Starting phenix.real_space_refine on Thu Jun 4 11:37:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28pr_56722/06_2026/28pr_56722.cif Found real_map, /net/cci-nas-00/data/ceres_data/28pr_56722/06_2026/28pr_56722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28pr_56722/06_2026/28pr_56722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28pr_56722/06_2026/28pr_56722.map" model { file = "/net/cci-nas-00/data/ceres_data/28pr_56722/06_2026/28pr_56722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28pr_56722/06_2026/28pr_56722.cif" } resolution = 2.4 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 6 7.16 5 S 44 5.16 5 C 7623 2.51 5 N 1899 2.21 5 O 2809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12383 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5608 Classifications: {'peptide': 711} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 676} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5606 Classifications: {'peptide': 710} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 674} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 155 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'HQE': 1, 'LMT': 1, 'UQ5': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UQ5:plan-2': 1, 'UQ5:plan-5': 1, 'UQ5:plan-6': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 162 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'HQE': 1, 'LMT': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 421 Classifications: {'water': 421} Link IDs: {None: 420} Chain: "B" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 431 Classifications: {'water': 431} Link IDs: {None: 430} Time building chain proxies: 3.37, per 1000 atoms: 0.27 Number of scatterers: 12383 At special positions: 0 Unit cell: (114.7, 92.5, 110.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 Ca 2 19.99 S 44 16.00 O 2809 8.00 N 1899 7.00 C 7623 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: 1.31 Conformation dependent library (CDL) restraints added in 427.2 milliseconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 6 sheets defined 79.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.766A pdb=" N GLY A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.547A pdb=" N ILE A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) 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: 3.968A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 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 307 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 323 through 355 Proline residue: A 352 - end of helix removed outlier: 3.919A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) 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 439 removed outlier: 3.719A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 512 through 537 removed outlier: 5.176A pdb=" N ILE A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) Proline residue: A 533 - end of helix Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.622A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 560 removed outlier: 3.869A pdb=" N GLU A 559 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 560' Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.569A pdb=" N MET A 583 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 585 " --> pdb=" O TRP A 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 585' Processing helix chain 'A' and resid 586 through 603 Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.523A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.006A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 4.769A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 682 removed outlier: 3.639A pdb=" N SER A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) 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 720 Processing helix chain 'A' and resid 720 through 744 Processing helix chain 'A' and resid 746 through 750 removed outlier: 3.522A pdb=" N ALA A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 removed outlier: 3.987A pdb=" N GLY B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 removed outlier: 3.556A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 112 through 129 removed outlier: 3.939A pdb=" N ALA B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 136 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 Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 307 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 323 through 355 Proline residue: B 352 - end of helix removed outlier: 3.887A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 390 removed outlier: 3.713A pdb=" N GLY B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) 