Starting phenix.real_space_refine on Tue Sep 24 03:47:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/09_2024/7mgw_23830.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/09_2024/7mgw_23830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/09_2024/7mgw_23830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/09_2024/7mgw_23830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/09_2024/7mgw_23830.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgw_23830/09_2024/7mgw_23830.cif" } resolution = 3.5 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= 0.041 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 S 34 5.16 5 Cl 1 4.86 5 C 4140 2.51 5 N 964 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6223 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4292 Classifications: {'peptide': 537} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 514} Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 160 Unusual residues: {' CL': 1, 'CLR': 1, 'D10': 1, 'D12': 4, 'HP6': 6, 'LNK': 1, 'SRO': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Time building chain proxies: 5.09, per 1000 atoms: 0.82 Number of scatterers: 6223 At special positions: 0 Unit cell: (69.336, 73.224, 121.824, 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) Cl 1 17.00 S 34 16.00 O 1084 8.00 N 964 7.00 C 4140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 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=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 868.9 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 7 sheets defined 54.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.846A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 114 through 120 removed outlier: 3.809A pdb=" N LEU A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU A 119 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Proline residue: A 120 - end of helix Processing helix chain 'A' and resid 121 through 144 Proline residue: A 131 - end of helix Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.524A pdb=" N TRP A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.598A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 190 removed outlier: 4.145A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.668A pdb=" N HIS A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 272 removed outlier: 4.364A pdb=" N LYS A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.642A pdb=" N VAL A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 removed outlier: 4.228A pdb=" N TYR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 356 through 391 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.783A pdb=" N GLU A 396 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 403 through 417 removed outlier: 4.749A pdb=" N PHE A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 454 removed outlier: 3.807A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 removed outlier: 4.511A pdb=" N LYS A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 482 removed outlier: 3.852A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 removed outlier: 4.318A pdb=" N VAL A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 517 through 530 removed outlier: 4.432A pdb=" N ASP A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 603 through 612 Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25 removed outlier: 3.515A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 30 removed outlier: 5.352A pdb=" N GLU B 29 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 112 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 69 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30 removed outlier: 5.352A pdb=" N GLU B 29 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 112 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.616A pdb=" N ALA C 39 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS C 43 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE C 95 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR C 94 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.605A