Starting phenix.real_space_refine on Tue Dec 31 01:37:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8siy_40522/12_2024/8siy_40522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8siy_40522/12_2024/8siy_40522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8siy_40522/12_2024/8siy_40522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8siy_40522/12_2024/8siy_40522.map" model { file = "/net/cci-nas-00/data/ceres_data/8siy_40522/12_2024/8siy_40522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8siy_40522/12_2024/8siy_40522.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 33 5.16 5 C 8443 2.51 5 N 2738 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14844 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2654 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 18, 'TRANS': 322} Chain breaks: 4 Chain: "C" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "D" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "E" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "F" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "G" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "H" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 697 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "K" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2993 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "L" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3034 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "B" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 137 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Time building chain proxies: 8.84, per 1000 atoms: 0.60 Number of scatterers: 14844 At special positions: 0 Unit cell: (112.32, 114.816, 123.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 294 15.00 O 3336 8.00 N 2738 7.00 C 8443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.3 seconds 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 18 sheets defined 51.3% alpha, 14.2% beta 144 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 7.41 Creating SS restraints... Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.678A pdb=" N ASN A 284 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 533 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'C' and resid 44 through 57 Processing helix chain 'C' and resid 63 through 77 removed outlier: 3.785A pdb=" N ASP C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.524A pdb=" N ILE C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.612A pdb=" N GLN D 27 " --> pdb=" O ASP D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.613A pdb=" N GLU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'E' and resid 16 through 22 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 45 through 73 removed outlier: 4.378A pdb=" N VAL E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 90 removed outlier: 3.516A pdb=" N LEU E 83 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'F' and resid 37 through 49 Processing helix chain 'F' and resid 55 through 84 Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 103 through 124 Processing helix chain 'G' and resid 44 through 57 Processing helix chain 'G' and resid 63 through 77 removed outlier: 3.927A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 82 through 93 removed outlier: 3.548A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 22 Processing helix chain 'I' and resid 26 through 36 Processing helix chain 'I' and resid 46 through 72 removed outlier: 3.544A pdb=" N LEU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 Processing helix chain 'I' and resid 90 through 97 Processing helix chain 'I' and resid 112 through 116 Processing helix chain 'J' and resid 37 through 49 Processing helix chain 'J' and resid 55 through 84 Processing helix chain 'J' and resid 90 through 102 Processing helix chain 'J' and resid 103 through 124 Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.595A pdb=" N VAL B 22 " --> pdb=" O ASP B 19 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 621 through 626 removed outlier: 3.769A pdb=" N THR A 623 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL A 642 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A 276 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 644 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N GLN B 15 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 276 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 298 removed outlier: 3.794A pdb=" N ALA A 295 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 321 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP A 326 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 332 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 335 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 351 removed outlier: 3.602A pdb=" N SER A 345 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 387 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS A 379 " --> pdb=" O CYS A 385 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N