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 435 removed outlier: 3.697A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.781A pdb=" N THR B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 488 Processing helix chain 'B' and resid 494 through 508 Processing helix chain 'B' and resid 512 through 537 removed outlier: 5.239A pdb=" N ILE B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) Proline residue: B 533 - end of helix Processing helix chain 'B' and resid 545 through 555 removed outlier: 3.618A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 560 removed outlier: 3.679A pdb=" N GLU B 559 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 560 " --> pdb=" O ALA B 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 560' Processing helix chain 'B' and resid 561 through 566 Processing helix chain 'B' and resid 571 through 576 removed outlier: 3.656A pdb=" N ARG B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.949A pdb=" N MET B 583 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN B 585 " --> pdb=" O TRP B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 585' Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 605 through 612 Processing helix chain 'B' and resid 613 through 621 removed outlier: 4.014A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 4.780A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 682 removed outlier: 3.646A pdb=" N SER B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) 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 720 Processing helix chain 'B' and resid 720 through 744 Processing helix chain 'B' and resid 746 through 750 removed outlier: 3.527A pdb=" N ALA B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.181A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU A 39 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 141 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.658A 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 'A' and resid 312 through 313 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.209A pdb=" N ARG B 47 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER B 42 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU B 39 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU B 141 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 41 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 313 771 hydrogen bonds defined for protein. 2241 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: 2.24 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 4655 1.38 - 1.55: 7166 1.55 - 1.73: 0 1.73 - 1.90: 84 1.90 - 2.07: 16 Bond restraints: 11921 Sorted by residual: bond pdb=" CB THR A 196 " pdb=" CG2 THR A 196 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 bond pdb=" CB THR B 196 " pdb=" CG2 THR B 196 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.72e+00 bond pdb=" CA GLU A 261 " pdb=" CB GLU A 261 " ideal model delta sigma weight residual 1.522 1.529 -0.007 7.00e-03 2.04e+04 1.01e+00 bond pdb=" CA ARG A 720 " pdb=" C ARG A 720 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.45e-02 4.76e+03 9.32e-01 bond pdb=" N ARG A 720 " pdb=" CA ARG A 720 " ideal model delta sigma weight residual 1.458 1.470 -0.012 1.29e-02 6.01e+03 9.25e-01 ... (remaining 11916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 16094 2.25 - 4.50: 181 4.50 - 6.76: 26 6.76 - 9.01: 7 9.01 - 11.26: 3 Bond angle restraints: 16311 Sorted by residual: angle pdb=" CB MET B 477 " pdb=" CG MET B 477 " pdb=" SD MET B 477 " ideal model delta sigma weight residual 112.70 122.07 -9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" C GLU B 407 " pdb=" N TYR B 408 " pdb=" CA TYR B 408 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.89e+00 angle pdb=" CA TRP A 338 " pdb=" CB TRP A 338 " pdb=" CG TRP A 338 " ideal model delta sigma weight residual 113.60 119.09 -5.49 1.90e+00 2.77e-01 8.36e+00 angle pdb=" CA TRP B 338 " pdb=" CB TRP B 338 " pdb=" CG TRP B 338 " ideal model delta sigma weight residual 113.60 119.08 -5.48 1.90e+00 2.77e-01 8.32e+00 angle pdb=" CB MET A 477 " pdb=" CG MET A 477 " pdb=" SD MET A 477 " ideal model delta sigma weight residual 112.70 120.95 -8.25 3.00e+00 1.11e-01 7.57e+00 ... (remaining 16306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5988 17.62 - 35.24: 545 35.24 - 52.86: 153 52.86 - 70.48: 41 70.48 - 88.10: 24 Dihedral angle restraints: 6751 sinusoidal: 2710 harmonic: 4041 Sorted by residual: dihedral pdb=" CA VAL B 560 " pdb=" C VAL B 560 " pdb=" N VAL B 561 " pdb=" CA VAL B 561 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLY B 491 " pdb=" C GLY B 491 " pdb=" N PHE B 492 " pdb=" CA PHE B 492 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLU A 490 " pdb=" C