 'B' and resid 597 through 601 Processing helix chain 'B' and resid 615 through 628 Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.718A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 660 removed outlier: 4.187A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 686 Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342 673 hydrogen bonds defined for protein. 1965 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: 4.34 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9780 1.03 - 1.23: 62 1.23 - 1.42: 4316 1.42 - 1.62: 5592 1.62 - 1.82: 72 Bond restraints: 19822 Sorted by residual: bond pdb=" N GLY B 527 " pdb=" CA GLY B 527 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.31e+00 bond pdb=" N GLY A 527 " pdb=" CA GLY A 527 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.12e+00 bond pdb=" CB PRO A 99 " pdb=" CG PRO A 99 " ideal model delta sigma weight residual 1.506 1.427 0.079 3.90e-02 6.57e+02 4.15e+00 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.506 1.434 0.072 3.90e-02 6.57e+02 3.41e+00 bond pdb=" N TRP A 464 " pdb=" CA TRP A 464 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 ... (remaining 19817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 32948 1.29 - 2.58: 2621 2.58 - 3.87: 127 3.87 - 5.16: 41 5.16 - 6.44: 7 Bond angle restraints: 35744 Sorted by residual: angle pdb=" N ASN B 96 " pdb=" CA ASN B 96 " pdb=" C ASN B 96 " ideal model delta sigma weight residual 109.81 116.25 -6.44 2.21e+00 2.05e-01 8.50e+00 angle pdb=" N VAL B 586 " pdb=" CA VAL B 586 " pdb=" C VAL B 586 " ideal model delta sigma weight residual 109.34 115.12 -5.78 2.08e+00 2.31e-01 7.71e+00 angle pdb=" CA TYR B 123 " pdb=" CB TYR B 123 " pdb=" CG TYR B 123 " ideal model delta sigma weight residual 113.90 118.80 -4.90 1.80e+00 3.09e-01 7.41e+00 angle pdb=" N ASN A 96 " pdb=" CA ASN A 96 " pdb=" C ASN A 96 " ideal model delta sigma weight residual 109.81 115.57 -5.76 2.21e+00 2.05e-01 6.80e+00 angle pdb=" CA TYR A 123 " pdb=" CB TYR A 123 " pdb=" CG TYR A 123 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.59e+00 ... (remaining 35739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8572 17.99 - 35.98: 460 35.98 - 53.98: 144 53.98 - 71.97: 142 71.97 - 89.96: 6 Dihedral angle restraints: 9324 sinusoidal: 4840 harmonic: 4484 Sorted by residual: dihedral pdb=" CA GLU A 600 " pdb=" C GLU A 600 " pdb=" N THR A 601 " pdb=" CA THR A 601 " ideal model delta harmonic sigma weight residual -180.00 -150.72 -29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLN A 400 " pdb=" C GLN A 400 " pdb=" N LYS A 401 " pdb=" CA LYS A 401 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ARG A 20 " pdb=" C ARG A 20 " pdb=" N ARG A 21 " pdb=" CA ARG A 21 " ideal model delta harmonic sigma weight residual -180.00 -152.60 -27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 9321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 861 0.035 - 0.069: 524 0.069 - 0.104: 125 0.104 - 0.139: 28 0.139 - 0.173: 14 Chirality restraints: 1552 Sorted by residual: chirality pdb=" CA PRO A 563 " pdb=" N PRO A 563 " pdb=" C PRO A 563 " pdb=" CB PRO A 563 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA ARG B 358 " pdb=" N ARG B 358 " pdb=" C ARG B 358 " pdb=" CB ARG B 358 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CA PRO A 138 " pdb=" N PRO A 138 " pdb=" C PRO A 138 " pdb=" CB PRO A 138 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1549 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 400 " 0.029 2.00e-02 2.50e+03 3.73e-02 2.09e+01 pdb=" CD GLN A 400 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 400 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN A 400 " -0.061 2.00e-02 2.50e+03 pdb="HE21 GLN A 400 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 