Starting phenix.real_space_refine on Tue Mar 3 15:35:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lia_23365/03_2026/7lia_23365.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lia_23365/03_2026/7lia_23365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lia_23365/03_2026/7lia_23365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lia_23365/03_2026/7lia_23365.map" model { file = "/net/cci-nas-00/data/ceres_data/7lia_23365/03_2026/7lia_23365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lia_23365/03_2026/7lia_23365.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 4190 2.51 5 N 966 2.21 5 O 1086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6279 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4305 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 23, 'TRANS': 515} 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: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} 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: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 203 Unusual residues: {' CL': 1, ' NA': 2, 'CLR': 1, 'D10': 5, 'HP6': 13, 'LNK': 1, 'SRO': 2} Classifications: {'undetermined': 25} Link IDs: {None: 24} Time building chain proxies: 1.48, per 1000 atoms: 0.24 Number of scatterers: 6279 At special positions: 0 Unit cell: (77.76, 78.408, 121.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 2 11.00 O 1086 8.00 N 966 7.00 C 4190 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 234.8 milliseconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 57.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 4.168A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 4.345A pdb=" N TRP A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 156 through 159 removed outlier: 3.533A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 160 through 190 removed outlier: 4.009A pdb=" N TYR A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.708A pdb=" N SER A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.717A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 313 removed outlier: 3.865A pdb=" N GLY A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.746A pdb=" N LEU A 321 " --> pdb=" O GLN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.884A pdb=" N TYR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 391 Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.607A pdb=" N PHE A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 454 removed outlier: 3.697A pdb=" N PHE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 458 Processing helix chain 'A' and resid 461 through 478 Processing helix chain 'A' and resid 484 through 496 removed outlier: 4.326A pdb=" N VAL A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.821A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.941A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Proline residue: A 546 - end of helix removed outlier: 3.885A pdb=" N MET A 558 " --> pdb=" O CYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 587 removed outlier: 4.112A pdb=" N ILE A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 603 through 613 Processing helix chain 'B' and resid 47 through 51 removed outlier: 4.078A pdb=" N SER B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.970A pdb=" N GLY B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.700A pdb=" N SER B 110 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 25 Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.790A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 56 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR B 129 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.790A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 56 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 24 through 27 removed outlier: 3.978A pdb=" N TYR C 94 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 32 removed outlier: 7.000A pdb=" N LEU C 31 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 996 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: 1.04 Time building geometry restraints manager: 0.94 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: 1822 1.34 - 1.46: 1600 1.46 - 1.58: 2971 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6442 Sorted by residual: bond pdb=" CD1 SRO A 905 " pdb=" NE1 SRO A 905 " ideal model delta sigma weight residual 1.377 1.323 0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" CD1 SRO A 901 " pdb=" NE1 SRO A 