Starting phenix.real_space_refine on Mon Apr 8 23:40:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8siy_40522/04_2024/8siy_40522_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8siy_40522/04_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8siy_40522/04_2024/8siy_40522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8siy_40522/04_2024/8siy_40522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8siy_40522/04_2024/8siy_40522_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8siy_40522/04_2024/8siy_40522_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 7.79, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.42 Conformation dependent library (CDL) restraints added in 1.7 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... running ksdssp... Secondary structure from input PDB file: 40 helices and 7 sheets defined 45.7% alpha, 11.7% beta 144 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 7.89 Creating SS restraints... Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 527 through 532 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 45 through 56 Processing helix chain 'C' and resid 64 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 86 through 113 Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 31 through 40 Processing helix chain 'D' and resid 48 through 75 removed outlier: 4.026A pdb=" N TYR D 51 " --> pdb=" O GLY D 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU D 52 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 66 " --> pdb=" O GLU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 27 through 36 Processing helix chain 'E' and resid 45 through 72 removed outlier: 4.378A pdb=" N VAL E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 56 through 83 Processing helix chain 'F' and resid 91 through 101 Processing helix chain 'F' and resid 104 through 123 Processing helix chain 'G' and resid 45 through 56 Processing helix chain 'G' and resid 64 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 86 through 113 Processing helix chain 'G' and resid 121 through 131 Processing helix chain 'H' and resid 26 through 28 No H-bonds generated for 'chain 'H' and resid 26 through 28' Processing helix chain 'H' and resid 31 through 40 Processing helix chain 'H' and resid 48 through 75 removed outlier: 3.632A pdb=" N TYR H 51 " --> pdb=" O GLY H 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE H 66 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 Processing helix chain 'I' and resid 17 through 21 Processing helix chain 'I' and resid 27 through 37 Processing helix chain 'I' and resid 47 through 73 removed outlier: 3.544A pdb=" N LEU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 89 Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'I' and resid 113 through 115 No H-bonds generated for 'chain 'I' and resid 113 through 115' Processing helix chain 'J' and resid 38 through 48 Processing helix chain 'J' and resid 56 through 83 Processing helix chain 'J' and resid 91 through 101 Processing helix chain 'J' and resid 104 through 123 Processing helix chain 'B' and resid 19 through 21 No H-bonds generated for 'chain 'B' and resid 19 through 21' Processing sheet with id= A, first strand: chain 'A' and resid 293 through 298 removed outlier: 7.080A pdb=" N CYS A 317 " --> pdb=" O TRP A 294 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N CYS A 296 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA A 315 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE A 298 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR A 313 " --> pdb=" O PHE A 298 " (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) Processing sheet with id= B, 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= C, first strand: chain 'A' and resid 396 through 400 removed outlier: 6.862A pdb=" N ALA A 412 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 399 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE A 410 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 438 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP A 422 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLN A 436 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.306A pdb=" N ASN A 487 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N CYS A 468 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 503 through 506 removed outlier: 6.331A pdb=" N SER A 526 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 544 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing sheet with id= F, 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= G, first strand: chain 'A' and resid 272 through 277 removed outlier: 6.692A pdb=" N ILE A 644 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A 276 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL A 642 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 623 " --> pdb=" O LEU A 636 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1131 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: 7.04 Time building geometry restraints manager: 7.93 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: 98.78 - 105.83: 1660 105.83 - 112.88: 8661 112.88 - 119.93: 5419 119.93 - 126.98: 6045 126.98 - 134.03: 762 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: 63 2.57 - 3.16: 11447 3.16 - 3.74: 26535 3.74 - 4.32: 37444 4.32 - 4.90: 54183 Nonbonded interactions: 129672 Sorted by model distance: nonbonded pdb=" OG1 THR F 90 " pdb=" OE1 GLU F 93 " model vdw 1.993 2.440 nonbonded pdb=" OE2 GLU A 299 " pdb=" ND2 ASN A 364 " model vdw 2.068 2.520 nonbonded pdb=" OG1 THR J 90 " pdb=" OE1 GLU J 93 " model vdw 2.087 2.440 nonbonded pdb=" NE2 GLN A 292 " pdb=" O ARG H 19 " model vdw 2.093 2.520 nonbonded pdb=" OG SER A 561 " pdb=" O VAL A 624 " model vdw 2.167 2.440 ... (remaining 129667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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: 1.290 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: 6.540 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 49.900 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.220 ------------------------------------------------------------------------------- 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= 0.333 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 fitting. rotamer outliers: 13 poor density : 271 time to evaluate : 1.247 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: 1.6670 time to fit residues: 498.3559 Evaluate side-chains 172 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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: 8.9990 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN A 567 ASN C 76 GLN C 108 ASN D 93 GLN G 76 GLN G 108 ASN I 112 GLN J 49 HIS J 67 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 15728 Z= 0.436 Angle : 0.662 7.243 22547 Z= 0.382 Chirality : 0.042 0.173 2575 Planarity : 0.006 0.059 1830 Dihedral : 30.215 172.092 4438 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.84 % Favored : 98.07 % Rotamer: Outliers : 4.68 % Allowed : 18.28 % Favored : 77.05 % 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: 1.41 (0.25), residues: 1087 helix: 2.23 (0.21), residues: 551 sheet: 0.49 (0.48), residues: 109 loop : -0.69 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 550 HIS 0.007 0.001 HIS A 392 PHE 0.012 0.002 PHE H 61 TYR 0.018 0.002 TYR A 632 ARG 0.013 0.001 ARG A 381 *********************** 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 224 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 180 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 120 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8959 (mtm) REVERT: E 64 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: G 59 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7349 (pp20) REVERT: G 97 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8266 (mt-10) REVERT: I 73 ASN cc_start: 0.8581 (t0) cc_final: 0.8210 (t0) outliers start: 44 outliers final: 16 residues processed: 208 average time/residue: 1.6614 time to fit residues: 372.6424 Evaluate side-chains 182 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 120 MET 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 F residue 115 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN D 93 GLN E 73 ASN E 104 GLN J 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 15728 Z= 0.345 Angle : 0.598 8.571 22547 Z= 0.347 Chirality : 0.038 0.146 2575 Planarity : 0.005 0.043 1830 Dihedral : 30.254 174.818 4434 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.12 % Favored : 97.79 % Rotamer: Outliers : 3.61 % Allowed : 19.66 % Favored : 76.73 % 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: 1.30 (0.25), residues: 1087 helix: 2.12 (0.22), residues: 554 sheet: 0.33 (0.49), residues: 112 loop : -0.71 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 471 HIS 0.011 0.001 HIS A 275 PHE 0.016 0.001 PHE A 630 TYR 0.015 0.002 TYR F 40 ARG 0.008 0.001 ARG J 86 *********************** 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 207 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.152 Fit side-chains REVERT: C 120 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8948 (mtm) REVERT: F 57 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8517 (mmtm) REVERT: G 59 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7410 (pp20) REVERT: H 77 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8577 (mmtp) REVERT: I 73 ASN cc_start: 0.8538 (t0) cc_final: 0.8184 (t0) outliers start: 34 outliers final: 18 residues processed: 190 average time/residue: 1.6830 time to fit residues: 343.4591 Evaluate side-chains 186 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 GLU 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 449 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain I residue 101 THR 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: 0.8980 chunk 13 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN H 27 GLN J 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 15728 Z= 0.321 Angle : 0.589 8.612 22547 Z= 0.341 Chirality : 0.037 0.143 2575 Planarity : 0.005 0.040 1830 Dihedral : 30.207 173.873 4434 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 4.36 % Allowed : 20.72 % Favored : 74.92 % 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: 1.33 (0.25), residues: 1087 helix: 2.11 (0.22), residues: 554 sheet: 0.16 (0.50), residues: 112 loop : -0.58 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 471 HIS 0.006 0.001 HIS A 275 PHE 0.019 0.001 PHE A 630 TYR 0.017 0.002 TYR F 40 ARG 0.011 0.001 ARG I 29 *********************** 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 208 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 167 time to evaluate : 1.359 Fit side-chains REVERT: C 120 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8928 (mtm) REVERT: F 57 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8506 (mmtm) REVERT: G 59 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7430 (pp20) REVERT: H 77 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8587 (mmtp) REVERT: I 73 ASN cc_start: 0.8527 (t0) cc_final: 0.8201 (t0) REVERT: B 27 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8156 (mm) outliers start: 41 outliers final: 22 residues processed: 193 average time/residue: 1.7125 time to fit residues: 355.4881 Evaluate side-chains 189 