Starting phenix.real_space_refine on Thu Aug 6 00:36:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/32fi_58853/08_2026/32fi_58853.cif Found real_map, /net/cci-nas-00/data/ceres_data/32fi_58853/08_2026/32fi_58853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/32fi_58853/08_2026/32fi_58853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/32fi_58853/08_2026/32fi_58853.map" model { file = "/net/cci-nas-00/data/ceres_data/32fi_58853/08_2026/32fi_58853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/32fi_58853/08_2026/32fi_58853.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 P 1 5.49 5 S 46 5.16 5 C 7980 2.51 5 N 1994 2.21 5 O 2128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12155 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5878 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 5897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5897 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Unusual residues: {' CA': 1, 'HEM': 2, 'LMO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {' CA': 1, 'HEM': 2, 'LMO': 1, 'LOP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Time building chain proxies: 3.04, per 1000 atoms: 0.25 Number of scatterers: 12155 At special positions: 0 Unit cell: (73.08, 105.27, 109.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 46 16.00 P 1 15.00 O 2128 8.00 N 1994 7.00 C 7980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 593.4 milliseconds 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 4 sheets defined 79.7% alpha, 1.4% 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 4 through 32 Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 82 through 104 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 112 through 129 removed outlier: 3.698A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 142 through 161 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 226 through 253 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 309 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.577A pdb=" N GLN A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 355 Proline residue: A 352 - end of helix Processing helix chain 'A' and resid 362 through 390 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 412 through 440 Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 445 through 458 Processing helix chain 'A' and resid 461 through 468 removed outlier: 4.121A pdb=" N TYR A 468 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 509 removed outlier: 4.521A pdb=" N GLU A 490 " --> pdb=" O HIS A 486 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 530 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.644A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.582A pdb=" N ASN A 585 " --> pdb=" O TRP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 603 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 613 through 621 removed outlier: 3.925A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 4.677A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 681 Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 710 through 719 Processing helix chain 'A' and resid 719 through 744 removed outlier: 4.573A pdb=" N GLY A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 32 removed outlier: 3.569A pdb=" N GLY B 27 " --> pdb=" O GLY B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 82 through 104 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 112 through 129 removed outlier: 3.765A pdb=" N ALA B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 161 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 182 through 202 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 226 through 253 Processing helix chain 'B' and resid 268 through 272 removed outlier: 3.627A pdb=" N THR B 272 " --> pdb=" O PRO B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 307 Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.858A pdb=" N GLN B 320 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 355 Proline residue: B 352 - end of helix Processing helix chain 'B' and resid 362 through 390 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 412 through 440 Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 445 through 461 Processing helix chain 'B' and resid 462 through 468 removed outlier: 4.049A pdb=" N TYR B 468 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 489 Processing helix chain 'B' and resid 491 through 509 Processing helix chain 'B' and resid 512 through 537 removed outlier: 4.637A pdb=" N ILE B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) Proline residue: B 533 - end of helix removed outlier: 3.585A pdb=" N PHE B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 555 removed outlier: 3.630A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 559 removed outlier: 4.136A pdb=" N GLU B 559 " --> pdb=" O SER B 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 559' Processing helix chain 'B' and resid 560 through 570 removed outlier: 4.102A pdb=" N ILE B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU B 569 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 575 Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.907A