400 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 353 " -0.025 2.00e-02 2.50e+03 3.56e-02 1.90e+01 pdb=" CD GLN A 353 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN A 353 " 0.007 2.00e-02 2.50e+03 pdb=" NE2 GLN A 353 " 0.062 2.00e-02 2.50e+03 pdb="HE21 GLN A 353 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 353 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 618 " 0.029 2.00e-02 2.50e+03 3.46e-02 1.79e+01 pdb=" CG ASN B 618 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 618 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 618 " -0.054 2.00e-02 2.50e+03 pdb="HD21 ASN B 618 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN B 618 " 0.052 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 757 2.17 - 2.77: 37991 2.77 - 3.38: 55461 3.38 - 3.99: 69546 3.99 - 4.60: 109924 Nonbonded interactions: 273679 Sorted by model distance: nonbonded pdb=" HG1 THR B 452 " pdb=" OD1 ASN B 454 " model vdw 1.556 2.450 nonbonded pdb=" O GLN B 54 " pdb=" HG SER B 55 " model vdw 1.568 2.450 nonbonded pdb=" HG1 THR A 452 " pdb=" OD1 ASN A 454 " model vdw 1.569 2.450 nonbonded pdb="HH11 ARG B 104 " pdb=" O GLY B 110 " model vdw 1.574 2.450 nonbonded pdb="HH11 ARG A 104 " pdb=" O GLY A 110 " model vdw 1.583 2.450 ... (remaining 273674 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' 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: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.010 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:8.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 : 0.006 0.079 10032 Z= 0.270 Angle : 0.736 6.444 13638 Z= 0.454 Chirality : 0.046 0.173 1552 Planarity : 0.008 0.131 1666 Dihedral : 12.557 89.961 3514 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.19 % Allowed : 5.29 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.24), residues: 1164 helix: -0.11 (0.16), residues: 864 sheet: None (None), residues: 0 loop : 1.07 (0.43), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.003 ARG B 279 TYR 0.025 0.005 TYR A 532 PHE 0.016 0.003 PHE B 57 TRP 0.027 0.004 TRP A 271 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00623 (10030) covalent geometry : angle 0.73547 (13634) SS BOND : bond 0.00631 ( 2) SS BOND : angle 1.46241 ( 4) hydrogen bonds : bond 0.11770 ( 673) hydrogen bonds : angle 5.87021 ( 1965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.7863 (t0) cc_final: 0.7452 (t0) REVERT: A 208 LEU cc_start: 0.8415 (tt) cc_final: 0.8192 (tp) REVERT: A 490 ASN cc_start: 0.8097 (t0) cc_final: 0.7777 (t0) REVERT: A 538 MET cc_start: 0.6634 (tmt) cc_final: 0.6314 (tmt) REVERT: B 324 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7224 (mtp85) REVERT: B 538 MET cc_start: 0.6887 (tmt) cc_final: 0.6379 (tmt) outliers start: 2 outliers final: 1 residues processed: 262 average time/residue: 1.3450 time to fit residues: 374.8759 Evaluate side-chains 226 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116074 restraints weight = 35671.509| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.69 r_work: 0.3324 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10032 Z= 0.239 Angle : 0.621 6.375 13638 Z= 0.337 Chirality : 0.040 0.145 1552 Planarity : 0.005 0.043 1666 Dihedral : 4.907 28.575 1292 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.32 % Allowed : 11.63 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1164 helix: 0.94 (0.17), residues: 882 sheet: None (None), residues: 0 loop : 0.94 (0.43), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 325 TYR 0.018 0.002 TYR A 568 PHE 0.017 0.002 PHE A 599 TRP 0.014 0.001 TRP A 223 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00555 (10030) covalent geometry : angle 0.62084 (13634) SS BOND : bond 0.00329 ( 2) SS BOND : angle 0.94498 ( 4) hydrogen bonds : bond 0.06207 ( 673) hydrogen bonds : angle 4.82127 ( 1965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8216 (t0) cc_final: 0.7863 (t0) REVERT: A 490 ASN cc_start: 0.8073 (t0) cc_final: 0.7724 (t0) REVERT: A 531 ARG cc_start: 0.6707 (ttm-80) cc_final: 0.6455 (ttm-80) REVERT: A 538 MET cc_start: 0.6632 (tmt) cc_final: 0.6323 (tmt) REVERT: B 39 ASP cc_start: 0.7746 (t0) cc_final: 0.7478 (t70) REVERT: B 66 ILE cc_start: 0.8359 (pt) cc_final: 0.7808 (mt) REVERT: B 69 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7579 (mtm110) REVERT: B 103 ASP cc_start: 0.8289 (t0) cc_final: 0.7912 (t0) REVERT: B 151 ARG cc_start: 0.7229 (tmt170) cc_final: 0.6990 (tmt170) REVERT: B 166 ASP cc_start: 0.7544 (m-30) cc_final: 0.7301 (m-30) REVERT: B 538 MET cc_start: 0.6937 (tmt) cc_final: 0.6394 (tmt) outliers start: 14 outliers final: 6 residues processed: 228 average time/residue: 1.4741 time to fit residues: 355.9603 Evaluate side-chains 213 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 207 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 605 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 104 optimal weight: 0.0040 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.145454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119431 restraints weight = 35343.450| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.71 r_work: 0.3329 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10032 Z= 0.196 Angle : 0.551 6.186 13638 Z= 0.300 Chirality : 0.038 0.132 1552 Planarity : 0.004 0.045 1666 Dihedral : 4.586 27.258 1292 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.51 % Allowed : 12.85 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.25), residues: 1164 helix: 1.36 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.80 (0.44), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 203 TYR 0.016 0.002 TYR A 568 PHE 0.023 0.002 PHE B 399 TRP 0.013 0.001 TRP A 223 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00460 (10030) covalent geometry : angle 0.55047 (13634) SS BOND : bond 0.00206 ( 2) SS BOND : angle 1.03157 ( 4) hydrogen bonds : bond 0.05732 ( 673) hydrogen bonds : angle 4.53411 ( 1965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8214 (t0) cc_final: 0.7874 (t0) REVERT: A 490 ASN cc_start: 0.8079 (t0) cc_final: 0.7712 (t0) REVERT: A 531 ARG cc_start: 0.6748 (ttm-80) cc_final: 0.6415 (ttm-80) REVERT: A 538 MET cc_start: 0.6660 (tmt) cc_final: 0.6293 (tmt) REVERT: B 39 ASP cc_start: 0.7708 (t0) cc_final: 0.7428 (t70) REVERT: B 65 PHE cc_start: 0.7853 (m-80) cc_final: 0.7534 (m-80) REVERT: B 66 ILE cc_start: 0.8344 (pt) cc_final: 0.8090 (mt) REVERT: B 94 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: B 151 ARG cc_start: 0.7198 (tmt170) cc_final: 0.6966 (tmt170) REVERT: B 538 MET cc_start: 0.6978 (tmt) cc_final: 0.6483 (tmt) REVERT: B 680 ASP cc_start: 0.7763 (m-30) cc_final: 0.7527 (m-30) outliers start: 16 outliers final: 5 residues processed: 219 average time/residue: 1.5078 time to fit residues: 349.4210 Evaluate side-chains 202 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 605 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 2 optimal weight: 0.0370 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN B 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.143181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117216 restraints weight = 35339.101| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.72 r_work: 0.3326 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10032 Z= 0.197 Angle : 0.548 6.198 13638 Z= 0.297 Chirality : 0.038 0.134 1552 Planarity : 0.004 0.053 1666 Dihedral : 4.476 25.605 1292 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.89 % Allowed : 13.42 