Starting phenix.real_space_refine on Tue Feb 11 23:05:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mgw_23830/02_2025/7mgw_23830.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mgw_23830/02_2025/7mgw_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/cci-nas-00/data/ceres_data/7mgw_23830/02_2025/7mgw_23830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mgw_23830/02_2025/7mgw_23830.map" model { file = "/net/cci-nas-00/data/ceres_data/7mgw_23830/02_2025/7mgw_23830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mgw_23830/02_2025/7mgw_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-5592/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: 6.03, per 1000 atoms: 0.97 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: 1.88 Conformation dependent library (CDL) restraints added in 886.9 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: 0.75 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: 1.89 Time building geometry restraints manager: 2.13 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: 3.370 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.350 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.020 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.639 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: 0.2148 time to fit residues: 41.4288 Evaluate side-chains 101 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.212382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.178970 restraints weight = 7574.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.184484 restraints weight = 4509.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.187995 restraints weight = 3206.604| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 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 to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.607 Fit side-chains REVERT: A 370 MET cc_start: 0.7375 (mmp) cc_final: 0.5287 (ttm) REVERT: A 389 MET cc_start: 0.6439 (mmt) cc_final: 0.6235 (mpp) REVERT: A 391 ASN cc_start: 0.6423 (t0) cc_final: 0.6202 (t0) REVERT: A 508 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 572 TYR cc_start: 0.7192 (t80) cc_final: 0.6979 (t80) outliers start: 21 outliers final: 8 residues processed: 118 average time/residue: 0.1726 time to fit residues: 27.0866 Evaluate side-chains 107 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 0.0570 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.198427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.161176 restraints weight = 7671.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.166518 restraints weight = 4713.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.170032 restraints weight = 3459.681| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6394 Z= 0.212 Angle : 0.573 9.815 8665 Z= 0.295 Chirality : 0.042 0.251 948 Planarity : 0.004 0.033 1049 Dihedral : 7.682 64.458 1015 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.30 % Allowed : 17.76 % 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: -1.23 (0.30), residues: 759 helix: 0.41 (0.26), residues: 359 sheet: -1.08 (0.51), residues: 96 loop : -2.24 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 197 HIS 0.003 0.001 HIS A 143 PHE 0.014 0.002 PHE A 465 TYR 0.023 0.001 TYR A 142 ARG 0.011 0.001 ARG A 144 *********************** 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 141 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.609 Fit side-chains REVERT: A 145 ASN cc_start: 0.8160 (t0) cc_final: 0.7953 (t0) REVERT: A 279 LYS cc_start: 0.5330 (tptt) cc_final: 0.4504 (ttpp) REVERT: A 280 VAL cc_start: 0.4114 (OUTLIER) cc_final: 0.3886 (t) REVERT: A 391 ASN cc_start: 0.6535 (t0) cc_final: 0.6187 (m-40) REVERT: A 478 LEU cc_start: 0.7687 (tt) cc_final: 0.7434 (tp) REVERT: A 508 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 550 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7793 (tt) REVERT: B 118 SER cc_start: 0.9380 (t) cc_final: 0.9123 (m) outliers start: 34 outliers final: 19 residues processed: 129 average time/residue: 0.1645 time to fit residues: 29.1688 Evaluate side-chains 114 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 275 LYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 VAL 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 549 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 599 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 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 456 HIS ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.180259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140112 restraints weight = 7781.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145364 restraints weight = 4698.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148839 restraints weight = 3439.588| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 6394 Z= 0.313 Angle : 0.630 10.043 8665 Z= 0.331 Chirality : 0.044 0.192 948 Planarity : 0.004 0.042 1049 Dihedral : 6.847 56.533 1015 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.14 % Allowed : 19.78 % 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: -1.37 (0.29), residues: 759 helix: 0.12 (0.25), residues: 365 sheet: -1.10 (0.51), residues: 101 loop : -2.12 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 151 HIS 0.006 0.001 HIS A 456 PHE 0.025 0.002 PHE A 407 TYR 0.016 0.002 TYR A 142 ARG 0.009 0.001 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 138 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.655 Fit side-chains REVERT: A 84 LYS cc_start: 0.6985 (pttm) cc_final: 0.6195 (ptpt) REVERT: A 165 ILE cc_start: 0.8843 (tp) cc_final: 0.8629 (tp) REVERT: A 328 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8342 (t0) REVERT: A 391 ASN cc_start: 0.6770 (t0) cc_final: 0.6303 (m-40) REVERT: A 508 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7604 (tm-30) REVERT: B 29 GLU cc_start: 0.8216 (mp0) cc_final: 0.7933 (mp0) outliers start: 33 outliers final: 22 residues processed: 125 average time/residue: 0.1619 time to fit residues: 28.0096 Evaluate side-chains 119 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 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 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 103 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 72 optimal weight: 0.4980 chunk 7 optimal weight: 0.0470 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 14 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.183861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145310 restraints weight = 7626.