CYS A 385 " --> pdb=" O HIS A 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 396 through 400 removed outlier: 3.882A pdb=" N ARG A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 418 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR A 439 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 420 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 446 through 451 removed outlier: 6.362A pdb=" N GLY A 463 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 449 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU A 461 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE A 459 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N CYS A 468 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASN A 487 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 503 through 506 removed outlier: 6.110A pdb=" N ILE A 522 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN A 547 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 524 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 560 through 563 removed outlier: 3.507A pdb=" N LEU A 568 " --> pdb=" O CYS A 563 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 610 through 611 Processing sheet with id=AA9, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.871A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'D' and resid 96 through 98 removed outlier: 6.640A pdb=" N THR D 96 " --> pdb=" O THR I 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 42 through 43 removed outlier: 7.261A pdb=" N ARG E 42 " --> pdb=" O ILE F 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 78 Processing sheet with id=AB5, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AB6, first strand: chain 'G' and resid 83 through 84 removed outlier: 7.216A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AB8, first strand: chain 'I' and resid 42 through 43 removed outlier: 7.442A pdb=" N ARG I 42 " --> pdb=" O ILE J 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 77 through 78 501 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 742 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 7.59 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3004 1.33 - 1.45: 4707 1.45 - 1.57: 7384 1.57 - 1.69: 586 1.69 - 1.81: 47 Bond restraints: 15728 Sorted by residual: bond pdb=" SG ML3 H 20 " pdb=" CD ML3 H 20 " ideal model delta sigma weight residual 1.815 1.752 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" CB ML3 H 20 " pdb=" SG ML3 H 20 " ideal model delta sigma weight residual 1.817 1.761 0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 1.533 1.495 0.038 1.42e-02 4.96e+03 7.09e+00 bond pdb=" C VAL A 338 " pdb=" N PRO A 339 " ideal model delta sigma weight residual 1.331 1.363 -0.031 1.20e-02 6.94e+03 6.82e+00 bond pdb=" CA PRO E 26 " pdb=" C PRO E 26 " ideal model delta sigma weight residual 1.521 1.505 0.015 9.30e-03 1.16e+04 2.71e+00 ... (remaining 15723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 21874 1.78 - 3.56: 649 3.56 - 5.33: 20 5.33 - 7.11: 2 7.11 - 8.89: 2 Bond angle restraints: 22547 Sorted by residual: angle pdb=" SG ML3 H 20 " pdb=" CD ML3 H 20 " pdb=" CE ML3 H 20 " ideal model delta sigma weight residual 115.60 106.71 8.89 3.00e+00 1.11e-01 8.78e+00 angle pdb=" CA ML3 H 20 " pdb=" CB ML3 H 20 " pdb=" SG ML3 H 20 " ideal model delta sigma weight residual 114.92 106.84 8.08 3.00e+00 1.11e-01 7.26e+00 angle pdb=" C TYR A 414 " pdb=" N ASP A 415 " pdb=" CA ASP A 415 " ideal model delta sigma weight residual 122.31 117.39 4.92 2.00e+00 2.50e-01 6.06e+00 angle pdb=" C3' DG K -70 " pdb=" C2' DG K -70 " pdb=" C1' DG K -70 " ideal model delta sigma weight residual 101.60 105.07 -3.47 1.50e+00 4.44e-01 5.35e+00 angle pdb=" O4' DG L 27 " pdb=" C1' DG L 27 " pdb=" C2' DG L 27 " ideal model delta sigma weight residual 106.40 103.19 3.21 1.50e+00 4.44e-01 4.59e+00 ... (remaining 22542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 7142 34.08 - 68.16: 1490 68.16 - 102.23: 14 102.23 - 136.31: 2 136.31 - 170.39: 2 Dihedral angle restraints: 8650 sinusoidal: 5411 harmonic: 3239 Sorted by residual: dihedral pdb=" C4' DC L -58 " pdb=" C3' DC L -58 " pdb=" O3' DC L -58 " pdb=" P DT L -57 " ideal model delta sinusoidal sigma weight residual 220.00 49.61 170.39 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG L 20 " pdb=" C3' DG L 20 " pdb=" O3' DG L 20 " pdb=" P DG L 21 " ideal model delta sinusoidal sigma weight residual 220.00 66.40 153.60 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA GLU A 406 " pdb=" C GLU A 406 " pdb=" N THR A 407 " pdb=" CA THR A 407 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 8647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1314 0.029 - 0.059: 766 0.059 - 0.088: 328 0.088 - 0.118: 134 0.118 - 0.147: 33 Chirality restraints: 2575 Sorted by residual: chirality pdb=" CA ILE A 418 " pdb=" N ILE A 418 " pdb=" C ILE A 418 " pdb=" CB ILE A 418 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA PRO E 80 " pdb=" N PRO E 80 " pdb=" C