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.25), residues: 1164 helix: 1.49 (0.17), residues: 886 sheet: None (None), residues: 0 loop : 0.72 (0.44), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 325 TYR 0.015 0.002 TYR A 141 PHE 0.014 0.002 PHE B 599 TRP 0.013 0.001 TRP A 223 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00464 (10030) covalent geometry : angle 0.54788 (13634) SS BOND : bond 0.00374 ( 2) SS BOND : angle 1.42531 ( 4) hydrogen bonds : bond 0.05556 ( 673) hydrogen bonds : angle 4.44604 ( 1965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8493 (m) cc_final: 0.7655 (p) REVERT: A 490 ASN cc_start: 0.8086 (t0) cc_final: 0.7727 (t0) REVERT: A 531 ARG cc_start: 0.6771 (ttm-80) cc_final: 0.6516 (ttm-80) REVERT: A 538 MET cc_start: 0.6676 (tmt) cc_final: 0.6303 (tmt) REVERT: B 39 ASP cc_start: 0.7789 (t0) cc_final: 0.7475 (t70) REVERT: B 66 ILE cc_start: 0.8354 (pt) cc_final: 0.8090 (mt) REVERT: B 94 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: B 151 ARG cc_start: 0.7182 (tmt170) cc_final: 0.6958 (tmt170) REVERT: B 166 ASP cc_start: 0.7420 (m-30) cc_final: 0.7075 (m-30) REVERT: B 538 MET cc_start: 0.6995 (tmt) cc_final: 0.6541 (tmt) REVERT: B 680 ASP cc_start: 0.7661 (m-30) cc_final: 0.7444 (m-30) outliers start: 20 outliers final: 7 residues processed: 209 average time/residue: 1.4722 time to fit residues: 326.5705 Evaluate side-chains 205 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116593 restraints weight = 35568.347| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.67 r_work: 0.3318 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10032 Z= 0.248 Angle : 0.569 6.194 13638 Z= 0.310 Chirality : 0.040 0.145 1552 Planarity : 0.004 0.049 1666 Dihedral : 4.495 25.390 1292 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.80 % Allowed : 13.80 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.25), residues: 1164 helix: 1.47 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.51 (0.44), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 325 TYR 0.017 0.002 TYR A 568 PHE 0.017 0.002 PHE A 67 TRP 0.012 0.001 TRP A 223 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00592 (10030) covalent geometry : angle 0.56814 (13634) SS BOND : bond 0.00654 ( 2) SS BOND : angle 2.32865 ( 4) hydrogen bonds : bond 0.05849 ( 673) hydrogen bonds : angle 4.47893 ( 1965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8492 (m) cc_final: 0.6919 (t) REVERT: A 490 ASN cc_start: 0.8098 (t0) cc_final: 0.7750 (t0) REVERT: A 531 ARG cc_start: 0.6783 (ttm-80) cc_final: 0.6507 (ttm-80) REVERT: B 39 ASP cc_start: 0.7788 (t0) cc_final: 0.7490 (t70) REVERT: B 65 PHE cc_start: 0.7883 (m-80) cc_final: 0.7486 (m-80) REVERT: B 66 ILE cc_start: 0.8359 (pt) cc_final: 0.8112 (mt) REVERT: B 151 ARG cc_start: 0.7168 (tmt170) cc_final: 0.6940 (tmt170) REVERT: B 166 ASP cc_start: 0.7402 (m-30) cc_final: 0.7063 (m-30) REVERT: B 169 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7875 (t) REVERT: B 538 MET cc_start: 0.7014 (tmt) cc_final: 0.6492 (tmt) REVERT: B 680 ASP cc_start: 0.7664 (m-30) cc_final: 0.7437 (m-30) outliers start: 19 outliers final: 10 residues processed: 215 average time/residue: 1.4345 time to fit residues: 327.1458 Evaluate side-chains 209 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 23 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116324 restraints weight = 35366.523| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.70 r_work: 0.3325 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10032 Z= 0.193 Angle : 0.543 6.030 13638 Z= 0.294 Chirality : 0.037 0.132 1552 Planarity : 0.004 0.056 1666 Dihedral : 4.384 24.558 1292 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.61 % Allowed : 14.93 