GLU A 490 " pdb=" N GLY A 491 " pdb=" CA GLY A 491 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 6748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1020 0.028 - 0.056: 427 0.056 - 0.083: 176 0.083 - 0.111: 83 0.111 - 0.139: 22 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA VAL A 489 " pdb=" N VAL A 489 " pdb=" C VAL A 489 " pdb=" CB VAL A 489 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA PRO B 627 " pdb=" N PRO B 627 " pdb=" C PRO B 627 " pdb=" CB PRO B 627 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.60e-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 2.39 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1725 not shown) Planarity restraints: 2017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 626 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO B 627 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 627 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 627 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 626 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 627 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 627 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 627 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 588 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO B 589 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.020 5.00e-02 4.00e+02 ... (remaining 2014 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 223 2.54 - 3.13: 9579 3.13 - 3.72: 21206 3.72 - 4.31: 30667 4.31 - 4.90: 48395 Nonbonded interactions: 110070 Sorted by model distance: nonbonded pdb="FE FE B 805 " pdb=" O HOH B1031 " model vdw 1.952 2.260 nonbonded pdb="FE FE A 804 " pdb=" O HOH A1021 " model vdw 1.960 2.260 nonbonded pdb=" NE2 HIS A 537 " pdb="FE FE A 804 " model vdw 2.126 2.340 nonbonded pdb=" NE2 HIS B 537 " pdb="FE FE B 805 " model vdw 2.145 2.340 nonbonded pdb=" OE1 GLU A 559 " pdb=" O HOH A 901 " model vdw 2.218 3.040 ... (remaining 110065 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 18 through 439 or resid 465 through 750)) selection = (chain 'B' and (resid 18 through 439 or resid 465 through 750)) } 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.570 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 11925 Z= 0.145 Angle : 0.613 11.261 16311 Z= 0.303 Chirality : 0.040 0.139 1728 Planarity : 0.004 0.036 2017 Dihedral : 16.234 88.097 4179 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.04 % Favored : 96.74 % Rotamer: Outliers : 1.71 % Allowed : 15.36 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.63 (0.23), residues: 1413 helix: 1.82 (0.17), residues: 994 sheet: 1.07 (1.17), residues: 20 loop : -0.78 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 31 TYR 0.019 0.002 TYR B 324 PHE 0.020 0.002 PHE B 635 TRP 0.023 0.002 TRP B 338 HIS 0.008 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (11921) covalent geometry : angle 0.61296 / 0.30 (16311) hydrogen bonds : bond 0.12931 / 8.61 ( 771) hydrogen bonds : angle 5.22706 / 3.81 ( 2241) Misc. bond : bond 0.06899 / 3.44 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.498 Fit side-chains REVERT: A 488 TRP cc_start: 0.6909 (m-10) cc_final: 0.6154 (m-90) REVERT: B 147 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: B 583 MET cc_start: 0.7320 (ppp) cc_final: 0.6941 (ppp) outliers start: 19 outliers final: 6 residues processed: 128 average time/residue: 0.7193 time to fit residues: 99.3060 Evaluate side-chains 94 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 568 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.067832 restraints weight = 19321.355| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.42 r_work: 0.2605 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 11925 Z= 0.139 Angle : 0.604 10.888 16311 Z= 0.288 Chirality : 0.040 0.144 1728 Planarity : 0.004 0.037 2017 Dihedral : 8.611 89.361 1775 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.26 % Favored : 96.53 % Rotamer: Outliers : 2.34 % Allowed : 16.80 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 2.04 (0.23), residues: 1413 helix: 2.14 (0.17), residues: 1008 sheet: 0.78 (1.11), residues: 20 loop : -0.76 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 51 TYR 0.011 0.001 TYR B 324 PHE 0.013 0.001 PHE B 635 TRP 0.021 0.001 TRP B 338 HIS 0.008 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (11921) covalent geometry : angle 0.60393 / 0.29 (16311) hydrogen bonds : bond 0.04942 / 3.28 ( 771) hydrogen bonds : angle 4.27828 / 3.12 ( 2241) Misc. bond : bond 0.09584 / 4.76 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8590 (ttp80) REVERT: A 477 MET cc_start: 0.8385 (tmm) cc_final: 0.8024 (tmm) REVERT: A 488 TRP