pdb=" N ASN B 585 " --> pdb=" O TRP B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 603 removed outlier: 3.506A pdb=" N LEU B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 Processing helix chain 'B' and resid 613 through 621 removed outlier: 3.899A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 4.473A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 681 Processing helix chain 'B' and resid 682 through 697 Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 704 through 709 Processing helix chain 'B' and resid 710 through 719 Processing helix chain 'B' and resid 719 through 744 removed outlier: 4.542A pdb=" N GLY B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.493A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU A 39 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU A 141 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA A 41 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.387A pdb=" N ARG B 47 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 42 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU B 39 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU B 141 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 41 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72 852 hydrogen bonds defined for protein. 2454 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: 2.30 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 4172 1.38 - 1.55: 8180 1.55 - 1.72: 11 1.72 - 1.89: 88 1.89 - 2.06: 16 Bond restraints: 12467 Sorted by residual: bond pdb=" N GLU B 572 " pdb=" CA GLU B 572 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 8.00e+00 bond pdb=" N TRP B 571 " pdb=" CA TRP B 571 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.72e+00 bond pdb=" N VAL A 455 " pdb=" CA VAL A 455 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.46e+00 bond pdb=" N ARG B 255 " pdb=" CA ARG B 255 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.44e+00 bond pdb=" N SER A 454 " pdb=" CA SER A 454 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.06e+00 ... (remaining 12462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 16938 3.29 - 6.57: 109 6.57 - 9.86: 10 9.86 - 13.15: 1 13.15 - 16.43: 2 Bond angle restraints: 17060 Sorted by residual: angle pdb=" N PRO A 262 " pdb=" CA PRO A 262 " pdb=" CB PRO A 262 " ideal model delta sigma weight residual 103.08 110.52 -7.44 9.70e-01 1.06e+00 5.88e+01 angle pdb=" N ALA A 457 " pdb=" CA ALA A 457 " pdb=" C ALA A 457 " ideal model delta sigma weight residual 113.28 107.83 5.45 1.22e+00 6.72e-01 1.99e+01 angle pdb=" CA TRP B 571 " pdb=" C TRP B 571 " pdb=" O TRP B 571 " ideal model delta sigma weight residual 120.51 115.48 5.03 1.43e+00 4.89e-01 1.24e+01 angle pdb=" N GLY A 456 " pdb=" CA GLY A 456 " pdb=" C GLY A 456 " ideal model delta sigma weight residual 113.18 105.34 7.84 2.37e+00 1.78e-01 1.09e+01 angle pdb=" CB MET A 477 " pdb=" CG MET A 477 " pdb=" SD MET A 477 " ideal model delta sigma weight residual 112.70 122.59 -9.89 3.00e+00 1.11e-01 1.09e+01 ... (remaining 17055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6223 17.92 - 35.85: 580 35.85 - 53.77: 166 53.77 - 71.69: 35 71.69 - 89.62: 15 Dihedral angle restraints: 7019 sinusoidal: 2761 harmonic: 4258 Sorted by residual: dihedral pdb=" C2D HEM B 801 " pdb=" C3D HEM B 801 " pdb=" CAD HEM B 801 " pdb=" CBD HEM B 801 " ideal model delta sinusoidal sigma weight residual 180.00 92.56 87.44 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2D HEM A 801 " pdb=" C3D HEM A 801 " pdb=" CAD HEM A 801 " pdb=" CBD HEM A 801 " ideal model delta sinusoidal sigma weight residual 180.00 93.56 86.44 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA TRP B 482 " pdb=" C TRP B 482 " pdb=" N TRP B 483 " pdb=" CA TRP B 483 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 7016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1318 0.039 - 0.078: 371 0.078 - 0.117: 112 0.117 - 0.156: 10 0.156 - 0.195: 2 Chirality restraints: 1813 Sorted by residual: chirality pdb=" CA PRO A 262 " pdb=" N PRO A 262 " pdb=" C PRO A 262 " pdb=" CB PRO A 262 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" CG LEU A 590 " pdb=" CB LEU A 590 " pdb=" CD1 LEU A 590 " pdb=" CD2 LEU A 590 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA THR B 546 " pdb=" N THR B 546 " pdb=" C THR B 546 " pdb=" CB THR B 546 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 1810 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 626 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 627 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 627 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 627 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 626 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO B 627 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 627 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 627 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 252 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ALA B 252 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA B 252 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE B 253 " 0.010 2.00e-02 