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.25), residues: 1164 helix: 1.61 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.45 (0.44), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 325 TYR 0.015 0.002 TYR A 256 PHE 0.027 0.002 PHE B 554 TRP 0.012 0.001 TRP A 223 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00457 (10030) covalent geometry : angle 0.54135 (13634) SS BOND : bond 0.00539 ( 2) SS BOND : angle 2.20702 ( 4) hydrogen bonds : bond 0.05470 ( 673) hydrogen bonds : angle 4.39292 ( 1965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8495 (m) cc_final: 0.6891 (t) REVERT: A 393 GLN cc_start: 0.7976 (mm110) cc_final: 0.7685 (mm110) REVERT: A 490 ASN cc_start: 0.8058 (t0) cc_final: 0.7713 (t0) REVERT: A 531 ARG cc_start: 0.6787 (ttm-80) cc_final: 0.6585 (ttm-80) REVERT: A 538 MET cc_start: 0.6710 (tmt) cc_final: 0.6217 (tmt) REVERT: A 682 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: B 39 ASP cc_start: 0.7742 (t0) cc_final: 0.7433 (t70) REVERT: B 65 PHE cc_start: 0.7890 (m-80) cc_final: 0.7514 (m-80) REVERT: B 66 ILE cc_start: 0.8352 (pt) cc_final: 0.8107 (mt) REVERT: B 94 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: B 151 ARG cc_start: 0.7146 (tmt170) cc_final: 0.6928 (tmt170) REVERT: B 166 ASP cc_start: 0.7409 (m-30) cc_final: 0.7058 (m-30) REVERT: B 169 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7892 (t) REVERT: B 538 MET cc_start: 0.7049 (tmt) cc_final: 0.6557 (tmt) REVERT: B 680 ASP cc_start: 0.7646 (m-30) cc_final: 0.7410 (m-30) outliers start: 17 outliers final: 8 residues processed: 211 average time/residue: 1.4506 time to fit residues: 324.4654 Evaluate side-chains 211 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 0.2980 chunk 91 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116185 restraints weight = 35591.494| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.70 r_work: 0.3322 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10032 Z= 0.191 Angle : 0.538 5.765 13638 Z= 0.292 Chirality : 0.037 0.134 1552 Planarity : 0.004 0.054 1666 Dihedral : 4.317 23.764 1292 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.17 % Allowed : 14.56 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.26), residues: 1164 helix: 1.68 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.45 (0.44), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 325 TYR 0.015 0.002 TYR A 256 PHE 0.017 0.001 PHE A 67 TRP 0.013 0.001 TRP A 223 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00449 (10030) covalent geometry : angle 0.53663 (13634) SS BOND : bond 0.00445 ( 2) SS BOND : angle 1.95708 ( 4) hydrogen bonds : bond 0.05395 ( 673) hydrogen bonds : angle 4.35338 ( 1965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8205 (t0) cc_final: 0.7881 (t0) REVERT: A 127 THR cc_start: 0.8494 (m) cc_final: 0.6887 (t) REVERT: A 490 ASN cc_start: 0.8032 (t0) cc_final: 0.7670 (t0) REVERT: A 538 MET cc_start: 0.6694 (tmt) cc_final: 0.6201 (tmt) REVERT: B 39 ASP cc_start: 0.7738 (t0) cc_final: 0.7428 (t70) REVERT: B 65 PHE cc_start: 0.7902 (m-80) cc_final: 0.7505 (m-80) REVERT: B 66 ILE cc_start: 0.8354 (pt) cc_final: 0.8116 (mt) REVERT: B 94 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: B 139 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8173 (tt) REVERT: B 151 ARG cc_start: 0.7122 (tmt170) cc_final: 0.6907 (tmt170) REVERT: B 166 ASP cc_start: 0.7414 (m-30) cc_final: 0.7057 (m-30) REVERT: B 169 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7876 (t) REVERT: B 538 MET cc_start: 0.7041 (tmt) cc_final: 0.6821 (tmt) REVERT: B 546 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7887 (mtt) REVERT: B 680 ASP cc_start: 0.7641 (m-30) cc_final: 0.7414 (m-30) outliers start: 23 outliers final: 10 residues processed: 214 average