cc_start: 0.6894 (m-10) cc_final: 0.5884 (m-90) REVERT: A 494 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7292 (tm-30) REVERT: B 147 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: B 477 MET cc_start: 0.8488 (tmm) cc_final: 0.8209 (tmm) REVERT: B 494 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7399 (tm-30) REVERT: B 583 MET cc_start: 0.7415 (ppp) cc_final: 0.6819 (ppp) outliers start: 26 outliers final: 7 residues processed: 114 average time/residue: 0.7600 time to fit residues: 93.1486 Evaluate side-chains 98 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 107 optimal weight: 0.8980 chunk 70 optimal weight: 0.0060 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 692 HIS B 213 ASN B 217 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.068598 restraints weight = 19719.849| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.43 r_work: 0.2617 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 11925 Z= 0.123 Angle : 0.567 10.464 16311 Z= 0.267 Chirality : 0.039 0.136 1728 Planarity : 0.004 0.050 2017 Dihedral : 8.242 89.489 1771 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.11 % Favored : 96.67 % Rotamer: Outliers : 1.89 % Allowed : 17.34 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.23), residues: 1413 helix: 2.35 (0.17), residues: 1000 sheet: 0.58 (1.10), residues: 20 loop : -0.83 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 267 TYR 0.009 0.001 TYR B 324 PHE 0.013 0.001 PHE B 635 TRP 0.019 0.001 TRP A 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (11921) covalent geometry : angle 0.56698 / 0.27 (16311) hydrogen bonds : bond 0.04473 / 2.95 ( 771) hydrogen bonds : angle 4.07037 / 2.97 ( 2241) Misc. bond : bond 0.07735 / 3.84 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.462 Fit side-chains REVERT: A 101 ARG cc_start: 0.8344 (tpt170) cc_final: 0.8083 (tpt170) REVERT: A 477 MET cc_start: 0.8341 (tmm) cc_final: 0.8017 (tmm) REVERT: A 488 TRP cc_start: 0.6953 (m-10) cc_final: 0.5934 (m-90) REVERT: A 494 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 559 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: A 583 MET cc_start: 0.8641 (tpp) cc_final: 0.8186 (mpp) REVERT: A 610 MET cc_start: 0.8974 (mmp) cc_final: 0.7860 (ttp) REVERT: B 168 ARG cc_start: 0.8445 (tpt90) cc_final: 0.8232 (tpt170) REVERT: B 477 MET cc_start: 0.8421 (tmm) cc_final: 0.8162 (tmm) REVERT: B 488 TRP cc_start: 0.6436 (m-10) cc_final: 0.5848 (m-90) REVERT: B 494 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7386 (tm-30) REVERT: B 583 MET cc_start: 0.7543 (ppp) cc_final: 0.6892 (ppp) outliers start: 21 outliers final: 8 residues processed: 107 average time/residue: 0.6728 time to fit residues: 78.0939 Evaluate side-chains 94 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 568 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.098093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.066091 restraints weight = 19748.672| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.44 r_work: 0.2578 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 11925 Z= 0.149 Angle : 0.599 12.452 16311 Z= 0.278 Chirality : 0.040 0.139 1728 Planarity : 0.004 0.037 2017 Dihedral : 7.938 87.833 1767 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.40 % Favored : 96.39 % Rotamer: Outliers : 1.89 % Allowed : 17.79 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.23), residues: 1413 helix: 2.31 (0.17), residues: 1004 sheet: 0.24 (1.13), residues: 20 loop : -0.76 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 267 TYR 0.012 0.001 TYR B 324 PHE 0.016 0.001 PHE A 635 TRP 0.018 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (11921) covalent geometry : angle 0.59936 / 0.28 (16311) hydrogen bonds : bond 0.04917 / 3.25 ( 771) hydrogen bonds : angle 4.05860 / 2.97 ( 2241) Misc. bond : bond 0.12360 / 6.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8296 (tpt170) cc_final: 0.7928 (tpt170) REVERT: A 488 TRP cc_start: 0.6994 (m-10) cc_final: 0.5961 (m-90) REVERT: A 494 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 583 MET cc_start: 0.8686 (tpp) cc_final: 0.8217 (mpp) REVERT: A 610 MET cc_start: 0.9006 (mmp) cc_final: 0.7909 (ttp) REVERT: B 126 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: B 488 TRP cc_start: 0.6526 (m-10) cc_final: 0.5926 (m-90) REVERT: B 494 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 583 MET cc_start: 0.7685 (ppp) cc_final: 0.7052 (ppp) outliers start: 21 outliers final: 14 residues processed: 105 average time/residue: 0.6845 time to fit residues: 78.0267 Evaluate side-chains 100 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 568 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 