901 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" CD2 SRO A 901 " pdb=" CE2 SRO A 901 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" CD2 SRO A 905 " pdb=" CE2 SRO A 905 " ideal model delta sigma weight residual 1.419 1.371 0.048 2.00e-02 2.50e+03 5.85e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 6437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 8346 1.19 - 2.37: 197 2.37 - 3.56: 80 3.56 - 4.74: 79 4.74 - 5.93: 10 Bond angle restraints: 8712 Sorted by residual: angle pdb=" C CYS A 588 " pdb=" N ILE A 589 " pdb=" CA ILE A 589 " ideal model delta sigma weight residual 120.33 122.59 -2.26 8.00e-01 1.56e+00 8.00e+00 angle pdb=" N GLY A 128 " pdb=" CA GLY A 128 " pdb=" C GLY A 128 " ideal model delta sigma weight residual 113.18 118.19 -5.01 2.37e+00 1.78e-01 4.47e+00 angle pdb=" CA GLY B 131 " pdb=" C GLY B 131 " pdb=" N GLN B 132 " ideal model delta sigma weight residual 114.61 117.13 -2.52 1.26e+00 6.30e-01 3.99e+00 angle pdb=" N VAL A 542 " pdb=" CA VAL A 542 " pdb=" C VAL A 542 " ideal model delta sigma weight residual 113.42 111.10 2.32 1.17e+00 7.31e-01 3.92e+00 angle pdb=" C13 CLR A 925 " pdb=" C17 CLR A 925 " pdb=" C20 CLR A 925 " ideal model delta sigma weight residual 119.60 113.67 5.93 3.00e+00 1.11e-01 3.90e+00 ... (remaining 8707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3401 17.83 - 35.66: 293 35.66 - 53.49: 47 53.49 - 71.32: 10 71.32 - 89.15: 7 Dihedral angle restraints: 3758 sinusoidal: 1552 harmonic: 2206 Sorted by residual: dihedral pdb=" CB GLU A 527 " pdb=" CG GLU A 527 " pdb=" CD GLU A 527 " pdb=" OE1 GLU A 527 " ideal model delta sinusoidal sigma weight residual 0.00 -89.15 89.15 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 615 " pdb=" CG GLU A 615 " pdb=" CD GLU A 615 " pdb=" OE1 GLU A 615 " ideal model delta sinusoidal sigma weight residual 0.00 -85.88 85.88 1 3.00e+01 1.11e-03 9.90e+00 dihedral pdb=" CB MET A 370 " pdb=" CG MET A 370 " pdb=" SD MET A 370 " pdb=" CE MET A 370 " ideal model delta sinusoidal sigma weight residual 60.00 117.91 -57.91 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 949 0.321 - 0.641: 1 0.641 - 0.962: 0 0.962 - 1.282: 0 1.282 - 1.603: 1 Chirality restraints: 951 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 -0.80 -1.60 2.00e-02 2.50e+03 6.42e+03 chirality pdb=" C14 CLR A 925 " pdb=" C13 CLR A 925 " pdb=" C15 CLR A 925 " pdb=" C8 CLR A 925 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C17 CLR A 925 " pdb=" C13 CLR A 925 " pdb=" C16 CLR A 925 " pdb=" C20 CLR A 925 " both_signs ideal model delta sigma weight residual False 2.55 2.78 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 948 not shown) Planarity restraints: 1052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 548 " -0.011 2.00e-02 2.50e+03 8.96e-03 1.40e+00 pdb=" CG PHE A 548 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 548 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 548 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 548 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 548 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 548 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 125 " 0.004 2.00e-02 2.50e+03 8.57e-03 7.35e-01 pdb=" C ALA A 125 " -0.015 2.00e-02 2.50e+03 pdb=" O ALA A 125 " 0.006 2.00e-02 2.50e+03 pdb=" N ILE A 126 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 406 " 0.004 2.00e-02 2.50e+03 8.44e-03 7.12e-01 pdb=" C LEU A 406 " -0.015 2.00e-02 2.50e+03 pdb=" O LEU A 406 " 0.006 2.00e-02 2.50e+03 pdb=" N PHE A 407 " 0.005 2.00e-02 2.50e+03 ... (remaining 1049 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1608 2.79 - 3.32: 5702 3.32 - 3.85: 10809 3.85 - 4.37: 12450 4.37 - 4.90: 21788 Nonbonded interactions: 52357 Sorted by model distance: nonbonded pdb=" O CYS A 147 " pdb=" NE1 TRP A 151 " model vdw 2.266 3.120 nonbonded pdb=" O SER A 395 " pdb=" OG SER A 395 " model vdw 2.283 3.040 nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR A 210 " pdb=" OG SER A 224 " model vdw 2.324 3.040 nonbonded pdb=" O ARG A 607 " pdb=" OG SER A 611 " model vdw 2.326 3.040 ... (remaining 52352 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.680 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 0.064 6447 Z= 0.144 Angle : 0.684 21.606 8724 Z= 0.311 Chirality : 0.065 1.603 951 Planarity : 0.003 0.020 1051 Dihedral : 13.551 89.147 2349 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.71 % Allowed : 8.85 