2.50e+03 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1245 2.74 - 3.28: 12720 3.28 - 3.82: 23457 3.82 - 4.36: 27220 4.36 - 4.90: 46160 Nonbonded interactions: 110802 Sorted by model distance: nonbonded pdb=" OG SER B 42 " pdb=" OD1 ASP B 44 " model vdw 2.200 3.040 nonbonded pdb=" O ALA A 304 " pdb=" OG1 THR A 307 " model vdw 2.225 3.040 nonbonded pdb=" O ASN B 214 " pdb=" OH TYR B 618 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 324 " pdb=" O1A HEM A 801 " model vdw 2.244 3.040 nonbonded pdb=" O TYR A 618 " pdb=" O HOH A 901 " model vdw 2.245 3.040 ... (remaining 110797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 245 or (resid 246 and (name N or name CA or name \ C or name O or name CB )) or resid 247 through 576 or (resid 577 and (name N or \ name CA or name C or name O or name CB )) or resid 578 through 803)) selection = (chain 'B' and (resid 1 through 253 or (resid 254 through 255 and (name N or nam \ e CA or name C or name O or name CB )) or resid 256 or (resid 257 through 262 an \ d (name N or name CA or name C or name O or name CB )) or resid 263 through 803) \ ) } 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.510 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 : 0.004 0.128 12471 Z= 0.154 Angle : 0.638 16.435 17060 Z= 0.314 Chirality : 0.039 0.195 1813 Planarity : 0.004 0.046 2110 Dihedral : 15.905 89.618 4315 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.81 % Favored : 95.79 % Rotamer: Outliers : 2.15 % Allowed : 14.21 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.53 (0.22), residues: 1496 helix: 1.66 (0.16), residues: 1088 sheet: -0.87 (1.10), residues: 20 loop : -0.67 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 328 TYR 0.016 0.001 TYR A 30 PHE 0.014 0.001 PHE B 461 TRP 0.024 0.002 TRP A 488 HIS 0.006 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (12467) covalent geometry : angle 0.63847 / 0.31 (17060) hydrogen bonds : bond 0.12652 / 8.66 ( 852) hydrogen bonds : angle 5.21736 / 4.02 ( 2454) Misc. bond : bond 0.08959 / 4.44 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7235 (mtp-110) cc_final: 0.6832 (ttp-170) REVERT: A 101 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7880 (ttp-170) REVERT: A 246 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7697 (tm) REVERT: A 313 PHE cc_start: 0.8390 (t80) cc_final: 0.8170 (t80) REVERT: A 320 GLN cc_start: 0.8297 (mt0) cc_final: 0.7762 (mm-40) REVERT: A 467 PHE cc_start: 0.7624 (m-10) cc_final: 0.7274 (m-10) REVERT: A 483 TRP cc_start: 0.7903 (t60) cc_final: 0.7664 (t-100) REVERT: A 583 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8420 (ttm) REVERT: B 31 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8208 (ttp80) REVERT: B 38 GLU cc_start: 0.8657 (tp30) cc_final: 0.8262 (tp30) REVERT: B 101 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7553 (mmm160) REVERT: B 168 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7788 (tpm-80) REVERT: B 430 MET cc_start: 0.8835 (mmm) cc_final: 0.8557 (mmm) REVERT: B 578 THR cc_start: 0.4354 (OUTLIER) cc_final: 0.4049 (m) REVERT: B 609 PHE cc_start: 0.8430 (m-10) cc_final: 0.7864 (t80) outliers start: 25 outliers final: 13 residues processed: 134 average time/residue: 0.5084 time to fit residues: 74.9871 Evaluate side-chains 126 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 732 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN B 32 GLN ** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.086959 restraints weight = 17790.017| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.30 r_work: 0.3013 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 12471 Z= 0.124 Angle : 0.599 12.704 17060 Z= 0.287 Chirality : 0.039 0.208 1813 Planarity : 0.004 0.054 2110 Dihedral : 9.406 87.061 1838 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.54 % Favored : 96.12 % Rotamer: Outliers : 3.19 % Allowed : 13.01 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.70 (0.22), residues: 1496 helix: 1.75 (0.16), residues: 1104 sheet: -1.23 (1.10), residues: 20 loop : -0.56 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 186 TYR 0.011 0.001 TYR B 78 PHE 0.012 0.001 PHE B 19 TRP 0.017 0.001 TRP A 338 HIS 0.006 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (12467) covalent geometry : angle 0.59866 / 0.29 (17060) hydrogen bonds : bond 0.03949 / 2.72 ( 852) hydrogen bonds : angle 4.49618 / 3.42 ( 2454) Misc. bond : bond 0.09959 / 4.98 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.446 Fit side-chains REVERT: A 5 ARG cc_start: 0.7332 (mtp-110) cc_final: 0.6896 (ttp-170) REVERT: A 101 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7949 (ttp-170) REVERT: A 246 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7667 (tm) REVERT: A 313 PHE cc_start: 0.8279 (t80) cc_final: 0.8014 (t80) REVERT: A 320 GLN cc_start: 0.8293 (mt0) cc_final: 0.7798 (mm-40) REVERT: A 467 PHE cc_start: 0.7571 (m-10) cc_final: 0.7168 (m-10) REVERT: A 483 TRP cc_start: 0.7813 (t60) cc_final: 0.7584 (t-100) REVERT: A 490 GLU cc_start: 0.5724 (mt-10) cc_final: 0.5185 (mt-10) REVERT: A 514 ARG cc_start: 0.7351 (mmm-85) cc_final: 0.6988 (ttm110) REVERT: A 583 MET