122 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 141 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.067397 restraints weight = 19781.784| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.46 r_work: 0.2610 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 11925 Z= 0.121 Angle : 0.565 11.238 16311 Z= 0.263 Chirality : 0.038 0.134 1728 Planarity : 0.004 0.042 2017 Dihedral : 7.797 87.948 1767 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.97 % Favored : 96.82 % Rotamer: Outliers : 1.71 % Allowed : 18.60 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.23), residues: 1413 helix: 2.41 (0.17), residues: 999 sheet: -0.02 (1.13), residues: 20 loop : -0.83 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 267 TYR 0.009 0.001 TYR B 324 PHE 0.012 0.001 PHE B 635 TRP 0.019 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (11921) covalent geometry : angle 0.56548 / 0.26 (16311) hydrogen bonds : bond 0.04373 / 2.89 ( 771) hydrogen bonds : angle 3.94841 / 2.88 ( 2241) Misc. bond : bond 0.07157 / 3.57 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.446 Fit side-chains REVERT: A 101 ARG cc_start: 0.8382 (tpt170) cc_final: 0.8027 (tpt170) REVERT: A 477 MET cc_start: 0.8393 (tmm) cc_final: 0.8049 (tmm) REVERT: A 488 TRP cc_start: 0.6991 (m-10) cc_final: 0.5928 (m-90) REVERT: A 494 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 559 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: A 583 MET cc_start: 0.8680 (tpp) cc_final: 0.8052 (mpp) REVERT: A 610 MET cc_start: 0.9003 (mmp) cc_final: 0.7894 (ttp) REVERT: B 51 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7436 (ttm-80) REVERT: B 126 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: B 477 MET cc_start: 0.8464 (tmm) cc_final: 0.8168 (tmm) REVERT: B 494 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 583 MET cc_start: 0.7750 (ppp) cc_final: 0.7100 (ppp) outliers start: 19 outliers final: 11 residues processed: 106 average time/residue: 0.7171 time to fit residues: 82.0528 Evaluate side-chains 101 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 73 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.068155 restraints weight = 19613.773| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.45 r_work: 0.2568 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 11925 Z= 0.114 Angle : 0.562 10.545 16311 Z= 0.262 Chirality : 0.038 0.133 1728 Planarity : 0.004 0.036 2017 Dihedral : 7.707 88.760 1767 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.04 % Favored : 96.74 % Rotamer: Outliers : 1.89 % Allowed : 18.51 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.23), residues: 1413 helix: 2.46 (0.17), residues: 999 sheet: -0.09 (1.14), residues: 20 loop : -0.82 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 267 TYR 0.014 0.001 TYR B 638 PHE 0.016 0.001 PHE B 635 TRP 0.018 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (11921) covalent geometry : angle 0.56156 / 0.26 (16311) hydrogen bonds : bond 0.04130 / 2.72 ( 771) hydrogen bonds : angle 3.90807 / 2.86 ( 2241) Misc. bond : bond 0.06579 / 3.28 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.536 Fit side-chains REVERT: A 51 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7410 (ttm-80) REVERT: A 101 ARG cc_start: 0.8326 (tpt170) cc_final: 0.7996 (tpt170) REVERT: A 477 MET cc_start: 0.8339 (tmm) cc_final: 0.8017 (tmm) REVERT: A 488 TRP cc_start: 0.6878 (m-10) cc_final: 0.5865 (m-90) REVERT: A 494 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7266 (tm-30) REVERT: A 559 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: A 583 MET cc_start: 0.8693 (tpp) cc_final: 0.8214 (mpp) REVERT: A 610 MET cc_start: 0.8912 (mmp) cc_final: 0.7872 (ttp) REVERT: B 51 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7375 (ttm-80) REVERT: B 126 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: B 477 MET cc_start: 0.8374 (tmm) cc_final: 0.8129 (tmm) REVERT: B 494 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7440 (tm-30) REVERT: B 583 MET cc_start: 0.7709 (ppp) cc_final: 0.7030 (ppp) outliers start: 21 outliers final: 12 residues processed: 107 average time/residue: 0.7298 time to fit residues: 84.4429 Evaluate side-chains 104 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 63 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 141 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.098143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.066130 restraints weight = 19720.188| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.44 r_work: 0.2585 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 11925 Z= 0.143 Angle : 0.585 11.847 16311 Z= 0.272 Chirality : 0.039 0.136 1728 Planarity : 