pdb=" N ASN C 51 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 removed outlier: 6.930A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 121 " --> pdb=" O GLN C 114 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1816 1.34 - 1.46: 1680 1.46 - 1.58: 2849 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6394 Sorted by residual: bond pdb=" CD1 SRO A 712 " pdb=" NE1 SRO A 712 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" CD1 SRO A 715 " pdb=" NE1 SRO A 715 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" CD2 SRO A 712 " pdb=" CE2 SRO A 712 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" CD2 SRO A 715 " pdb=" CE2 SRO A 715 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" CB SRO A 715 " pdb=" CG SRO A 715 " ideal model delta sigma weight residual 1.498 1.527 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 6389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 8486 2.07 - 4.13: 161 4.13 - 6.20: 16 6.20 - 8.27: 1 8.27 - 10.34: 1 Bond angle restraints: 8665 Sorted by residual: angle pdb=" C GLU C 47 " pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 121.70 132.04 -10.34 1.80e+00 3.09e-01 3.30e+01 angle pdb=" C LEU A 119 " pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta sigma weight residual 121.65 119.11 2.54 1.01e+00 9.80e-01 6.34e+00 angle pdb=" CA GLU C 47 " pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 115.60 118.96 -3.36 1.48e+00 4.57e-01 5.16e+00 angle pdb=" C20 CLR A 716 " pdb=" C22 CLR A 716 " pdb=" C23 CLR A 716 " ideal model delta sigma weight residual 115.57 109.14 6.43 3.00e+00 1.11e-01 4.59e+00 angle pdb=" N VAL A 236 " pdb=" CA VAL A 236 " pdb=" C VAL A 236 " ideal model delta sigma weight residual 113.39 110.26 3.13 1.47e+00 4.63e-01 4.53e+00 ... (remaining 8660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.03: 3447 19.03 - 38.06: 230 38.06 - 57.09: 37 57.09 - 76.11: 5 76.11 - 95.14: 10 Dihedral angle restraints: 3729 sinusoidal: 1529 harmonic: 2200 Sorted by residual: dihedral pdb=" C2 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" C5 NAG D 1 " ideal model delta sinusoidal sigma weight residual 53.78 -41.36 95.14 1 3.00e+01 1.11e-03 1.16e+01 dihedral pdb=" C2 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sinusoidal sigma weight residual 175.11 81.72 93.39 1 3.00e+01 1.11e-03 1.13e+01 dihedral pdb=" C5 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O3 NAG D 1 " ideal model delta sinusoidal sigma weight residual -174.13 -81.26 -92.87 1 3.00e+01 1.11e-03 1.12e+01 ... (remaining 3726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 869 0.068 - 0.137: 74 0.137 - 0.205: 2 0.205 - 0.273: 2 0.273 - 0.341: 1 Chirality restraints: 948 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.95e+01 chirality pdb=" C14 CLR A 716 " pdb=" C13 CLR A 716 " pdb=" C15 CLR A 716 " pdb=" C8 CLR A 716 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C9 CLR A 716 " pdb=" C10 CLR A 716 " pdb=" C11 CLR A 716 " pdb=" C8 CLR A 716 " both_signs ideal model delta sigma weight residual False -2.45 -2.68 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 945 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 570 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 571 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 100 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.48e+00 pdb=" N PRO C 101 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 101 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 101 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 589 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 590 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 590 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 590 " 0.015 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1875 2.81 - 3.34: 5836 3.34 - 3.86: 10538 3.86 - 4.38: 11412 4.38 - 4.90: 19850 Nonbonded interactions: 49511 Sorted by model distance: nonbonded pdb=" OG1 THR B 106 " pdb=" OD1 ASP B 109 " model vdw 2.292 3.040 nonbonded pdb=" O ILE A 108 " pdb=" ND2 ASN A 112 " model vdw 2.297 3.120 nonbonded pdb=" OG SER C 76 " pdb=" OD1 ASN C 77 " model vdw 2.310 3.040 nonbonded pdb=" OG SER C 55 " pdb=" O ALA C 74 " model vdw 2.313 3.040 nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.323 3.040 ... (remaining 49506 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 3.860 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6394 Z= 0.175 Angle : 0.636 10.336 8665 Z= 0.301 Chirality : 0.041 0.341 948 Planarity : 0.003 0.031 1049 Dihedral : 13.533 95.142 2324 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.40 % Allowed : 9.66 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -2.49 (0.28), residues: 759 helix: -0.76 (0.23), residues: 354 sheet: -1.78 (0.51), residues: 93 loop : -2.62 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 317 HIS 0.001 0.000 HIS A 143 PHE 0.015 0.001 PHE A 474 TYR 0.009 0.000 TYR A 176 ARG 0.001 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 0.689 Fit side-chains REVERT: A 144 ARG cc_start: 0.6293 (mtm110) cc_final: 0.6074 (ttm110) REVERT: A 145 ASN cc_start: 0.6109 (t0) cc_final: 0.5464 (t0) REVERT: A 243 LYS cc_start: 0.7231 (mtmm) cc_final: 0.7008 (mmtm) REVERT: A 267 TYR cc_start: 0.5156 (t80) cc_final: 0.4873 (t80) REVERT: A 370 MET cc_start: 0.6126 (mmp) cc_final: 0.4205 (ttm) REVERT: A 391 ASN cc_start: 0.7447 (t0) cc_final: 0.7161 (t0) REVERT: A 430 MET cc_start: 0.6276 (ttm) cc_final: 0.6050 (tmm) REVERT: A 466 VAL cc_start: 0.3864 (p) cc_final: 0.3450 (t) REVERT: A 508 GLU cc_start: 0.6099 (tm-30) cc_final: 0.5663 (tm-30) REVERT: A 572 TYR cc_start: 0.6178 (t80) cc_final: 0.5765 (t80) REVERT: B 76 ASP cc_start: 0.7630 (t0) cc_final: 0.6898 (t0) REVERT: C 78 GLN cc_start: 0.7740 (mt0) cc_final: 0.7485 (mt0) outliers start: 9 outliers final: 4 residues processed: 151 average time/residue: 0.2062 time to fit residues: 39.7004 Evaluate side-chains 101 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.0170 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.0270 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN A 205 ASN A 316 ASN A 332 GLN A 355 ASN B 25 GLN B 54 ASN B 101 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5141 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6394 Z= 0.176 Angle : 0.538 9.853 8665 Z= 0.273 Chirality : 0.040 0.209 948 Planarity : 0.004 0.029 1049 Dihedral : 9.392 77.120 1018 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.27 % Allowed : 16.67 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 (0.30), residues: 759 helix: 0.30 (0.26), residues: 353 sheet: -1.24 (0.52), residues: 95 loop : -2.33 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 326 HIS 0.001 0.000 HIS A 223 PHE 0.025 0.001 PHE A 428 TYR 0.015 0.001 TYR A 358 ARG 0.004 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.667 Fit side-chains REVERT: A 144 ARG cc_start: 0.6254 (mtm110) cc_final: 0.6044 (ttm110) REVERT: A 243 LYS cc_start: 0.7348 (mtmm) cc_final: 0.7110 (mmtm) REVERT: A 370 MET cc_start: 0.6244 (mmp) cc_final: 0.4094 (ttm) REVERT: A 389 MET cc_start: 0.4496 (mmt) cc_final: 0.4131 (mpp) REVERT: A 391 ASN cc_start: 0.7415 (t0) cc_final: 0.7160 (t0) REVERT: A 430 MET cc_start: 0.6505 (OUTLIER) cc_final: 0.6211 (tmm) REVERT: A 508 GLU cc_start: 0.6144 (tm-30) cc_final: 0.5733 (tm-30) REVERT: A 572 TYR cc_start: 0.6181 (t80) cc_final: 0.5799 (t80) REVERT: C 78 GLN cc_start: 0.7727 (mt0) cc_final: 0.7408 (mt0) outliers start: 21 outliers final: 8 residues processed: 118 average time/residue: 0.1757 time to fit residues: 27.7922 Evaluate side-chains 109 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 0.0370 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 0.0370 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN B 25 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5243 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6394 Z= 0.187 Angle : 0.540 9.784 8665 Z= 0.276 Chirality : 0.041 0.248 948 Planarity : 0.004 0.031 1049 Dihedral : 7.790 65.463 1015 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.52 % Allowed : 18.54 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.10 (0.30), residues: 759 helix: 0.56 (0.26), residues: 355 sheet: -1.03 (0.52), residues: 96 loop : -2.19 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 197 HIS 0.002 0.001 HIS A 143 PHE 0.015 0.001 PHE A 407 TYR 0.022 0.001 TYR A 142 ARG 0.004 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 0.654 Fit side-chains REVERT: A 144 ARG cc_start: 0.5994 (mtm110) cc_final: 0.5743 (ttm110) REVERT: A 279 LYS cc_start: 0.3982 (tptt) cc_final: 0.3335 (ttpp) REVERT: A 391 ASN cc_start: 0.7483 (t0) cc_final: 0.6862 (m-40) REVERT: A 508 GLU cc_start: 0.6174 (tm-30) cc_final: 0.5702 (tm-30) REVERT: A 572 TYR cc_start: 0.6079 (t80) cc_final: 0.5775 (t80) outliers start: 29 outliers final: 17 residues processed: 123 average time/residue: 0.1727 time to fit residues: 28.7356 Evaluate side-chains 110 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 416 ASN A 456 HIS B 25 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5307 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6394 Z= 0.214 Angle : 0.562 9.850 8665 Z= 0.292 Chirality : 0.041 0.192 948 Planarity : 0.004 0.041 1049 Dihedral : 6.524 55.910 1015 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.52 % Allowed : 20.09 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.05 (0.30), residues: 759 helix: 0.50 (0.26), residues: 359 sheet: -0.92 (0.52), residues: 101 loop : -2.09 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 326 HIS 0.006 0.001 HIS A 456 PHE 0.020 0.002 PHE A 407 TYR 0.016 0.001 TYR A 142 ARG 0.006 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.677 Fit side-chains REVERT: A 84 LYS cc_start: 0.6157 (pttm) cc_final: 0.5601 (ptpt) REVERT: A 144 ARG cc_start: 0.5878 (mtm110) cc_final: 0.5622 (ttm110) REVERT: A 317 TRP cc_start: 0.6786 (m100) cc_final: 0.6399 (m100) REVERT: A 391 ASN cc_start: 0.7528 (t0) cc_final: 0.6909 (m-40) REVERT: A 562 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7321 (mm-40) REVERT: A 572 TYR cc_start: 0.5825 (t80) cc_final: 0.5573 (t80) outliers start: 29 outliers final: 20 residues processed: 119 average time/residue: 0.1636 time to fit residues: 26.7251 Evaluate side-chains 111 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN B 101 GLN C 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5317 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6394 Z= 0.217 Angle : 0.553 9.902 8665 Z= 0.289 Chirality : 0.040 0.203 948 Planarity : 0.004 0.050 1049 Dihedral : 5.852 58.530 1015 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.36 % Allowed : 20.72 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.95 (0.30), residues: 759 helix: 0.50 (0.26), residues: 362 sheet: -0.81 (0.52), residues: 101 loop : -1.99 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS A 456 PHE 0.018 0.002 PHE A 454 TYR 0.012 0.001 TYR A 267 ARG 0.009 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.662 Fit side-chains REVERT: A 84 LYS cc_start: 0.6101 (pttm) cc_final: 0.5562 (ptpt) REVERT: A 317 TRP cc_start: 0.6758 (m100) cc_final: 0.6379 (m100) REVERT: A 391 ASN cc_start: 0.7494 (t0) cc_final: 0.6861 (m-40) REVERT: A 508 GLU cc_start: 0.6226 (tm-30) cc_final: 0.5801 (tm-30) REVERT: A 562 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7284 (mm-40) REVERT: A 572 TYR cc_start: 0.5743 (t80) cc_final: 0.5533 (t80) REVERT: C 85 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7504 (mtm110) outliers start: 28 outliers final: 21 residues processed: 118 average time/residue: 0.1650 time to fit residues: 26.6958 Evaluate side-chains 117 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.7980 chunk 14 optimal weight: 0.0270 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 0.0970 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5312 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6394 Z= 0.192 Angle : 0.550 9.843 8665 Z= 0.285 Chirality : 0.040 0.201 948 Planarity : 0.004 0.049 1049 Dihedral : 5.503 54.921 1015 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.05 % Allowed : 20.87 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.90 (0.30), residues: 759 helix: 0.51 (0.26), residues: 362 sheet: -0.72 (0.52), residues: 101 loop : -1.94 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 204 HIS 0.002 0.001 HIS A 456 PHE 0.016 0.001 PHE A 353 TYR 0.011 0.001 TYR A 110 ARG 0.009 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.662 Fit side-chains REVERT: A 84 LYS cc_start: 0.6153 (pttm) cc_final: 0.5653 (ptpt) REVERT: A 144 ARG cc_start: 0.5682 (mtm110) cc_final: 0.5434 (ttm110) REVERT: A 391 ASN cc_start: 0.7521 (t0) cc_final: 0.6880 (m-40) REVERT: A 508 GLU cc_start: 0.6185 (tm-30) cc_final: 0.5778 (tm-30) REVERT: A 562 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7263 (mm-40) REVERT: C 85 ARG cc_start: 0.7744 (mtm110) cc_final: 0.7352 (mtm110) outliers start: 26 outliers final: 20 residues processed: 120 average time/residue: 0.1639 time to fit residues: 26.7045 Evaluate side-chains 115 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5363 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 6394 Z= 0.276 Angle : 0.589 9.837 8665 Z= 0.311 Chirality : 0.042 0.232 948 Planarity : 0.004 0.050 1049 Dihedral : 5.672 53.638 1015 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.89 % Allowed : 21.18 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -1.03 (0.30), residues: 759 helix: 0.34 (0.26), residues: 362 sheet: -0.76 (0.52), residues: 101 loop : -1.92 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 151 HIS 0.002 0.001 HIS A 235 PHE 0.028 0.002 PHE A 407 TYR 0.021 0.002 TYR A 267 ARG 0.002 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.6102 (pttm) cc_final: 0.5612 (ptpt) REVERT: A 167 ILE cc_start: 0.6649 (mm) cc_final: 0.6444 (mt) REVERT: A 317 TRP cc_start: 0.6775 (m100) cc_final: 0.6534 (m100) REVERT: A 391 ASN cc_start: 0.7538 (t0) cc_final: 0.6891 (m-40) REVERT: A 514 TRP cc_start: 0.6057 (m100) cc_final: 0.5723 (m-10) REVERT: A 562 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7370 (mm-40) REVERT: B 79 TYR cc_start: 0.7768 (m-80) cc_final: 0.7250 (m-80) REVERT: C 85 ARG cc_start: 0.7684 (mtm110) cc_final: 0.7382 (mtm110) outliers start: 25 outliers final: 24 residues processed: 120 average time/residue: 0.1593 time to fit residues: 26.4949 Evaluate side-chains 124 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 0.0270 chunk 69 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 GLN B 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6394 Z= 0.237 Angle : 0.575 9.913 8665 Z= 0.303 Chirality : 0.041 0.225 948 Planarity : 0.004 0.049 1049 Dihedral : 5.563 51.997 1015 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.83 % Allowed : 21.81 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.99 (0.30), residues: 759 helix: 0.43 (0.26), residues: 357 sheet: -0.69 (0.52), residues: 101 loop : -1.95 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 151 HIS 0.002 0.001 HIS A 143 PHE 0.030 0.001 PHE A 407 TYR 0.013 0.001 TYR A 267 ARG 0.002 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.6098 (pttm) cc_final: 0.5627 (ptpt) REVERT: A 259 ILE cc_start: 0.4490 (OUTLIER) cc_final: 0.4276 (mm) REVERT: A 317 TRP cc_start: 0.6829 (m100) cc_final: 0.6591 (m100) REVERT: A 391 ASN cc_start: 0.7550 (t0) cc_final: 0.6892 (m-40) REVERT: A 508 GLU cc_start: 0.6283 (tm-30) cc_final: 0.5855 (tm-30) REVERT: A 514 TRP cc_start: 0.6109 (m100) cc_final: 0.5715 (m-10) REVERT: A 562 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7351 (mm-40) REVERT: B 25 GLN cc_start: 0.7767 (tt0) cc_final: 0.7454 (tt0) REVERT: B 29 GLU cc_start: 0.7971 (mp0) cc_final: 0.7717 (mp0) REVERT: B 79 TYR cc_start: 0.7793 (m-80) cc_final: 0.7270 (m-80) REVERT: C 85 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7357 (mtm110) outliers start: 31 outliers final: 26 residues processed: 122 average time/residue: 0.1452 time to fit residues: 25.0757 Evaluate side-chains 125 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 71 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5343 