cc_start: 0.8578 (ttm) cc_final: 0.8362 (ttm) REVERT: B 24 PHE cc_start: 0.7592 (t80) cc_final: 0.7336 (t80) REVERT: B 31 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.8078 (ttp80) REVERT: B 38 GLU cc_start: 0.8677 (tp30) cc_final: 0.8269 (tp30) REVERT: B 101 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7556 (mmm160) REVERT: B 168 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7911 (tpm-80) REVERT: B 251 TRP cc_start: 0.6861 (t60) cc_final: 0.6646 (t60) REVERT: B 430 MET cc_start: 0.8698 (mmm) cc_final: 0.8418 (mmm) REVERT: B 514 ARG cc_start: 0.7990 (mtp85) cc_final: 0.7580 (tmt170) REVERT: B 578 THR cc_start: 0.3797 (OUTLIER) cc_final: 0.3357 (m) REVERT: B 601 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7868 (tpp) REVERT: B 609 PHE cc_start: 0.8392 (m-10) cc_final: 0.7871 (t80) outliers start: 37 outliers final: 11 residues processed: 152 average time/residue: 0.4810 time to fit residues: 80.7137 Evaluate side-chains 131 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 486 HIS ** 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 = 0.3558 r_free = 0.3558 target = 0.114012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.085524 restraints weight = 17925.972| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.28 r_work: 0.2987 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 12471 Z= 0.141 Angle : 0.620 16.424 17060 Z= 0.288 Chirality : 0.040 0.208 1813 Planarity : 0.004 0.054 2110 Dihedral : 9.225 87.646 1827 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.94 % Favored : 95.79 % Rotamer: Outliers : 2.93 % Allowed : 13.87 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.75 (0.22), residues: 1496 helix: 1.83 (0.16), residues: 1098 sheet: -1.35 (1.10), residues: 20 loop : -0.65 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 358 TYR 0.012 0.001 TYR B 652 PHE 0.012 0.001 PHE A 635 TRP 0.017 0.001 TRP A 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (12467) covalent geometry : angle 0.62040 / 0.29 (17060) hydrogen bonds : bond 0.03883 / 2.67 ( 852) hydrogen bonds : angle 4.43580 / 3.37 ( 2454) Misc. bond : bond 0.12651 / 6.37 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.414 Fit side-chains REVERT: A 5 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.6887 (ttp-170) REVERT: A 101 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7981 (ttp-170) REVERT: A 246 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7644 (tm) REVERT: A 272 THR cc_start: 0.8886 (t) cc_final: 0.8610 (p) REVERT: A 313 PHE cc_start: 0.8368 (t80) cc_final: 0.8016 (t80) REVERT: A 320 GLN cc_start: 0.8298 (mt0) cc_final: 0.7772 (mm-40) REVERT: A 467 PHE cc_start: 0.7588 (m-10) cc_final: 0.7387 (m-10) REVERT: A 483 TRP cc_start: 0.7884 (t60) cc_final: 0.7622 (t-100) REVERT: A 490 GLU cc_start: 0.5564 (mt-10) cc_final: 0.5051 (mt-10) REVERT: A 493 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.6427 (m-10) REVERT: A 514 ARG cc_start: 0.7394 (mmm-85) cc_final: 0.7107 (ttm110) REVERT: A 577 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6715 (mmtp) REVERT: B 24 PHE cc_start: 0.7646 (t80) cc_final: 0.7383 (t80) REVERT: B 31 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.8134 (tmm160) REVERT: B 38 GLU cc_start: 0.8638 (tp30) cc_final: 0.8269 (tp30) REVERT: B 101 ARG cc_start: 0.8045 (tpp80) cc_final: 0.7538 (mmm160) REVERT: B 168 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.7860 (tpm-80) REVERT: B 205 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8824 (tp30) REVERT: B 430 MET cc_start: 0.8748 (mmm) cc_final: 0.8360 (mmm) REVERT: B 514 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7733 (tpt170) REVERT: B 578 THR cc_start: 0.3684 (OUTLIER) cc_final: 0.3399 (m) REVERT: B 601 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7871 (tpp) REVERT: B 609 PHE cc_start: 0.8347 (m-10) cc_final: 0.7806 (t80) outliers start: 34 outliers final: 13 residues processed: 148 average time/residue: 0.5083 time to fit residues: 82.8125 Evaluate side-chains 134 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 121 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 141 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 486 HIS ** 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 = 0.3548 r_free = 0.3548 target = 0.113449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.084268 restraints weight = 17887.757| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.33 r_work: 0.2971 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 12471 Z= 0.152 Angle : 0.621 16.779 17060 Z= 0.289 Chirality : 0.040 0.155 1813 Planarity : 0.004 0.055 2110 Dihedral : 9.292 87.438 1826 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.01 % Favored : 95.79 % Rotamer: Outliers : 3.53 % Allowed : 13.78 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.73 (0.22), residues: 1496 helix: 1.82 (0.16), residues: 1098 sheet: -1.55 (1.09), residues: 20 loop : -0.68 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 358 TYR 0.010 0.001 TYR A 30 PHE 0.013 0.001 PHE A 635 TRP 0.018 0.001 TRP A 338 HIS 0.006 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (12467) covalent geometry : angle 