0.004 0.037 2017 Dihedral : 7.762 88.078 1767 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.18 % Favored : 96.60 % Rotamer: Outliers : 1.71 % Allowed : 18.96 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.23), residues: 1413 helix: 2.40 (0.17), residues: 1000 sheet: -0.20 (1.17), residues: 20 loop : -0.77 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 267 TYR 0.014 0.001 TYR B 638 PHE 0.017 0.001 PHE B 635 TRP 0.017 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (11921) covalent geometry : angle 0.58541 / 0.27 (16311) hydrogen bonds : bond 0.04709 / 3.11 ( 771) hydrogen bonds : angle 3.96244 / 2.89 ( 2241) Misc. bond : bond 0.11310 / 5.64 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.431 Fit side-chains REVERT: A 51 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7430 (ttm-80) REVERT: A 101 ARG cc_start: 0.8398 (tpt170) cc_final: 0.8097 (tpt170) REVERT: A 477 MET cc_start: 0.8430 (tmm) cc_final: 0.8068 (tmm) REVERT: A 488 TRP cc_start: 0.6944 (m-10) cc_final: 0.5895 (m-90) REVERT: A 494 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 559 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: A 583 MET cc_start: 0.8774 (tpp) cc_final: 0.8110 (mpp) REVERT: A 610 MET cc_start: 0.8994 (mmp) cc_final: 0.7970 (ttp) REVERT: B 51 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7375 (ttm-80) REVERT: B 126 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: B 477 MET cc_start: 0.8441 (tmm) cc_final: 0.8160 (tmm) REVERT: B 494 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7552 (tm-30) REVERT: B 583 MET cc_start: 0.7819 (ppp) cc_final: 0.7141 (ppp) outliers start: 19 outliers final: 11 residues processed: 101 average time/residue: 0.7238 time to fit residues: 78.7811 Evaluate side-chains 100 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 0.0040 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.067823 restraints weight = 19659.611| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.46 r_work: 0.2563 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 11925 Z= 0.114 Angle : 0.560 10.143 16311 Z= 0.262 Chirality : 0.038 0.166 1728 Planarity : 0.004 0.040 2017 Dihedral : 7.633 88.368 1767 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.11 % Favored : 96.67 % Rotamer: Outliers : 1.71 % Allowed : 18.87 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.23), residues: 1413 helix: 2.47 (0.17), residues: 1000 sheet: -0.26 (1.18), residues: 20 loop : -0.78 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 267 TYR 0.016 0.001 TYR B 638 PHE 0.015 0.001 PHE A 492 TRP 0.019 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (11921) covalent geometry : angle 0.55967 / 0.26 (16311) hydrogen bonds : bond 0.04138 / 2.73 ( 771) hydrogen bonds : angle 3.88959 / 2.85 ( 2241) Misc. bond : bond 0.06399 / 3.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.487 Fit side-chains REVERT: A 101 ARG cc_start: 0.8352 (tpt170) cc_final: 0.8000 (tpt170) REVERT: A 126 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8617 (tt0) REVERT: A 477 MET cc_start: 0.8330 (tmm) cc_final: 0.8030 (tmm) REVERT: A 488 TRP cc_start: 0.6890 (m-10) cc_final: 0.5839 (m-90) REVERT: A 494 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 559 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: A 583 MET cc_start: 0.8706 (tpp) cc_final: 0.8221 (mpp) REVERT: A 610 MET cc_start: 0.8932 (mmp) cc_final: 0.7920 (ttp) REVERT: B 126 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: B 477 MET cc_start: 0.8365 (tmm) cc_final: 0.8129 (tmm) REVERT: B 494 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 577 LYS cc_start: 0.8682 (mmpt) cc_final: 0.7916 (tmmm) REVERT: B 583 MET cc_start: 0.7755 (ppp) cc_final: 0.7046 (ppp) outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 0.6762 time to fit residues: 78.2531 Evaluate side-chains 104 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 101 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.100819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.070988 restraints weight = 20385.467| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.37 r_work: 0.2776 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 11925 Z= 0.123 Angle : 0.564 11.160 16311 Z= 0.262 Chirality : 0.038 0.175 1728 Planarity : 0.004 0.041 2017 Dihedral : 7.628 88.539 1767 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.26 % Favored : 96.53 % Rotamer: Outliers : 1.35 % Allowed : 19.32 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.23), residues: 1413 helix: 2.45 (0.17), residues: 1000 sheet: -0.34 (1.17), residues: 20 loop : -0.78 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 267 TYR 0.013 0.001 TYR B 638 PHE 0.016 0.001 PHE B 635 TRP 0.018 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (11921) covalent geometry : angle 0.56421 / 0.26 (16311) hydrogen bonds : bond 0.04310 / 2.84 ( 771) hydrogen bonds : angle 3.89631 / 2.85 ( 2241) Misc. bond : bond 0.08637 / 4.