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150545 restraints weight = 4607.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153917 restraints weight = 3356.464| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6394 Z= 0.186 Angle : 0.561 9.997 8665 Z= 0.292 Chirality : 0.040 0.186 948 Planarity : 0.004 0.052 1049 Dihedral : 5.991 57.893 1015 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.52 % Allowed : 20.25 % Favored : 75.23 % 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: -1.13 (0.30), residues: 759 helix: 0.29 (0.26), residues: 366 sheet: -0.88 (0.52), residues: 101 loop : -2.02 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 220 HIS 0.003 0.001 HIS A 143 PHE 0.019 0.001 PHE A 407 TYR 0.016 0.001 TYR A 142 ARG 0.003 0.000 ARG A 144 *********************** 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 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.752 Fit side-chains REVERT: A 84 LYS cc_start: 0.6991 (pttm) cc_final: 0.6210 (ptpt) REVERT: A 220 TRP cc_start: 0.5769 (m-90) cc_final: 0.5497 (m-90) REVERT: A 391 ASN cc_start: 0.6723 (t0) cc_final: 0.6296 (m-40) REVERT: A 508 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 537 TRP cc_start: 0.6756 (m100) cc_final: 0.5631 (m-90) outliers start: 29 outliers final: 23 residues processed: 123 average time/residue: 0.1595 time to fit residues: 27.0720 Evaluate side-chains 119 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 381 THR 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 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 C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 562 GLN A 567 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.181984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143283 restraints weight = 7579.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148343 restraints weight = 4696.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151764 restraints weight = 3478.167| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6394 Z= 0.212 Angle : 0.569 9.897 8665 Z= 0.298 Chirality : 0.041 0.200 948 Planarity : 0.004 0.049 1049 Dihedral : 5.705 56.241 1015 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.45 % Allowed : 21.03 % Favored : 73.52 % 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: -1.13 (0.30), residues: 759 helix: 0.26 (0.26), residues: 366 sheet: -0.86 (0.52), residues: 101 loop : -1.98 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 220 HIS 0.002 0.001 HIS A 143 PHE 0.023 0.001 PHE A 407 TYR 0.011 0.001 TYR A 110 ARG 0.003 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 138 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7037 (pttm) cc_final: 0.6257 (ptpt) REVERT: A 220 TRP cc_start: 0.5799 (m-90) cc_final: 0.5590 (m-90) REVERT: A 259 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.6616 (mm) REVERT: A 391 ASN cc_start: 0.6746 (t0) cc_final: 0.6265 (m-40) REVERT: A 508 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 25 GLN cc_start: 0.8553 (mt0) cc_final: 0.8168 (tt0) outliers start: 35 outliers final: 30 residues processed: 127 average time/residue: 0.1536 time to fit residues: 27.0251 Evaluate side-chains 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE 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 301 THR 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 430 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 550 LEU 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 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 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 0.0070 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN A 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.183670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.145116 restraints weight = 7717.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150238 restraints weight = 4772.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.153598 restraints weight = 3519.889| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6394 Z= 0.196 Angle : 0.549 9.857 8665 Z= 0.289 Chirality : 0.040 0.202 948 Planarity : 0.004 0.050 1049 Dihedral : 5.431 54.430 1015 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.98 % Allowed : 22.12 % Favored : 72.90 % 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: 0.25 (0.26), residues: 369 sheet: -0.80 (0.52), residues: 101 loop : -1.80 (0.37), residues: 289 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 0.024 0.001 PHE A 407 TYR 0.018 0.001 TYR A 267 ARG 0.002 0.000 ARG A 144 *********************** 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 128 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.593 Fit side-chains REVERT: A 84 LYS cc_start: 0.7009 (pttm) cc_final: 0.6294 (ptpt) REVERT: A 200 CYS cc_start: 0.2151 (OUTLIER) cc_final: 0.0272 (t) REVERT: A 259 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6694 (mm) REVERT: A 391 ASN cc_start: 0.6755 (t0) cc_final: 0.6225 (m-40) REVERT: A 454 PHE cc_start: 0.6147 (m-10) cc_final: 0.5929 (m-10) REVERT: A 508 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7589 (tm-30) outliers start: 32 outliers final: 26 residues processed: 122 average time/residue: 0.1472 time to fit residues: 25.0538 Evaluate side-chains 120 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ILE 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 430 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL 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 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS A 368 ASN A 562 GLN B 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.182747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144334 restraints weight = 7552.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149505 restraints weight = 4595.