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.28), residues: 761 helix: -0.17 (0.25), residues: 364 sheet: -2.68 (0.45), residues: 101 loop : -2.86 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 152 TYR 0.008 0.001 TYR A 175 PHE 0.020 0.001 PHE A 548 TRP 0.011 0.001 TRP A 220 HIS 0.001 0.000 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6442) covalent geometry : angle 0.63273 ( 8712) SS BOND : bond 0.00054 ( 3) SS BOND : angle 0.09228 ( 6) hydrogen bonds : bond 0.16389 ( 341) hydrogen bonds : angle 6.83203 ( 996) link_BETA1-4 : bond 0.06417 ( 1) link_BETA1-4 : angle 13.92840 ( 3) link_NAG-ASN : bond 0.00539 ( 1) link_NAG-ASN : angle 1.97672 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.165 Fit side-chains REVERT: A 410 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: A 538 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7707 (mtt-85) outliers start: 11 outliers final: 10 residues processed: 71 average time/residue: 0.1074 time to fit residues: 9.8461 Evaluate side-chains 61 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 615 GLU 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 223 HIS A 316 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 416 ASN C 26 GLN C 77 ASN C 78 GLN C 113 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.165750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.151400 restraints weight = 6360.203| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 0.64 r_work: 0.3291 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6447 Z= 0.155 Angle : 0.538 12.142 8724 Z= 0.270 Chirality : 0.041 0.193 951 Planarity : 0.003 0.023 1051 Dihedral : 7.291 82.320 1054 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.86 % Allowed : 12.73 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.30), residues: 761 helix: 0.76 (0.26), residues: 376 sheet: -1.93 (0.46), residues: 101 loop : -2.21 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 44 TYR 0.012 0.001 TYR A 312 PHE 0.025 0.002 PHE A 548 TRP 0.014 0.001 TRP A 103 HIS 0.005 0.001 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6442) covalent geometry : angle 0.53648 ( 8712) SS BOND : bond 0.00193 ( 3) SS BOND : angle 0.63063 ( 6) hydrogen bonds : bond 0.03717 ( 341) hydrogen bonds : angle 4.89527 ( 996) link_BETA1-4 : bond 0.00662 ( 1) link_BETA1-4 : angle 0.70942 ( 3) link_NAG-ASN : bond 0.01023 ( 1) link_NAG-ASN : angle 2.44088 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.196 Fit side-chains REVERT: A 538 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7952 (mtt-85) REVERT: B 88 THR cc_start: 0.8797 (m) cc_final: 0.8519 (p) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.0809 time to fit residues: 7.9526 Evaluate side-chains 63 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 615 GLU 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 3 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 211 ASN A 223 HIS A 355 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.159327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.147140 restraints weight = 6374.785| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 0.78 r_work: 0.3246 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6447 Z= 0.150 Angle : 0.510 8.940 8724 Z= 0.261 Chirality : 0.042 0.379 951 Planarity : 0.004 0.059 1051 Dihedral : 6.366 81.389 1046 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.64 % Allowed : 14.44 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.30), residues: 761 helix: 1.01 (0.26), residues: 373 sheet: -1.32 (0.48), residues: 102 loop : -1.97 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.011 0.001 TYR A 312 PHE 0.025 0.002 PHE A 548 TRP 0.011 0.001 TRP A 103 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6442) covalent geometry : angle 0.50587 ( 8712) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.42055 ( 6) hydrogen bonds : bond 0.04079 ( 341) hydrogen bonds : angle 4.67121 ( 996) link_BETA1-4 : bond 0.01153 ( 1) link_BETA1-4 : angle 0.76971 ( 3) link_NAG-ASN : bond 0.00773 ( 1) link_NAG-ASN : angle 3.61970 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.219 Fit side-chains REVERT: A 127 PHE cc_start: 0.7034 (m-10) cc_final: 0.6301 (m-80) REVERT: A 260 MET cc_start: 0.8074 (mtt) cc_final: 0.7769 (mtt) REVERT: A 538 ARG cc_start: 0.8241 (mtp180) cc_final: 0.8007 (mtt-85) outliers start: 17 outliers final: 12 residues processed: 66 average time/residue: 0.0704 time to fit residues: 