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.457 Fit side-chains REVERT: A 101 ARG cc_start: 0.8414 (tpt170) cc_final: 0.8099 (tpt170) REVERT: A 126 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8788 (tt0) REVERT: A 477 MET cc_start: 0.8434 (tmm) cc_final: 0.8123 (tmm) REVERT: A 488 TRP cc_start: 0.6981 (m-10) cc_final: 0.5934 (m-90) REVERT: A 494 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7316 (tm-30) REVERT: A 559 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A 583 MET cc_start: 0.8820 (tpp) cc_final: 0.8266 (mpp) REVERT: A 610 MET cc_start: 0.9015 (mmp) cc_final: 0.8023 (ttp) REVERT: B 126 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: B 477 MET cc_start: 0.8434 (tmm) cc_final: 0.8179 (tmm) REVERT: B 494 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 583 MET cc_start: 0.7858 (ppp) cc_final: 0.7168 (ppp) outliers start: 15 outliers final: 11 residues processed: 102 average time/residue: 0.6984 time to fit residues: 77.1536 Evaluate side-chains 101 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 610 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 107 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 0.0870 chunk 141 optimal weight: 0.0470 chunk 7 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.072754 restraints weight = 20338.157| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.37 r_work: 0.2761 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11925 Z= 0.108 Angle : 0.557 10.045 16311 Z= 0.261 Chirality : 0.038 0.169 1728 Planarity : 0.004 0.045 2017 Dihedral : 7.469 89.102 1765 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.11 % Favored : 96.67 % Rotamer: Outliers : 1.35 % Allowed : 19.41 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.23), residues: 1413 helix: 2.49 (0.17), residues: 1000 sheet: -0.42 (1.67), residues: 10 loop : -0.79 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 267 TYR 0.013 0.001 TYR B 638 PHE 0.018 0.001 PHE A 492 TRP 0.020 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (11921) covalent geometry : angle 0.55716 / 0.26 (16311) hydrogen bonds : bond 0.03920 / 2.58 ( 771) hydrogen bonds : angle 3.84303 / 2.81 ( 2241) Misc. bond : bond 0.05278 / 2.63 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.409 Fit side-chains REVERT: A 101 ARG cc_start: 0.8395 (tpt170) cc_final: 0.8033 (tpt170) REVERT: A 126 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: A 477 MET cc_start: 0.8412 (tmm) cc_final: 0.8118 (tmm) REVERT: A 488 TRP cc_start: 0.6983 (m-10) cc_final: 0.5940 (m-90) REVERT: A 494 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 559 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: A 583 MET cc_start: 0.8715 (tpp) cc_final: 0.8274 (mpp) REVERT: A 610 MET cc_start: 0.9015 (mmp) cc_final: 0.8006 (ttp) REVERT: B 126 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: B 477 MET cc_start: 0.8418 (tmm) cc_final: 0.8192 (tmm) REVERT: B 494 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7545 (tm-30) REVERT: B 583 MET cc_start: 0.7882 (ppp) cc_final: 0.7230 (ppp) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.6669 time to fit residues: 72.5692 Evaluate side-chains 99 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 0.0970 chunk 129 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 138 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.072419 restraints weight = 20112.246| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.36 r_work: 0.2735 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 11925 Z= 0.112 Angle : 0.554 10.695 16311 Z= 0.258 Chirality : 0.038 0.181 1728 Planarity : 0.004 0.045 2017 Dihedral : 7.448 89.476 1765 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.18 % Favored : 96.60 % Rotamer: Outliers : 0.90 % Allowed : 19.77 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.23), residues: 1413 helix: 2.49 (0.17), residues: 1000 sheet: -0.39 (1.69), residues: 10 loop : -0.80 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 267 TYR 0.012 0.001 TYR B 638 PHE 0.014 0.001 PHE B 635 TRP 0.018 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (11921) covalent geometry : angle 0.55419 / 0.26 (16311) hydrogen bonds : bond 0.04009 / 2.64 ( 771) hydrogen bonds : angle 3.84333 / 2.81 ( 2241) Misc. bond : bond 0.06963 / 3.47 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5345.31 seconds wall clock time: 91 minutes 36.18 seconds (5496.18 seconds total)