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 396 ILE Chi-restraints excluded: chain A residue 398 THR 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 580 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 642 VAL 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 114 VAL Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 115 THR 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 49 LEU Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain B residue 27 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.5980 chunk 1 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN E 104 GLN H 27 GLN I 31 HIS I 110 ASN J 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15728 Z= 0.277 Angle : 0.569 9.064 22547 Z= 0.332 Chirality : 0.036 0.138 2575 Planarity : 0.004 0.040 1830 Dihedral : 30.118 174.019 4434 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.12 % Favored : 97.79 % Rotamer: Outliers : 3.61 % Allowed : 21.15 % 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: 1.42 (0.26), residues: 1087 helix: 2.16 (0.22), residues: 554 sheet: 0.27 (0.49), residues: 112 loop : -0.51 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 525 HIS 0.014 0.001 HIS A 275 PHE 0.012 0.001 PHE A 506 TYR 0.020 0.002 TYR F 40 ARG 0.008 0.000 ARG H 23 *********************** 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 204 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: C 120 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8902 (mtm) REVERT: G 59 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7405 (pp20) REVERT: I 73 ASN cc_start: 0.8484 (t0) cc_final: 0.8241 (t0) REVERT: B 27 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8133 (mm) outliers start: 34 outliers final: 21 residues processed: 190 average time/residue: 1.6808 time to fit residues: 343.5365 Evaluate side-chains 187 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 443 SER 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 623 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain C residue 120 MET 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 E residue 113 SER Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 115 THR 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 49 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain B residue 27 LEU 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: 0.0970 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 125 GLN H 27 GLN J 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 15728 Z= 0.422 Angle : 0.632 11.095 22547 Z= 0.360 Chirality : 0.040 0.158 2575 Planarity : 0.005 0.039 1830 Dihedral : 30.419 175.495 4434 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.76 % Favored : 97.15 % Rotamer: Outliers : 3.83 % Allowed : 21.25 % Favored : 74.92 % 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: 1.29 (0.26), residues: 1087 helix: 2.02 (0.22), residues: 554 sheet: 0.25 (0.47), residues: 114 loop : -0.55 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 471 HIS 0.006 0.001 HIS A 379 PHE 0.012 0.002 PHE B 16 TYR 0.020 0.002 TYR F 40 ARG 0.011 0.001 ARG F 33 *********************** 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 200 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 1.278 Fit side-chains REVERT: C 120 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8952 (mtm) REVERT: G 59 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7599 (pp20) REVERT: H 77 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8609 (mmtp) REVERT: B 27 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8160 (mm) outliers start: 36 outliers final: 22 residues processed: 185 average time/residue: 1.7425 time to fit residues: 346.0272 Evaluate side-chains 181 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 GLU 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 443 SER Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain D residue 24 ASP 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 E residue 113 SER Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 115 THR 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 77 LYS Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain B residue 27 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN E 104 GLN I 24 GLN J 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15728 Z= 0.190 Angle : 0.578 10.902 22547 Z= 0.331 Chirality : 0.036 0.257 2575 Planarity : 0.004 0.041 1830 Dihedral : 29.989 174.028 4434 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 2.66 % Allowed : 22.85 % Favored : 74.50 % 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: 1.46 (0.26), residues: 1087 helix: 2.14 (0.22), residues: 553 sheet: 0.32 (0.48), residues: 114 loop : -0.42 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 471 HIS 0.009 0.001 HIS A 275 PHE 0.009 0.001 PHE A 630 TYR 0.022 0.001 TYR F 40 ARG 0.009 0.001 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 200 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 175 time to evaluate : 1.388 Fit side-chains REVERT: C 120 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8870 (mtm) REVERT: F 42 TYR cc_start: 0.8295 (t80) cc_final: 0.7962 (t80) REVERT: G 59 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7440 (pp20) REVERT: B 27 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8178 (mm) outliers start: 25 outliers final: 17 residues processed: 188 average time/residue: 1.6672 time to fit residues: 337.7116 Evaluate side-chains 184 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 623 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 642 VAL 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 G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain H residue 18 HIS Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain B residue 27 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 87 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN I 24 GLN J 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15728 Z= 0.259 Angle : 0.589 10.973 22547 Z= 0.336 Chirality : 0.037 0.269 2575 Planarity : 0.004 0.049 1830 Dihedral : 29.961 174.503 4434 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.67 % Favored : 97.24 % Rotamer: Outliers : 2.76 % Allowed : 23.80 % Favored : 73.43 % 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: 1.48 (0.26), residues: 1087 helix: 2.15 (0.22), residues: 553 sheet: 0.36 (0.48), residues: 115 loop : -0.40 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 471 HIS 0.004 0.001 HIS A 392 PHE 0.027 0.001 PHE B 16 TYR 0.024 0.002 TYR F 40 ARG 0.012 0.001 ARG F 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 192 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.345 Fit side-chains REVERT: C 120 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8906 (mtm) REVERT: F 42 TYR cc_start: 0.8316 (t80) cc_final: 0.7995 (t80) REVERT: G 59 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7474 (pp20) outliers start: 26 outliers final: 13 residues processed: 181 average time/residue: 1.7123 time to fit residues: 333.5518 Evaluate side-chains 176 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL 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 623 THR Chi-restraints excluded: chain A residue 642 VAL 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 F residue 115 THR 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 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: 1.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15728 Z= 0.330 Angle : 0.608 12.654 22547 Z= 0.344 Chirality : 0.038 0.240 2575 Planarity : 0.004 0.040 1830 Dihedral : 30.029 175.141 4434 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 2.55 % Allowed : 24.12 % Favored : 73.33 % 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: 1.40 (0.26), residues: 1087 helix: 2.09 (0.22), residues: 554 sheet: 0.09 (0.46), residues: 120 loop : -0.37 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 471 HIS 0.006 0.001 HIS A 275 PHE 0.023 0.001 PHE B 16 TYR 0.026 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 185 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 1.190 Fit side-chains REVERT: C 120 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8911 (mtm) REVERT: F 42 TYR cc_start: 0.8365 (t80) cc_final: 0.8077 (t80) REVERT: G 59 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7550 (pp20) REVERT: H 23 ARG cc_start: 0.8525 (mtt90) cc_final: 0.8306 (mmt-90) outliers start: 24 outliers final: 16 residues processed: 175 average time/residue: 1.6744 time to fit residues: 315.4967 Evaluate side-chains 173 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 623 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 642 VAL 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 F residue 36 SER Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 18 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN F 47 GLN J 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15728 Z= 0.199 Angle : 0.602 12.875 22547 Z= 0.338 Chirality : 0.037 0.346 2575 Planarity : 0.005 0.104 1830 Dihedral : 30.024 174.905 4434 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.76 % Favored : 97.15 % Rotamer: Outliers : 2.13 % Allowed : 25.19 % Favored : 72.69 % 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: 1.41 (0.26), residues: 1087 helix: 2.09 (0.22), residues: 552 sheet: 0.11 (0.47), residues: 120 loop : -0.36 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 471 HIS 0.008 0.001 HIS A 275 PHE 0.024 0.001 PHE B 16 TYR 0.025 0.002 TYR F 40 ARG 0.010 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 182 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.276 Fit side-chains REVERT: C 120 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8893 (mtm) REVERT: F 42 TYR cc_start: 0.8288 (t80) cc_final: 0.7969 (t80) REVERT: G 59 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: H 23 ARG cc_start: 0.8473 (mtt90) cc_final: 0.8255 (mmt-90) outliers start: 20 outliers final: 14 residues processed: 173 average time/residue: 1.7061 time to fit residues: 317.8920 Evaluate side-chains 174 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 623 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 642 VAL 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 F residue 115 THR Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 18 HIS 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: 4.9990 chunk 15 optimal weight: 0.0970 chunk 29 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.048296 restraints weight = 43680.248| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.26 r_work: 0.2588 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 15728 Z= 0.402 Angle : 0.636 13.486 22547 Z= 0.358 Chirality : 0.040 0.327 2575 Planarity : 0.005 0.045 1830 Dihedral : 30.157 175.674 4434 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.42 % Rotamer: Outliers : 2.23 % Allowed : 24.55 % Favored : 73.22 % 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: 1.33 (0.26), residues: 1087 helix: 2.01 (0.22), residues: 554 sheet: 0.08 (0.46), residues: 119 loop : -0.40 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 471 HIS 0.009 0.001 HIS A 275 PHE 0.019 0.002 PHE B 16 TYR 0.026 0.002 TYR F 40 ARG 0.009 0.001 ARG E 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5609.23 seconds wall clock time: 104 minutes 5.46 seconds (6245.46 seconds total)