6.7437 Evaluate side-chains 56 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.156499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.143122 restraints weight = 6447.765| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 0.84 r_work: 0.3173 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6447 Z= 0.155 Angle : 0.510 8.861 8724 Z= 0.262 Chirality : 0.042 0.278 951 Planarity : 0.003 0.045 1051 Dihedral : 6.366 82.697 1046 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.64 % Allowed : 15.06 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.31), residues: 761 helix: 0.98 (0.26), residues: 378 sheet: -0.83 (0.51), residues: 102 loop : -1.76 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.011 0.001 TYR A 312 PHE 0.026 0.002 PHE A 548 TRP 0.012 0.001 TRP A 103 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6442) covalent geometry : angle 0.50499 ( 8712) SS BOND : bond 0.00171 ( 3) SS BOND : angle 0.45056 ( 6) hydrogen bonds : bond 0.04021 ( 341) hydrogen bonds : angle 4.59924 ( 996) link_BETA1-4 : bond 0.00111 ( 1) link_BETA1-4 : angle 0.79867 ( 3) link_NAG-ASN : bond 0.01165 ( 1) link_NAG-ASN : angle 3.99162 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.230 Fit side-chains REVERT: A 127 PHE cc_start: 0.7242 (m-10) cc_final: 0.6617 (m-80) REVERT: A 212 TYR cc_start: 0.4683 (OUTLIER) cc_final: 0.4377 (m-80) REVERT: A 416 ASN cc_start: 0.8301 (t160) cc_final: 0.7507 (t0) REVERT: A 538 ARG cc_start: 0.8300 (mtp180) cc_final: 0.8043 (mtt-85) outliers start: 17 outliers final: 12 residues processed: 63 average time/residue: 0.0720 time to fit residues: 6.4318 Evaluate side-chains 60 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 70 optimal weight: 0.0770 chunk 42 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.156384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.143969 restraints weight = 6465.664| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 0.79 r_work: 0.3225 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6447 Z= 0.129 Angle : 0.501 10.345 8724 Z= 0.253 Chirality : 0.040 0.268 951 Planarity : 0.003 0.042 1051 Dihedral : 6.280 83.888 1046 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.42 % Allowed : 14.29 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.31), residues: 761 helix: 1.11 (0.26), residues: 378 sheet: -0.57 (0.52), residues: 102 loop : -1.64 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.011 0.001 TYR A 175 PHE 0.025 0.001 PHE A 548 TRP 0.017 0.001 TRP A 306 HIS 0.001 0.000 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6442) covalent geometry : angle 0.49596 ( 8712) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.29606 ( 6) hydrogen bonds : bond 0.03910 ( 341) hydrogen bonds : angle 4.50611 ( 996) link_BETA1-4 : bond 0.00439 ( 1) link_BETA1-4 : angle 0.98491 ( 3) link_NAG-ASN : bond 0.00937 ( 1) link_NAG-ASN : angle 3.74750 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.225 Fit side-chains REVERT: A 212 TYR cc_start: 0.4601 (OUTLIER) cc_final: 0.4308 (m-80) REVERT: A 416 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7473 (t0) outliers start: 22 outliers final: 16 residues processed: 62 average time/residue: 0.0719 time to fit residues: 6.3786 Evaluate side-chains 62 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 TYR 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 274 VAL Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.155904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.143761 restraints weight = 6427.432| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 0.79 r_work: 0.3189 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6447 Z= 0.149 Angle : 0.509 8.185 8724 Z= 0.261 Chirality : 0.041 0.267 951 Planarity : 0.003 0.038 1051 Dihedral : 6.422 85.139 1046 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.42 % Allowed : 15.53 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.31), residues: 761 helix: 1.09 (0.26), residues: 380 sheet: -0.44 (0.52), residues: 102 loop : -1.53 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.011 0.001 TYR A 175 PHE 0.025 0.001 PHE A 548 TRP 0.011 0.001 TRP A 103 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6442) covalent geometry : angle 0.50432 ( 8712) SS BOND : bond 0.00078 ( 3) SS BOND : angle 0.30299 ( 6) hydrogen bonds : bond 0.03978 ( 341) hydrogen bonds : angle 4.50898 ( 996) link_BETA1-4 : bond 0.00381 ( 1) link_BETA1-4 : angle 1.08020 ( 