time/residue: 1.4446 time to fit residues: 327.8302 Evaluate side-chains 214 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.140178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115537 restraints weight = 35664.234| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.63 r_work: 0.3323 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10032 Z= 0.225 Angle : 0.561 5.732 13638 Z= 0.304 Chirality : 0.039 0.149 1552 Planarity : 0.005 0.077 1666 Dihedral : 4.372 24.159 1292 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.98 % Allowed : 15.78 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.26), residues: 1164 helix: 1.59 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.50 (0.44), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 325 TYR 0.016 0.002 TYR A 256 PHE 0.025 0.002 PHE A 554 TRP 0.012 0.001 TRP A 223 HIS 0.003 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00538 (10030) covalent geometry : angle 0.55984 (13634) SS BOND : bond 0.00526 ( 2) SS BOND : angle 2.02001 ( 4) hydrogen bonds : bond 0.05595 ( 673) hydrogen bonds : angle 4.39966 ( 1965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8211 (t0) cc_final: 0.7883 (t0) REVERT: A 127 THR cc_start: 0.8529 (m) cc_final: 0.6898 (t) REVERT: A 393 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7745 (mm110) REVERT: A 490 ASN cc_start: 0.8071 (t0) cc_final: 0.7706 (t0) REVERT: A 682 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: B 39 ASP cc_start: 0.7732 (t0) cc_final: 0.7417 (t70) REVERT: B 65 PHE cc_start: 0.7936 (m-80) cc_final: 0.7721 (m-80) REVERT: B 66 ILE cc_start: 0.8362 (pt) cc_final: 0.8132 (mt) REVERT: B 139 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8158 (tt) REVERT: B 151 ARG cc_start: 0.7132 (tmt170) cc_final: 0.6932 (tmt170) REVERT: B 166 ASP cc_start: 0.7437 (m-30) cc_final: 0.7099 (m-30) REVERT: B 169 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7942 (t) REVERT: B 334 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7451 (tt) REVERT: B 538 MET cc_start: 0.7076 (tmt) cc_final: 0.6863 (tmt) REVERT: B 680 ASP cc_start: 0.7728 (m-30) cc_final: 0.7500 (m-30) outliers start: 21 outliers final: 10 residues processed: 218 average time/residue: 1.3965 time to fit residues: 323.6084 Evaluate side-chains 212 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 35 optimal weight: 0.0570 chunk 34 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.140200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116166 restraints weight = 36203.981| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.65 r_work: 0.3341 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10032 Z= 0.152 Angle : 0.523 5.733 13638 Z= 0.284 Chirality : 0.036 0.128 1552 Planarity : 0.004 0.052 1666 Dihedral : 4.216 23.289 1292 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.95 % Allowed : 16.82 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.26), residues: 1164 helix: 1.80 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.58 (0.45), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 325 TYR 0.014 0.001 TYR B 256 PHE 0.016 0.001 PHE A 67 TRP 0.013 0.001 TRP A 223 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00348 (10030) covalent geometry : angle 0.52228 (13634) SS BOND : bond 0.00336 ( 2) SS BOND : angle 1.55766 ( 4) hydrogen bonds : bond 0.05105 ( 673) hydrogen bonds : angle 4.28877 ( 1965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8149 (t0) cc_final: 0.7797 (t0) REVERT: A 127 THR cc_start: 0.8478 (m) cc_final: 0.6854 (t) REVERT: A 490 ASN cc_start: 0.8010 (t0) cc_final: 0.7637 (t0) REVERT: A 538 MET cc_start: 0.6656 (tmt) cc_final: 0.6294 (tmt) REVERT: A 682 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: B 39 ASP cc_start: 0.7734 (t0) cc_final: 0.7415 (t70) REVERT: B 65 PHE cc_start: 0.8007 (m-80) cc_final: 0.7600 (m-80) REVERT: B 66 ILE cc_start: 0.8360 (pt) cc_final: 0.8131 (mt) REVERT: B 139 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8108 (tt) REVERT: B 166 ASP cc_start: 0.7475 (m-30) cc_final: 0.7116 (m-30) REVERT: B 538 MET cc_start: 0.7063 (tmt) cc_final: 0.6732 (tmt) REVERT: B 680 ASP cc_start: 0.7735 (m-30) cc_final: 0.7523 (m-30) outliers start: 10 outliers final: 7 residues processed: 212 average time/residue: 1.4874 time to fit residues: 334.5060 Evaluate side-chains 213 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.141594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115951 restraints weight = 35314.036| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.70 r_work: 0.3318 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10032 Z= 0.226 Angle : 0.570 6.070 13638 Z= 0.308 Chirality : 0.039 0.151 1552 Planarity : 0.006 0.082 1666 Dihedral : 4.335 23.801 1292 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.04 % Allowed : 16.92 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.26), residues: 1164 helix: 1.68 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.45 (0.44), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 325 TYR 0.016 0.002 TYR A 568 PHE 0.025 0.002 PHE A 67 TRP 0.012 0.001 TRP A 223 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00538 (10030) covalent geometry : angle 0.56946 (13634) SS BOND : bond 0.00533 ( 2) SS BOND : angle 2.07485 ( 4) hydrogen bonds : bond 0.05567 ( 673) hydrogen bonds : angle 4.37405 ( 1965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8198 (t0) cc_final: 0.7796 (t0) REVERT: A 127 THR cc_start: 0.8530 (m) cc_final: 0.6882 (t) REVERT: A 490 ASN cc_start: 0.8047 (t0) cc_final: 0.7682 (t0) REVERT: B 39 ASP cc_start: 0.7759 (t0) cc_final: 0.7438 (t70) REVERT: B 65 PHE cc_start: 0.8030 (m-80) cc_final: 0.7715 (m-80) REVERT: B 66 ILE cc_start: 0.8352 (pt) cc_final: 0.8139 (mt) REVERT: B 139 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8157 (tt) REVERT: B 169 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7936 (t) REVERT: B 538 MET cc_start: 0.7075 (tmt) cc_final: 0.6708 (tmt) REVERT: B 680 ASP cc_start: 0.7733 (m-30) cc_final: 0.7511 (m-30) outliers start: 11 outliers final: 7 residues processed: 210 average time/residue: 1.4804 time to fit residues: 329.6637 Evaluate side-chains 213 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 50 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 80 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 32 optimal weight: 0.0170 chunk 108 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.142407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116895 restraints weight = 35462.455| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.70 r_work: 0.3333 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10032 Z= 0.150 Angle : 0.531 5.858 13638 Z= 0.287 Chirality : 0.035 0.131 1552 Planarity : 0.005 0.103 1666 Dihedral : 4.208 23.070 1292 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.85 % Allowed : 17.01 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.26), residues: 1164 helix: 1.83 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.55 (0.45), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 325 TYR 0.014 0.001 TYR B 256 PHE 0.017 0.001 PHE A 67 TRP 0.013 0.001 TRP A 223 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00342 (10030) covalent geometry : angle 0.53088 (13634) SS BOND : bond 0.00314 ( 2) SS BOND : angle 1.55867 ( 4) hydrogen bonds : bond 0.05062 ( 673) hydrogen bonds : angle 4.27824 ( 1965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8596.78 seconds wall clock time: 145 minutes 22.51 seconds (8722.51 seconds total)