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152950 restraints weight = 3380.319| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6394 Z= 0.205 Angle : 0.566 9.858 8665 Z= 0.297 Chirality : 0.040 0.208 948 Planarity : 0.004 0.049 1049 Dihedral : 5.370 53.540 1015 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.30 % Allowed : 22.27 % Favored : 72.43 % 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: 363 sheet: -0.74 (0.52), residues: 101 loop : -1.74 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 220 HIS 0.002 0.001 HIS A 143 PHE 0.021 0.001 PHE A 407 TYR 0.014 0.001 TYR A 267 ARG 0.002 0.000 ARG A 144 *********************** 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 129 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7049 (pttm) cc_final: 0.6352 (ptpt) REVERT: A 200 CYS cc_start: 0.2222 (OUTLIER) cc_final: 0.0359 (t) REVERT: A 259 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6524 (mm) REVERT: A 391 ASN cc_start: 0.6727 (t0) cc_final: 0.6197 (m-40) REVERT: A 454 PHE cc_start: 0.6364 (m-10) cc_final: 0.5868 (m-80) REVERT: A 508 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7795 (tm-30) REVERT: B 25 GLN cc_start: 0.8528 (mt0) cc_final: 0.8256 (tt0) outliers start: 34 outliers final: 28 residues processed: 120 average time/residue: 0.1496 time to fit residues: 25.3605 Evaluate side-chains 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE 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 301 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ILE 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 410 TYR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL 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 597 LEU Chi-restraints excluded: chain A residue 599 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 Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.0370 chunk 51 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.181775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142760 restraints weight = 7595.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148042 restraints weight = 4519.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151564 restraints weight = 3284.780| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6394 Z= 0.220 Angle : 0.582 9.847 8665 Z= 0.308 Chirality : 0.040 0.214 948 Planarity : 0.004 0.050 1049 Dihedral : 5.371 52.627 1015 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.83 % Allowed : 22.43 % 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: -0.92 (0.30), residues: 759 helix: 0.37 (0.26), residues: 361 sheet: -0.79 (0.51), residues: 101 loop : -1.72 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 220 HIS 0.002 0.001 HIS A 143 PHE 0.021 0.001 PHE A 407 TYR 0.012 0.001 TYR B 79 ARG 0.002 0.000 ARG A 144 *********************** 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 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7050 (pttm) cc_final: 0.6343 (ptpt) REVERT: A 200 CYS cc_start: 0.2282 (OUTLIER) cc_final: 0.0361 (t) REVERT: A 259 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6542 (mm) REVERT: A 391 ASN cc_start: 0.6776 (t0) cc_final: 0.6256 (m-40) REVERT: A 454 PHE cc_start: 0.6382 (m-10) cc_final: 0.5936 (m-80) REVERT: A 508 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 25 GLN cc_start: 0.8584 (mt0) cc_final: 0.8215 (tt0) outliers start: 31 outliers final: 27 residues processed: 116 average time/residue: 0.1559 time to fit residues: 25.6569 Evaluate side-chains 122 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE 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 301 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ILE 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 430 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL 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 597 LEU Chi-restraints excluded: chain A residue 599 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 Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.180412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141902 restraints weight = 7633.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146984 restraints weight = 4624.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150414 restraints weight = 3383.011| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6394 Z= 0.235 Angle : 0.591 9.851 8665 Z= 0.311 Chirality : 0.041 0.227 948 Planarity : 0.004 0.050 1049 Dihedral : 5.396 51.511 1015 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.52 % Allowed : 23.21 % Favored : 72.27 % 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: -0.97 (0.30), residues: 759 helix: 0.42 (0.26), residues: 355 sheet: -0.80 (0.52), residues: 96 loop : -1.83 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 220 HIS 0.002 0.001 HIS A 143 PHE 0.022 0.001 PHE A 407 TYR 0.012 0.001 TYR A 110 ARG 0.002 0.000 ARG B 38 ********************** 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 121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7086 (pttm) cc_final: 0.6402 (ptpt) REVERT: A 223 HIS cc_start: 0.7830 (m-70) cc_final: 0.7559 (m-70) REVERT: A 259 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6784 (mm) REVERT: A 391 ASN cc_start: 0.6705 (t0) cc_final: 0.6176 (m-40) REVERT: A 454 PHE cc_start: 0.6477 (m-10) cc_final: 0.6034 (m-80) REVERT: A 508 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 25 GLN cc_start: 0.8624 (mt0) cc_final: 0.8274 (tt0) outliers start: 29 outliers final: 28 residues processed: 114 average time/residue: 0.1598 time to fit residues: 25.2796 Evaluate side-chains 121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE 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 301 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ILE 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 430 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL 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 597 LEU Chi-restraints excluded: chain A residue 599 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 Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 72 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.181384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142838 restraints weight = 7689.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.147990 restraints weight = 4663.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151411 restraints weight = 3422.467| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6394 Z= 0.210 Angle : 0.580 9.930 8665 Z= 0.305 Chirality : 0.040 0.224 948 Planarity : 0.004 0.050 1049 Dihedral : 5.344 51.105 1015 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.52 % Allowed : 23.21 % Favored : 72.27 % 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: 0.32 (0.26), residues: 366 sheet: -0.95 (0.51), residues: 96 loop : -1.65 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 220 HIS 0.002 0.001 HIS A 143 PHE 0.022 0.001 PHE A 407 TYR 0.014 0.001 TYR B 99 ARG 0.005 0.000 ARG B 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2428.53 seconds wall clock time: 44 minutes 21.28 seconds (2661.28 seconds total)