0.62051 / 0.29 (17060) hydrogen bonds : bond 0.03841 / 2.64 ( 852) hydrogen bonds : angle 4.42617 / 3.36 ( 2454) Misc. bond : bond 0.13600 / 6.85 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.455 Fit side-chains REVERT: A 5 ARG cc_start: 0.7304 (mtp-110) cc_final: 0.6873 (ttp-170) REVERT: A 38 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: A 101 ARG cc_start: 0.8282 (mtp85) cc_final: 0.7905 (tpp80) REVERT: A 246 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7635 (tm) REVERT: A 272 THR cc_start: 0.8878 (t) cc_final: 0.8560 (p) REVERT: A 313 PHE cc_start: 0.8387 (t80) cc_final: 0.8034 (t80) REVERT: A 320 GLN cc_start: 0.8289 (mt0) cc_final: 0.7725 (mm-40) REVERT: A 483 TRP cc_start: 0.7908 (t60) cc_final: 0.7643 (t-100) REVERT: A 490 GLU cc_start: 0.5573 (mt-10) cc_final: 0.5039 (mt-10) REVERT: A 493 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6438 (m-10) REVERT: A 577 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6710 (mmtp) REVERT: B 24 PHE cc_start: 0.7683 (t80) cc_final: 0.7415 (t80) REVERT: B 31 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.8115 (ttp80) REVERT: B 38 GLU cc_start: 0.8662 (tp30) cc_final: 0.8278 (tp30) REVERT: B 51 ARG cc_start: 0.8715 (ttt-90) cc_final: 0.8438 (ttm-80) REVERT: B 101 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7521 (mmm160) REVERT: B 168 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.7870 (tpm-80) REVERT: B 251 TRP cc_start: 0.6637 (t60) cc_final: 0.6286 (t60) REVERT: B 430 MET cc_start: 0.8752 (mmm) cc_final: 0.8269 (mmm) REVERT: B 514 ARG cc_start: 0.8021 (mtp85) cc_final: 0.7665 (tmt170) REVERT: B 609 PHE cc_start: 0.8357 (m-10) cc_final: 0.7816 (t80) REVERT: B 612 ASN cc_start: 0.9304 (t160) cc_final: 0.9062 (t0) outliers start: 41 outliers final: 15 residues processed: 151 average time/residue: 0.5107 time to fit residues: 85.0579 Evaluate side-chains 132 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.083990 restraints weight = 17785.788| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.32 r_work: 0.2964 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.187 12471 Z= 0.159 Angle : 0.629 17.839 17060 Z= 0.291 Chirality : 0.041 0.160 1813 Planarity : 0.004 0.055 2110 Dihedral : 9.291 87.364 1825 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.21 % Favored : 95.59 % Rotamer: Outliers : 3.36 % Allowed : 14.64 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.70 (0.22), residues: 1496 helix: 1.81 (0.16), residues: 1098 sheet: -1.68 (1.09), residues: 20 loop : -0.71 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.020 0.001 TYR A 362 PHE 0.013 0.001 PHE A 635 TRP 0.018 0.001 TRP A 338 HIS 0.007 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (12467) covalent geometry : angle 0.62939 / 0.29 (17060) hydrogen bonds : bond 0.03885 / 2.66 ( 852) hydrogen bonds : angle 4.43595 / 3.36 ( 2454) Misc. bond : bond 0.14765 / 7.44 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.435 Fit side-chains REVERT: A 5 ARG cc_start: 0.7226 (mtp-110) cc_final: 0.6820 (ttp-170) REVERT: A 38 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: A 101 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7886 (tpp80) REVERT: A 246 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7596 (tm) REVERT: A 272 THR cc_start: 0.8862 (t) cc_final: 0.8555 (p) REVERT: A 313 PHE cc_start: 0.8401 (t80) cc_final: 0.8028 (t80) REVERT: A 320 GLN cc_start: 0.8275 (mt0) cc_final: 0.7628 (mm-40) REVERT: A 483 TRP cc_start: 0.7893 (t60) cc_final: 0.7621 (t-100) REVERT: A 493 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6433 (m-10) REVERT: A 577 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6723 (mmtp) REVERT: B 24 PHE cc_start: 0.7618 (t80) cc_final: 0.7356 (t80) REVERT: B 31 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.8077 (ttp80) REVERT: B 38 GLU cc_start: 0.8669 (tp30) cc_final: 0.8267 (tp30) REVERT: B 51 ARG cc_start: 0.8690 (ttt-90) cc_final: 0.8405 (ttm-80) REVERT: B 101 ARG cc_start: 0.8034 (tpp80) cc_final: 0.7564 (mmm160) REVERT: B 168 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7840 (tpm-80) REVERT: B 251 TRP cc_start: 0.6589 (t60) cc_final: 0.6210 (t60) REVERT: B 430 MET cc_start: 0.8704 (mmm) cc_final: 0.8247 (mmm) REVERT: B 445 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6085 (pptt) REVERT: B 514 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7674 (tpt170) REVERT: B 609 PHE cc_start: 0.8357 (m-10) cc_final: 0.7821 (t80) outliers start: 39 outliers final: 17 residues processed: 147 average time/residue: 0.5445 time to fit residues: 88.1505 Evaluate side-chains 133 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.112465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083734 restraints weight = 17915.564| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.31 r_work: 0.2960 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.179 12471 Z= 0.155 Angle : 0.630 17.804 17060 Z= 0.291 Chirality : 0.041 0.173 1813 Planarity : 0.004 0.055 2110 Dihedral : 9.268 87.583 1825 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.14 % Favored : 95.66 % Rotamer: Outliers : 3.19 % Allowed : 14.90 