PRO E 80 " pdb=" CB PRO E 80 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE B 26 " pdb=" N ILE B 26 " pdb=" C ILE B 26 " pdb=" CB ILE B 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 2572 not shown) Planarity restraints: 1830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 598 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 599 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 599 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 599 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 450 " 0.045 5.00e-02 4.00e+02 6.93e-02 7.67e+00 pdb=" N PRO A 451 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 272 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO A 273 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " -0.033 5.00e-02 4.00e+02 ... (remaining 1827 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 61 2.57 - 3.16: 11356 3.16 - 3.74: 26526 3.74 - 4.32: 37287 4.32 - 4.90: 54158 Nonbonded interactions: 129388 Sorted by model distance: nonbonded pdb=" OG1 THR F 90 " pdb=" OE1 GLU F 93 " model vdw 1.993 3.040 nonbonded pdb=" OE2 GLU A 299 " pdb=" ND2 ASN A 364 " model vdw 2.068 3.120 nonbonded pdb=" OG1 THR J 90 " pdb=" OE1 GLU J 93 " model vdw 2.087 3.040 nonbonded pdb=" NE2 GLN A 292 " pdb=" O ARG H 19 " model vdw 2.093 3.120 nonbonded pdb=" OG SER A 561 " pdb=" O VAL A 624 " model vdw 2.167 3.040 ... (remaining 129383 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 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 24 through 102) } ncs_group { reference = (chain 'E' and resid 11 through 117) selection = chain 'I' } ncs_group { reference = (chain 'F' and resid 32 through 124) selection = chain 'J' } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 42.410 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 15728 Z= 0.329 Angle : 0.644 8.890 22547 Z= 0.388 Chirality : 0.046 0.147 2575 Planarity : 0.006 0.102 1830 Dihedral : 26.203 170.390 6552 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.38 % Allowed : 9.14 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1087 helix: 2.11 (0.21), residues: 554 sheet: 0.38 (0.48), residues: 113 loop : -0.58 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 645 HIS 0.011 0.001 HIS A 275 PHE 0.008 0.001 PHE C 84 TYR 0.012 0.002 TYR J 121 ARG 0.006 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 271 time to evaluate : 1.471 Fit side-chains REVERT: I 73 ASN cc_start: 0.8454 (t0) cc_final: 0.8202 (t0) outliers start: 13 outliers final: 3 residues processed: 278 average time/residue: 1.6697 time to fit residues: 500.1312 Evaluate side-chains 172 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 567 ASN C 76 GLN C 108 ASN D 25 ASN E 73 ASN F 47 GLN G 76 GLN G 108 ASN I 112 GLN J 49 HIS J 67 ASN B 15 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 15728 Z= 0.354 Angle : 0.653 7.880 22547 Z= 0.375 Chirality : 0.040 0.163 2575 Planarity : 0.005 0.055 1830 Dihedral : 29.807 174.005 4438 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.83 % Allowed : 17.64 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1087 helix: 2.53 (0.21), residues: 557 sheet: 0.40 (0.48), residues: 118 loop : -0.61 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 471 HIS 0.020 0.002 HIS A 275 PHE 0.009 0.001 PHE A 506 TYR 0.024 0.002 TYR A 632 ARG 0.011 0.001 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 396 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7977 (tp) REVERT: E 64 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: E 90 ASP cc_start: 0.8307 (t0) cc_final: 0.8101 (t0) REVERT: G 59 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7170 (pp20) REVERT: I 73 ASN cc_start: 0.8428 (t0) cc_final: 0.8093 (t0) outliers start: 36 outliers final: 16 residues processed: 203 average time/residue: 1.7527 time to fit residues: 384.3105 Evaluate side-chains 180 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 622 ASN C 76 GLN D 27 GLN E 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 15728 Z= 0.321 Angle : 0.606 8.020 22547 Z= 0.351 Chirality : 0.038 0.170 2575 Planarity : 0.004 0.048 1830 Dihedral : 30.112 173.508 4436 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 3.93 % Allowed : 18.49 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.26), residues: 1087 helix: 2.65 (0.21), residues: 558 sheet: 0.51 (0.52), residues: 104 loop : -0.77 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 471 HIS 0.004 0.001 HIS H 75 PHE 0.023 0.001 PHE A 276 TYR 0.018 0.002 TYR A 336 ARG 0.008 0.001 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 1.352 Fit side-chains REVERT: A 439 THR cc_start: 0.6828 (m) cc_final: 0.6589 (m) REVERT: F 35 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8251 (mt-10) REVERT: F 57 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8501 (mmtm) REVERT: G 59 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7258 (pp20) REVERT: I 73 ASN cc_start: 0.8485 (t0) cc_final: 0.8082 (t0) REVERT: J 105 GLU cc_start: 0.7980 (tp30) cc_final: 