3) link_NAG-ASN : bond 0.00861 ( 1) link_NAG-ASN : angle 3.83721 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.227 Fit side-chains REVERT: A 127 PHE cc_start: 0.7351 (m-10) cc_final: 0.6876 (m-10) REVERT: A 212 TYR cc_start: 0.4652 (OUTLIER) cc_final: 0.4325 (m-80) REVERT: A 416 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7466 (t0) outliers start: 22 outliers final: 18 residues processed: 69 average time/residue: 0.0768 time to fit residues: 7.4396 Evaluate side-chains 68 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 TYR 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 274 VAL Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.153865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.141353 restraints weight = 6386.538| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 0.78 r_work: 0.3163 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6447 Z= 0.161 Angle : 0.517 8.090 8724 Z= 0.265 Chirality : 0.041 0.264 951 Planarity : 0.004 0.038 1051 Dihedral : 6.544 85.451 1046 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.42 % Allowed : 16.61 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.31), residues: 761 helix: 1.12 (0.26), residues: 379 sheet: -0.14 (0.52), residues: 102 loop : -1.50 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.012 0.001 TYR A 175 PHE 0.026 0.002 PHE A 548 TRP 0.019 0.001 TRP A 306 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6442) covalent geometry : angle 0.51194 ( 8712) SS BOND : bond 0.00072 ( 3) SS BOND : angle 0.33923 ( 6) hydrogen bonds : bond 0.04119 ( 341) hydrogen bonds : angle 4.51615 ( 996) link_BETA1-4 : bond 0.00354 ( 1) link_BETA1-4 : angle 1.17416 ( 3) link_NAG-ASN : bond 0.00895 ( 1) link_NAG-ASN : angle 3.91660 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.142 Fit side-chains REVERT: A 127 PHE cc_start: 0.7466 (m-10) cc_final: 0.6998 (m-10) REVERT: A 212 TYR cc_start: 0.4873 (OUTLIER) cc_final: 0.4511 (m-80) REVERT: A 416 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.7547 (t0) outliers start: 22 outliers final: 19 residues processed: 69 average time/residue: 0.0624 time to fit residues: 6.2133 Evaluate side-chains 72 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 TYR 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 274 VAL Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 57 optimal weight: 0.0370 chunk 26 optimal weight: 0.0970 chunk 52 optimal weight: 5.9990 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.158688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.146946 restraints weight = 6392.669| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 0.74 r_work: 0.3272 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6447 Z= 0.098 Angle : 0.459 8.076 8724 Z= 0.236 Chirality : 0.039 0.245 951 Planarity : 0.003 0.039 1051 Dihedral : 6.178 86.612 1046 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.95 % Allowed : 18.01 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.31), residues: 761 helix: 1.40 (0.26), residues: 379 sheet: 0.11 (0.53), residues: 102 loop : -1.43 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 564 TYR 0.012 0.001 TYR A 175 PHE 0.023 0.001 PHE A 548 TRP 0.010 0.001 TRP B 66 HIS 0.002 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 6442) covalent geometry : angle 0.45399 ( 8712) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.22538 ( 6) hydrogen bonds : bond 0.03577 ( 341) hydrogen bonds : angle 4.29758 ( 996) link_BETA1-4 : bond 0.00298 ( 1) link_BETA1-4 : angle 1.36387 ( 3) link_NAG-ASN : bond 0.00998 ( 1) link_NAG-ASN : angle 3.40966 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.226 Fit side-chains REVERT: A 212 TYR cc_start: 0.4604 (OUTLIER) cc_final: 0.4265 (m-80) REVERT: A 230 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8240 (mt-10) REVERT: A 416 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7752 (t0) outliers start: 19 outliers final: 14 residues processed: 63 average time/residue: 0.0680 time to fit residues: 6.2787 Evaluate side-chains 60 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 127 MET 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 55 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 49 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 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 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.156268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.143018 restraints