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6394 Z= 0.202 Angle : 0.563 9.907 8665 Z= 0.297 Chirality : 0.040 0.214 948 Planarity : 0.004 0.051 1049 Dihedral : 5.447 52.015 1015 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.52 % Allowed : 22.74 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.89 (0.30), residues: 759 helix: 0.40 (0.26), residues: 362 sheet: -0.66 (0.53), residues: 101 loop : -1.78 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 204 HIS 0.002 0.001 HIS A 143 PHE 0.027 0.001 PHE A 407 TYR 0.010 0.001 TYR A 110 ARG 0.002 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.606 Fit side-chains REVERT: A 84 LYS cc_start: 0.6058 (pttm) cc_final: 0.5580 (ptpt) REVERT: A 144 ARG cc_start: 0.5610 (mtm110) cc_final: 0.5374 (ttm110) REVERT: A 259 ILE cc_start: 0.4453 (OUTLIER) cc_final: 0.4160 (mm) REVERT: A 317 TRP cc_start: 0.6873 (m100) cc_final: 0.6638 (m100) REVERT: A 391 ASN cc_start: 0.7527 (t0) cc_final: 0.6850 (m-40) REVERT: A 514 TRP cc_start: 0.6086 (m100) cc_final: 0.5694 (m-10) REVERT: A 562 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7326 (mm-40) REVERT: B 79 TYR cc_start: 0.7794 (m-80) cc_final: 0.7281 (m-80) REVERT: C 85 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7415 (mtm110) outliers start: 29 outliers final: 21 residues processed: 122 average time/residue: 0.1555 time to fit residues: 26.3262 Evaluate side-chains 121 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 0.0870 chunk 18 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5350 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6394 Z= 0.210 Angle : 0.578 9.915 8665 Z= 0.305 Chirality : 0.040 0.221 948 Planarity : 0.004 0.050 1049 Dihedral : 5.466 51.305 1015 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.05 % Allowed : 22.59 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.87 (0.30), residues: 759 helix: 0.50 (0.26), residues: 354 sheet: -0.67 (0.53), residues: 101 loop : -1.82 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 326 HIS 0.002 0.001 HIS A 143 PHE 0.026 0.001 PHE A 407 TYR 0.014 0.001 TYR A 110 ARG 0.002 0.000 ARG A 564 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 0.668 Fit side-chains REVERT: A 84 LYS cc_start: 0.6073 (pttm) cc_final: 0.5602 (ptpt) REVERT: A 144 ARG cc_start: 0.5699 (mtm110) cc_final: 0.5487 (ttm110) REVERT: A 259 ILE cc_start: 0.4455 (OUTLIER) cc_final: 0.4166 (mm) REVERT: A 317 TRP cc_start: 0.6897 (m100) cc_final: 0.6656 (m100) REVERT: A 391 ASN cc_start: 0.7521 (t0) cc_final: 0.6837 (m-40) REVERT: A 514 TRP cc_start: 0.6089 (m100) cc_final: 0.5690 (m-10) REVERT: A 562 GLN cc_start: 0.7626 (mm-40) cc_final: 0.7335 (mm-40) REVERT: B 79 TYR cc_start: 0.7829 (m-80) cc_final: 0.7296 (m-80) REVERT: C 85 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7450 (mtm110) outliers start: 26 outliers final: 21 residues processed: 115 average time/residue: 0.1541 time to fit residues: 24.5369 Evaluate side-chains 118 residues out of total 642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.179977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140591 restraints weight = 7684.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145844 restraints weight = 4677.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149312 restraints weight = 3434.090| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6394 Z= 0.235 Angle : 0.581 9.919 8665 Z= 0.308 Chirality : 0.041 0.237 948 Planarity : 0.004 0.051 1049 Dihedral : 5.536 50.534 1015 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.05 % Allowed : 22.27 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.93 (0.30), residues: 759 helix: 0.35 (0.26), residues: 359 sheet: -0.61 (0.54), residues: 96 loop : -1.76 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 220 HIS 0.002 0.001 HIS A 143 PHE 0.027 0.001 PHE A 407 TYR 0.014 0.001 TYR A 110 ARG 0.002 0.000 ARG A 564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1814.96 seconds wall clock time: 33 minutes 9.95 seconds (1989.95 seconds total)