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.68 (0.22), residues: 1496 helix: 1.80 (0.16), residues: 1098 sheet: -1.79 (1.09), residues: 20 loop : -0.74 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 358 TYR 0.011 0.001 TYR A 30 PHE 0.013 0.001 PHE B 19 TRP 0.019 0.001 TRP A 338 HIS 0.006 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 (12467) covalent geometry : angle 0.62959 / 0.29 (17060) hydrogen bonds : bond 0.03834 / 2.63 ( 852) hydrogen bonds : angle 4.42634 / 3.36 ( 2454) Misc. bond : bond 0.14417 / 7.26 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.441 Fit side-chains REVERT: A 5 ARG cc_start: 0.7258 (mtp-110) cc_final: 0.6838 (ttp-170) REVERT: A 38 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 101 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7904 (tpp80) REVERT: A 208 SER cc_start: 0.8874 (m) cc_final: 0.8550 (t) REVERT: A 228 GLU cc_start: 0.7906 (mp0) cc_final: 0.7517 (mp0) REVERT: A 246 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7604 (tm) REVERT: A 272 THR cc_start: 0.8882 (t) cc_final: 0.8567 (p) REVERT: A 313 PHE cc_start: 0.8387 (t80) cc_final: 0.8015 (t80) REVERT: A 320 GLN cc_start: 0.8318 (mt0) cc_final: 0.7671 (mm-40) REVERT: A 483 TRP cc_start: 0.7900 (t60) cc_final: 0.7646 (t-100) REVERT: A 493 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6414 (m-10) REVERT: A 577 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6705 (mmtp) REVERT: A 583 MET cc_start: 0.8505 (ttm) cc_final: 0.8117 (ttp) REVERT: A 699 MET cc_start: 0.7581 (tpt) cc_final: 0.7112 (tpt) REVERT: B 24 PHE cc_start: 0.7704 (t80) cc_final: 0.7431 (t80) REVERT: B 31 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8110 (ttp80) REVERT: B 38 GLU cc_start: 0.8623 (tp30) cc_final: 0.8226 (tp30) REVERT: B 51 ARG cc_start: 0.8706 (ttt-90) cc_final: 0.8412 (ttm-80) REVERT: B 101 ARG cc_start: 0.8039 (tpp80) cc_final: 0.7604 (mmm160) REVERT: B 168 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7842 (tpm-80) REVERT: B 251 TRP cc_start: 0.6671 (t60) cc_final: 0.6314 (t60) REVERT: B 430 MET cc_start: 0.8741 (mmm) cc_final: 0.8291 (mmm) REVERT: B 445 LYS cc_start: 0.6690 (OUTLIER) cc_final: 0.6080 (pptt) REVERT: B 514 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7740 (ttt180) REVERT: B 609 PHE cc_start: 0.8368 (m-10) cc_final: 0.7801 (t80) outliers start: 37 outliers final: 16 residues processed: 144 average time/residue: 0.5361 time to fit residues: 85.0268 Evaluate side-chains 133 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 625 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 85 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.084831 restraints weight = 17814.624| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.29 r_work: 0.2975 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 12471 Z= 0.138 Angle : 0.619 16.682 17060 Z= 0.285 Chirality : 0.040 0.161 1813 Planarity : 0.004 0.055 2110 Dihedral : 9.109 88.314 1821 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.28 % Favored : 95.52 % Rotamer: Outliers : 2.84 % Allowed : 15.25 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.72 (0.22), residues: 1496 helix: 1.84 (0.16), residues: 1098 sheet: -1.82 (1.10), residues: 20 loop : -0.74 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.009 0.001 TYR B 324 PHE 0.013 0.001 PHE A 635 TRP 0.019 0.001 TRP A 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (12467) covalent geometry : angle 0.61859 / 0.29 (17060) hydrogen bonds : bond 0.03702 / 2.55 ( 852) hydrogen bonds : angle 4.39231 / 3.33 ( 2454) Misc. bond : bond 0.12685 / 6.38 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.453 Fit side-chains REVERT: A 5 ARG cc_start: 0.7335 (mtp-110) cc_final: 0.6853 (ttp-170) REVERT: A 38 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: A 101 ARG cc_start: 0.8297 (mtp85) cc_final: 0.7958 (tpp80) REVERT: A 208 SER cc_start: 0.8864 (m) cc_final: 0.8548 (t) REVERT: A 228 GLU cc_start: 0.7901 (mp0) cc_final: 0.7510 (mp0) REVERT: A 272 THR cc_start: 0.8881 (t) cc_final: 0.8571 (p) REVERT: A 313 PHE cc_start: 0.8408 (t80) cc_final: 0.8056 (t80) REVERT: A 320 GLN cc_start: 0.8315 (mt0) cc_final: 0.7682 (mm-40) REVERT: A 483 TRP cc_start: 0.7840 (t60) cc_final: 0.7523 (t-100) REVERT: A 493 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6426 (m-10) REVERT: A 577 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6675 (mmtp) REVERT: B 24 PHE cc_start: 0.7698 (t80) cc_final: 0.7420 (t80) REVERT: B 31 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8109 (ttp80) REVERT: B 38 GLU cc_start: 0.8596 (tp30) cc_final: 0.8209 (tp30) REVERT: B 51 ARG cc_start: 0.8698 (ttt-90) cc_final: 0.8404 (ttm-80) REVERT: B 101 ARG cc_start: 0.8031 (tpp80) cc_final: 0.7603 (mmm160) REVERT: B 168 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7856 (tpm-80) REVERT: B 251 TRP cc_start: 0.6700 (t60) cc_final: 0.6259 (t60) REVERT: B 430 MET cc_start: 0.8749 (mmm) cc_final: 0.8314 (mmm) REVERT: B 514 ARG cc_start: 0.8054 (mtp85) cc_final: 0.7740 (ttt180) REVERT: B 609 PHE cc_start: 0.8381 (m-10) cc_final: 0.7780 (t80) REVERT: B 612 ASN cc_start: 0.9302 (t160) cc_final: 0.9049 (t0) outliers start: 33 outliers final: 17 residues processed: 145 average time/residue: 0.5493 time to fit residues: 87.5467 Evaluate side-chains 134 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 70 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084577 restraints weight = 17806.611| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.30 r_work: 0.2973 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 12471 Z= 0.142 Angle : 0.628 17.258 17060 Z= 0.288 Chirality : 0.040 0.161 1813 Planarity : 0.004 0.056 2110 Dihedral : 9.060 88.409 1819 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.14 % Favored : 95.66 % Rotamer: Outliers : 2.84 % Allowed : 15.68 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1496 helix: 1.85 (0.16), residues: 1096 sheet: -1.87 (1.10), residues: 20 loop : -0.70 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.013 0.001 TYR A 30 PHE 0.013 0.001 PHE B 19 TRP 0.019 0.001 TRP A 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (12467) covalent geometry : angle 0.62828 / 0.29 (17060) hydrogen bonds : bond 0.03699 / 2.55 ( 852) hydrogen bonds : angle 4.38143 / 3.32 ( 2454) Misc. bond : bond 0.12961 / 6.52 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.445 Fit side-chains REVERT: A 5 ARG cc_start: 0.7326 (mtp-110) cc_final: 0.6829 (ttp-170) REVERT: A 38 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: A 101 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7956 (tpp80) REVERT: A 208 SER cc_start: 0.8866 (m) cc_final: 0.8550 (t) REVERT: A 228 GLU cc_start: 0.7896 (mp0) cc_final: 0.7502 (mp0) REVERT: A 246 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7623 (tm) REVERT: A 272 THR cc_start: 0.8876 (t) cc_final: 0.8573 (p) REVERT: A 313 PHE cc_start: 0.8408 (t80) cc_final: 0.8050 (t80) REVERT: A 320 GLN cc_start: 0.8310 (mt0) cc_final: 0.7633 (mm-40) REVERT: A 483 TRP cc_start: 0.7814 (t60) cc_final: 0.7523 (t-100) REVERT: A 493 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.6392 (m-10) REVERT: A 577 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6670 (mmtp) REVERT: B 24 PHE cc_start: 0.7713 (t80) cc_final: 0.7434 (t80) REVERT: B 31 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.8136 (tmm160) REVERT: B 38 GLU cc_start: 0.8587 (tp30) cc_final: 0.8249 (tp30) REVERT: B 51 ARG cc_start: 0.8705 (ttt-90) cc_final: 0.8411 (ttm-80) REVERT: B 101 ARG cc_start: 0.8008 (tpp80) cc_final: 0.7584 (mmm160) REVERT: B 168 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.7858 (tpm-80) REVERT: B 251 TRP cc_start: 0.6790 (t60) cc_final: 0.6391 (t60) REVERT: B 430 MET cc_start: 0.8753 (mmm) cc_final: 0.8300 (mmm) REVERT: B 445 LYS cc_start: 0.6690 (OUTLIER) cc_final: 0.6079 (pptt) REVERT: B 514 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7720 (ttt180) REVERT: B 609 PHE cc_start: 0.8379 (m-10) cc_final: 0.7786 (t80) REVERT: B 612 ASN cc_start: 0.9307 (t160) cc_final: 0.9047 (t0) outliers start: 33 outliers final: 17 residues processed: 141 average time/residue: 0.5601 time to fit residues: 86.5203 Evaluate side-chains 134 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 625 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 111 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 0.0040 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.083230 restraints weight = 17813.917| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.30 r_work: 0.2950 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 12471 Z= 0.167 Angle : 0.658 19.191 17060 Z= 0.300 Chirality : 0.041 0.232 1813 Planarity : 0.004 0.056 2110 Dihedral : 9.116 87.207 1819 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.08 % Favored : 95.72 % Rotamer: Outliers : 2.41 % Allowed : 15.85 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.70 (0.22), residues: 1496 helix: 1.81 (0.16), residues: 1098 sheet: None (None), residues: 0 loop : -0.79 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 720 TYR 0.014 0.001 TYR B 652 PHE 0.014 0.001 PHE A 194 TRP 0.019 0.001 TRP A 251 HIS 0.007 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (12467) covalent geometry : angle 0.65777 / 0.30 (17060) hydrogen bonds : bond 0.03863 / 2.66 ( 852) hydrogen bonds : angle 4.42670 / 3.35 ( 2454) Misc. bond : bond 0.15785 / 7.95 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.273 Fit side-chains REVERT: A 5 ARG cc_start: 0.7312 (mtp-110) cc_final: 0.6813 (ttp-170) REVERT: A 38 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: A 101 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7952 (tpp80) REVERT: A 208 SER cc_start: 0.8885 (m) cc_final: 0.8557 (t) REVERT: A 228 GLU cc_start: 0.7916 (mp0) cc_final: 0.7534 (mp0) REVERT: A 246 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7607 (tm) REVERT: A 272 THR cc_start: 0.8877 (t) cc_final: 0.8562 (p) REVERT: A 313 PHE cc_start: 0.8415 (t80) cc_final: 0.8051 (t80) REVERT: A 320 GLN cc_start: 0.8321 (mt0) cc_final: 0.7650 (mm-40) REVERT: A 493 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6457 (m-10) REVERT: A 577 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6697 (mmtp) REVERT: A 699 MET cc_start: 0.7611 (tpt) cc_final: 0.7323 (tpt) REVERT: B 31 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8128 (ttp80) REVERT: B 38 GLU cc_start: 0.8589 (tp30) cc_final: 0.8250 (tp30) REVERT: B 51 ARG cc_start: 0.8716 (ttt-90) cc_final: 0.8420 (ttm-80) REVERT: B 101 ARG cc_start: 0.8000 (tpp80) cc_final: 0.7584 (mmm160) REVERT: B 168 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7842 (tpm-80) REVERT: B 251 TRP cc_start: 0.6826 (t60) cc_final: 0.6562 (t-100) REVERT: B 430 MET cc_start: 0.8734 (mmm) cc_final: 0.8286 (mmm) REVERT: B 445 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6085 (pptt) REVERT: B 514 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7735 (ttt180) REVERT: B 609 PHE cc_start: 0.8374 (m-10) cc_final: 0.7798 (t80) outliers start: 28 outliers final: 14 residues processed: 135 average time/residue: 0.6064 time to fit residues: 89.2982 Evaluate side-chains 130 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 625 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 90 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.084873 restraints weight = 17808.684| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.31 r_work: 0.2981 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 12471 Z= 0.134 Angle : 0.632 16.240 17060 Z= 0.291 Chirality : 0.040 0.227 1813 Planarity : 0.004 0.056 2110 Dihedral : 9.028 88.573 1819 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.14 % Favored : 95.66 % Rotamer: Outliers : 1.98 % Allowed : 16.28 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.81 (0.22), residues: 1496 helix: 1.89 (0.16), residues: 1096 sheet: None (None), residues: 0 loop : -0.73 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.013 0.001 TYR A 30 PHE 0.013 0.001 PHE A 635 TRP 0.020 0.001 TRP A 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (12467) covalent geometry : angle 0.63156 / 0.29 (17060) hydrogen bonds : bond 0.03628 / 2.51 ( 852) hydrogen bonds : angle 4.37385 / 3.31 ( 2454) Misc. bond : bond 0.12122 / 6.09 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.432 Fit side-chains REVERT: A 5 ARG cc_start: 0.7303 (mtp-110) cc_final: 0.6811 (ttp-170) REVERT: A 38 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 101 ARG cc_start: 0.8303 (mtp85) cc_final: 0.7971 (tpp80) REVERT: A 208 SER cc_start: 0.8869 (m) cc_final: 0.8555 (t) REVERT: A 228 GLU cc_start: 0.7918 (mp0) cc_final: 0.7541 (mp0) REVERT: A 246 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7645 (tm) REVERT: A 272 THR cc_start: 0.8872 (t) cc_final: 0.8552 (p) REVERT: A 313 PHE cc_start: 0.8391 (t80) cc_final: 0.8041 (t80) REVERT: A 320 GLN cc_start: 0.8329 (mt0) cc_final: 0.7626 (mm-40) REVERT: A 483 TRP cc_start: 0.7846 (t60) cc_final: 0.7548 (t-100) REVERT: A 493 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6399 (m-10) REVERT: A 577 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6712 (mmtp) REVERT: A 583 MET cc_start: 0.8503 (ttm) cc_final: 0.8241 (ttp) REVERT: B 38 GLU cc_start: 0.8561 (tp30) cc_final: 0.7984 (mm-30) REVERT: B 51 ARG cc_start: 0.8713 (ttt-90) cc_final: 0.8423 (ttm-80) REVERT: B 101 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7609 (mmm160) REVERT: B 168 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.7865 (tpm-80) REVERT: B 251 TRP cc_start: 0.6801 (t60) cc_final: 0.6512 (t-100) REVERT: B 430 MET cc_start: 0.8738 (mmm) cc_final: 0.8278 (mmm) REVERT: B 445 LYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6094 (pptt) REVERT: B 514 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7738 (ttt180) REVERT: B 609 PHE cc_start: 0.8392 (m-10) cc_final: 0.7793 (t80) REVERT: B 612 ASN cc_start: 0.9297 (t160) cc_final: 0.9052 (t0) outliers start: 23 outliers final: 13 residues processed: 137 average time/residue: 0.5746 time to fit residues: 86.3768 Evaluate side-chains 130 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 555 PHE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 625 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 93 optimal weight: 0.0030 chunk 64 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.114172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.085650 restraints weight = 17766.079| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.31 r_work: 0.2993 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 12471 Z= 0.127 Angle : 0.632 15.687 17060 Z= 0.290 Chirality : 0.040 0.261 1813 Planarity : 0.004 0.056 2110 Dihedral : 8.979 89.484 1819 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 1.81 % Allowed : 16.71 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.86 (0.22), residues: 1496 helix: 1.93 (0.16), residues: 1096 sheet: None (None), residues: 0 loop : -0.69 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 31 TYR 0.012 0.001 TYR B 652 PHE 0.013 0.001 PHE B 19 TRP 0.021 0.001 TRP A 338 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (12467) covalent geometry : angle 0.63237 / 0.29 (17060) hydrogen bonds : bond 0.03539 / 2.45 ( 852) hydrogen bonds : angle 4.33606 / 3.28 ( 2454) Misc. bond : bond 0.11004 / 5.54 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4216.67 seconds wall clock time: 72 minutes 41.05 seconds (4361.05 seconds total)