0.7575 (tp30) REVERT: J 108 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8404 (ttpt) outliers start: 37 outliers final: 14 residues processed: 199 average time/residue: 1.6156 time to fit residues: 348.1244 Evaluate side-chains 181 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 519 GLN A 622 ASN C 76 GLN J 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 15728 Z= 0.386 Angle : 0.619 7.522 22547 Z= 0.357 Chirality : 0.039 0.149 2575 Planarity : 0.005 0.049 1830 Dihedral : 30.371 174.965 4436 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.67 % Favored : 97.24 % Rotamer: Outliers : 4.04 % Allowed : 19.77 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1087 helix: 2.59 (0.22), residues: 558 sheet: 0.35 (0.51), residues: 107 loop : -0.74 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 471 HIS 0.013 0.001 HIS A 275 PHE 0.023 0.002 PHE A 630 TYR 0.018 0.002 TYR A 336 ARG 0.010 0.001 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 1.259 Fit side-chains REVERT: F 35 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8143 (mt-10) REVERT: G 59 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7505 (pp20) REVERT: I 73 ASN cc_start: 0.8506 (t0) cc_final: 0.8064 (t0) REVERT: J 105 GLU cc_start: 0.8093 (tp30) cc_final: 0.7663 (tp30) REVERT: J 108 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8492 (ttpt) outliers start: 38 outliers final: 16 residues processed: 200 average time/residue: 1.8162 time to fit residues: 391.6952 Evaluate side-chains 177 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN A 622 ASN C 76 GLN C 125 GLN E 104 GLN I 31 HIS J 47 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15728 Z= 0.313 Angle : 0.607 10.349 22547 Z= 0.347 Chirality : 0.038 0.138 2575 Planarity : 0.004 0.045 1830 Dihedral : 30.215 174.486 4436 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 3.29 % Allowed : 21.68 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.26), residues: 1087 helix: 2.67 (0.22), residues: 558 sheet: 0.77 (0.52), residues: 105 loop : -0.69 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 471 HIS 0.027 0.001 HIS A 275 PHE 0.010 0.001 PHE A 630 TYR 0.017 0.002 TYR F 40 ARG 0.006 0.000 ARG J 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.215 Fit side-chains REVERT: D 92 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8444 (ttp80) REVERT: E 15 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8566 (tptm) REVERT: G 59 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7549 (pp20) REVERT: J 108 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8639 (ttpt) outliers start: 31 outliers final: 17 residues processed: 190 average time/residue: 1.6875 time to fit residues: 345.6392 Evaluate side-chains 182 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain B residue 14 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN C 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 15728 Z= 0.385 Angle : 0.630 9.113 22547 Z= 0.359 Chirality : 0.040 0.180 2575 Planarity : 0.004 0.044 1830 Dihedral : 30.335 175.208 4434 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.76 % Favored : 97.15 % Rotamer: Outliers : 4.57 % Allowed : 19.98 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.26), residues: 1087 helix: 2.64 (0.22), residues: 558 sheet: 0.65 (0.50), residues: 105 loop : -0.69 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 471 HIS 0.016 0.001 HIS A 275 PHE 0.017 0.002 PHE B 16 TYR 0.020 0.002 TYR F 40 ARG 0.013 0.001 ARG I 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.319 Fit side-chains REVERT: E 15 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8572 (tptm) REVERT: F 57 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8568 (mmtt) REVERT: G 59 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7619 (pp20) REVERT: H 77 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8771 (mmtp) REVERT: J 108 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8618 (tttt) outliers start: 43 outliers final: 24 residues processed: 190 average time/residue: 1.7125 time to fit residues: 350.3234 Evaluate side-chains 185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain I residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN A 622 ASN C 68 GLN C 76 GLN D 93 GLN E 104 GLN H 27 GLN I 24 GLN J 47 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15728 Z= 0.184 Angle : 0.596 10.649 22547 Z= 0.337 Chirality : 0.036 0.159 2575 Planarity : 0.004 0.043 1830 Dihedral : 29.951 173.983 4434 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.67 % Favored : 97.24 % Rotamer: Outliers : 2.76 % Allowed : 22.00 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.26), residues: 1087 helix: 2.80 (0.22), residues: 558 sheet: 0.67 (0.53), residues: 104 loop : -0.57 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 471 HIS 0.012 0.001 HIS A 275 PHE 0.013 0.001 PHE B 16 TYR 0.021 0.001 TYR F 40 ARG 0.009 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.206 Fit side-chains REVERT: C 120 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8937 (mtm) REVERT: G 59 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7515 (pp20) REVERT: J 108 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8606 (ttpt) outliers start: 26 outliers final: 15 residues processed: 191 average time/residue: 1.7022 time to fit residues: 350.3517 Evaluate side-chains 185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain H residue 18 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS A 280 HIS A 283 ASN A 622 ASN C 68 GLN C 76 GLN H 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15728 Z= 0.290 Angle : 0.610 10.991 22547 Z= 0.345 Chirality : 0.038 0.213 2575 Planarity : 0.004 0.044 1830 Dihedral : 30.012 174.522 4434 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.76 % Favored : 97.15 % Rotamer: Outliers : 2.66 % Allowed : 22.95 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.26), residues: 1087 helix: 2.79 (0.21), residues: 558 sheet: 0.65 (0.50), residues: 109 loop : -0.61 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 471 HIS 0.010 0.001 HIS A 275 PHE 0.008 0.001 PHE B 16 TYR 0.022 0.002 TYR F 40 ARG 0.007 0.001 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.355 Fit side-chains REVERT: D 92 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8212 (ttp80) REVERT: G 59 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7562 (pp20) REVERT: J 105 GLU cc_start: 0.7996 (tp30) cc_final: 0.7742 (tp30) REVERT: J 108 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8615 (ttpt) outliers start: 25 outliers final: 16 residues processed: 185 average time/residue: 1.6894 time to fit residues: 338.5908 Evaluate side-chains 184 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 283 ASN A 622 ASN C 76 GLN D 25 ASN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15728 Z= 0.289 Angle : 0.622 14.550 22547 Z= 0.349 Chirality : 0.038 0.234 2575 Planarity : 0.004 0.044 1830 Dihedral : 29.991 174.701 4434 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 2.34 % Allowed : 23.38 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1087 helix: 2.77 (0.21), residues: 558 sheet: 0.77 (0.51), residues: 110 loop : -0.66 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 471 HIS 0.005 0.001 HIS A 280 PHE 0.010 0.001 PHE A 276 TYR 0.025 0.002 TYR F 40 ARG 0.010 0.001 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 1.425 Fit side-chains REVERT: G 59 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7626 (pp20) REVERT: J 108 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8665 (ttpt) outliers start: 22 outliers final: 18 residues processed: 183 average time/residue: 1.6621 time to fit residues: 328.8050 Evaluate side-chains 179 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 133 optimal weight: 0.0060 chunk 122 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN C 76 GLN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15728 Z= 0.266 Angle : 0.616 12.688 22547 Z= 0.345 Chirality : 0.037 0.202 2575 Planarity : 0.004 0.044 1830 Dihedral : 29.920 174.581 4434 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 2.23 % Allowed : 24.02 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.26), residues: 1087 helix: 2.79 (0.21), residues: 558 sheet: 0.72 (0.50), residues: 110 loop : -0.66 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 471 HIS 0.007 0.001 HIS A 275 PHE 0.010 0.001 PHE A 276 TYR 0.027 0.002 TYR F 40 ARG 0.009 0.001 ARG E 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 2.459 Fit side-chains REVERT: A 430 TYR cc_start: 0.6687 (m-80) cc_final: 0.6093 (p90) REVERT: G 59 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7653 (pp20) outliers start: 21 outliers final: 17 residues processed: 180 average time/residue: 1.6720 time to fit residues: 325.7117 Evaluate side-chains 177 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 49 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 10.0000 chunk 98 optimal weight: 0.0170 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 622 ASN C 68 GLN C 76 GLN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.080058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052048 restraints weight = 43489.759| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.26 r_work: 0.2689 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15728 Z= 0.178 Angle : 0.606 13.756 22547 Z= 0.338 Chirality : 0.036 0.251 2575 Planarity : 0.004 0.044 1830 Dihedral : 29.701 173.809 4434 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 2.23 % Allowed : 23.91 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.26), residues: 1087 helix: 2.82 (0.21), residues: 558 sheet: 0.70 (0.51), residues: 103 loop : -0.57 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 471 HIS 0.007 0.001 HIS A 275 PHE 0.013 0.001 PHE A 276 TYR 0.025 0.002 TYR F 40 ARG 0.010 0.001 ARG E 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5652.85 seconds wall clock time: 102 minutes 2.32 seconds (6122.32 seconds total)