weight = 6414.079| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 0.80 r_work: 0.3180 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6447 Z= 0.132 Angle : 0.486 7.358 8724 Z= 0.249 Chirality : 0.040 0.253 951 Planarity : 0.003 0.039 1051 Dihedral : 6.280 86.635 1046 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.80 % Allowed : 17.86 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.31), residues: 761 helix: 1.43 (0.26), residues: 379 sheet: 0.16 (0.53), residues: 103 loop : -1.42 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 44 TYR 0.012 0.001 TYR A 175 PHE 0.025 0.001 PHE A 548 TRP 0.010 0.001 TRP B 66 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6442) covalent geometry : angle 0.48145 ( 8712) SS BOND : bond 0.00105 ( 3) SS BOND : angle 0.25318 ( 6) hydrogen bonds : bond 0.03798 ( 341) hydrogen bonds : angle 4.35232 ( 996) link_BETA1-4 : bond 0.00338 ( 1) link_BETA1-4 : angle 1.28432 ( 3) link_NAG-ASN : bond 0.00839 ( 1) link_NAG-ASN : angle 3.57454 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.190 Fit side-chains REVERT: A 212 TYR cc_start: 0.4774 (OUTLIER) cc_final: 0.4401 (m-80) REVERT: A 230 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8328 (mt-10) REVERT: A 306 TRP cc_start: 0.7754 (t-100) cc_final: 0.7111 (p-90) REVERT: A 416 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7853 (t0) outliers start: 18 outliers final: 16 residues processed: 61 average time/residue: 0.0678 time to fit residues: 5.9383 Evaluate side-chains 64 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.155630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.142311 restraints weight = 6385.252| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 0.80 r_work: 0.3190 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6447 Z= 0.113 Angle : 0.473 7.530 8724 Z= 0.242 Chirality : 0.040 0.244 951 Planarity : 0.003 0.039 1051 Dihedral : 6.203 86.805 1046 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.26 % Allowed : 17.55 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.31), residues: 761 helix: 1.49 (0.26), residues: 379 sheet: 0.28 (0.54), residues: 103 loop : -1.37 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 44 TYR 0.012 0.001 TYR A 175 PHE 0.024 0.001 PHE A 548 TRP 0.009 0.001 TRP A 103 HIS 0.002 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6442) covalent geometry : angle 0.46790 ( 8712) SS BOND : bond 0.00100 ( 3) SS BOND : angle 0.24615 ( 6) hydrogen bonds : bond 0.03666 ( 341) hydrogen bonds : angle 4.30243 ( 996) link_BETA1-4 : bond 0.00392 ( 1) link_BETA1-4 : angle 1.33778 ( 3) link_NAG-ASN : bond 0.00921 ( 1) link_NAG-ASN : angle 3.43268 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.215 Fit side-chains REVERT: A 212 TYR cc_start: 0.4716 (OUTLIER) cc_final: 0.4317 (m-80) REVERT: A 230 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8342 (mt-10) REVERT: A 306 TRP cc_start: 0.7731 (t-100) cc_final: 0.7094 (p-90) REVERT: A 416 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7827 (t0) outliers start: 21 outliers final: 17 residues processed: 64 average time/residue: 0.0661 time to fit residues: 6.1784 Evaluate side-chains 64 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.153499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.140109 restraints weight = 6496.727| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.81 r_work: 0.3125 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6447 Z= 0.198 Angle : 0.528 7.299 8724 Z= 0.272 Chirality : 0.042 0.265 951 Planarity : 0.004 0.036 1051 Dihedral : 6.201 86.190 1044 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.95 % Allowed : 18.32 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.31), residues: 761 helix: 1.32 (0.26), residues: 379 sheet: 0.27 (0.53), residues: 103 loop : -1.35 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.012 0.001 TYR A 312 PHE 0.029 0.002 PHE A 548 TRP 0.012 0.001 TRP A 103 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 6442) covalent geometry : angle 0.52378 ( 8712) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.42985 ( 6) hydrogen bonds : bond 0.04095 ( 341) hydrogen bonds : angle 4.43544 ( 996) link_BETA1-4 : bond 0.00271 ( 1) link_BETA1-4 : angle 1.20945 ( 3) link_NAG-ASN : bond 0.00865 ( 1) link_NAG-ASN : angle 3.69037 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1425.54 seconds wall clock time: 25 minutes 16.12 seconds (1516.12 seconds total)