Starting phenix.real_space_refine on Thu Jul 2 04:32:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lia_23365/07_2026/7lia_23365.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lia_23365/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lia_23365/07_2026/7lia_23365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lia_23365/07_2026/7lia_23365.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lia_23365/07_2026/7lia_23365.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lia_23365/07_2026/7lia_23365.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lia_23365/07_2026/7lia_23365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lia_23365/07_2026/7lia_23365.map" } 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-6108/lib/python3.11/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 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: 1.41, per 1000 atoms: 0.22 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: 0.59 Conformation dependent library (CDL) restraints added in 356.4 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: 0.20 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: 1.19 Time building geometry restraints manager: 0.79 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: 3314 17.83 - 35.66: 283 35.66 - 53.49: 46 53.49 - 71.32: 10 71.32 - 89.15: 7 Dihedral angle restraints: 3660 sinusoidal: 1454 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 3657 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.840 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 7.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 13.655 89.147 2251 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/Z covalent geometry : bond 0.00260 / 0.14 ( 6442) covalent geometry : angle 0.63273 / 0.30 ( 8712) SS BOND : bond 0.00054 / 0.03 ( 3) SS BOND : angle 0.09228 / 0.05 ( 6) hydrogen bonds : bond 0.16389 / 10.28 ( 341) hydrogen bonds : angle 6.83203 / 4.84 ( 996) link_BETA1-4 : bond 0.06417 / 3.38 ( 1) link_BETA1-4 : angle 13.92840 / 8.02 ( 3) link_NAG-ASN : bond 0.00539 / 0.28 ( 1) link_NAG-ASN : angle 1.97672 / 1.07 ( 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 : 0.140 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: 0.0916 time to fit residues: 8.3819 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 : 0.138 ------------------------------------------------------------------------------- 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... A 143 HIS A 177 ASN A 223 HIS A 316 ASN A 355 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.211640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.170732 restraints weight = 61714.881| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 9.50 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6447 Z= 0.155 Angle : 0.520 11.954 8724 Z= 0.261 Chirality : 0.041 0.183 951 Planarity : 0.003 0.023 1051 Dihedral : 7.373 82.277 956 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.86 % Allowed : 11.80 % Favored : 86.34 % 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: -1.09 (0.30), residues: 761 helix: 0.76 (0.26), residues: 375 sheet: -1.93 (0.46), residues: 102 loop : -2.27 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.012 0.001 TYR A 312 PHE 0.025 0.002 PHE A 548 TRP 0.013 0.001 TRP A 103 HIS 0.008 0.002 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 6442) covalent geometry : angle 0.51797 / 0.26 ( 8712) SS BOND : bond 0.00215 / 0.11 ( 3) SS BOND : angle 0.59382 / 0.31 ( 6) hydrogen bonds : bond 0.03686 / 2.40 ( 341) hydrogen bonds : angle 4.91258 / 3.55 ( 996) link_BETA1-4 : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : angle 0.78579 / 0.40 ( 3) link_NAG-ASN : bond 0.00631 / 0.33 ( 1) link_NAG-ASN : angle 2.20465 / 1.18 ( 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 69 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.205 Fit side-chains REVERT: A 538 ARG cc_start: 0.7353 (mtp180) cc_final: 0.7132 (mtt-85) REVERT: B 88 THR cc_start: 0.8605 (m) cc_final: 0.8090 (p) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.0683 time to fit residues: 6.3818 Evaluate side-chains 57 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 27 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN A 223 HIS A 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.162415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.147458 restraints weight = 6403.160| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 0.64 r_work: 0.3235 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6447 Z= 0.135 Angle : 0.489 9.395 8724 Z= 0.250 Chirality : 0.040 0.201 951 Planarity : 0.004 0.062 1051 Dihedral : 6.271 82.194 948 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.33 % Allowed : 13.82 % Favored : 83.85 % 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: -0.57 (0.30), residues: 761 helix: 1.09 (0.26), residues: 373 sheet: -1.31 (0.48), residues: 102 loop : -2.02 (0.35), 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 175 PHE 0.024 0.001 PHE A 548 TRP 0.012 0.001 TRP A 103 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6442) covalent geometry : angle 0.48615 / 0.25 ( 8712) SS BOND : bond 0.00542 / 0.28 ( 3) SS BOND : angle 0.32910 / 0.19 ( 6) hydrogen bonds : bond 0.03823 / 2.51 ( 341) hydrogen bonds : angle 4.59714 / 3.31 ( 996) link_BETA1-4 : bond 0.00219 / 0.12 ( 1) link_BETA1-4 : angle 0.48749 / 0.24 ( 3) link_NAG-ASN : bond 0.00610 / 0.32 ( 1) link_NAG-ASN : angle 2.85961 / 1.51 ( 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 65 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.212 Fit side-chains REVERT: A 538 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7976 (mtt-85) REVERT: B 88 THR cc_start: 0.8832 (m) cc_final: 0.8560 (p) outliers start: 15 outliers final: 9 residues processed: 63 average time/residue: 0.0644 time to fit residues: 5.7027 Evaluate side-chains 55 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 0.0370 chunk 52 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.156039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.143767 restraints weight = 6406.885| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 0.80 r_work: 0.3220 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6447 Z= 0.148 Angle : 0.505 8.653 8724 Z= 0.258 Chirality : 0.041 0.215 951 Planarity : 0.004 0.047 1051 Dihedral : 6.406 83.776 948 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.80 % Allowed : 13.66 % Favored : 83.54 % 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: -0.39 (0.30), residues: 761 helix: 1.03 (0.26), residues: 378 sheet: -0.94 (0.49), 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 0.025 0.002 PHE A 548 TRP 0.012 0.001 TRP A 103 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 6442) covalent geometry : angle 0.50084 / 0.26 ( 8712) SS BOND : bond 0.00171 / 0.09 ( 3) SS BOND : angle 0.50783 / 0.29 ( 6) hydrogen bonds : bond 0.03985 / 2.59 ( 341) hydrogen bonds : angle 4.58075 / 3.30 ( 996) link_BETA1-4 : bond 0.00312 / 0.16 ( 1) link_BETA1-4 : angle 0.87889 / 0.45 ( 3) link_NAG-ASN : bond 0.00577 / 0.30 ( 1) link_NAG-ASN : angle 3.33611 / 1.76 ( 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 70 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.209 Fit side-chains REVERT: A 127 PHE cc_start: 0.7189 (m-10) cc_final: 0.6543 (m-80) REVERT: A 212 TYR cc_start: 0.4630 (OUTLIER) cc_final: 0.4371 (m-80) REVERT: A 260 MET cc_start: 0.8083 (mtt) cc_final: 0.7880 (mtt) REVERT: A 416 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7988 (t0) REVERT: A 538 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7998 (mtt-85) outliers start: 18 outliers final: 13 residues processed: 68 average time/residue: 0.0639 time to fit residues: 6.2499 Evaluate side-chains 64 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 56 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3593 r_free = 0.3593 target = 0.153999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.141738 restraints weight = 6404.949| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 0.76 r_work: 0.3199 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6447 Z= 0.163 Angle : 0.523 8.010 8724 Z= 0.268 Chirality : 0.042 0.336 951 Planarity : 0.003 0.040 1051 Dihedral : 6.586 84.387 948 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.26 % Allowed : 14.75 % Favored : 81.99 % 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: -0.19 (0.31), residues: 761 helix: 1.07 (0.26), residues: 378 sheet: -0.55 (0.51), residues: 102 loop : -1.60 (0.38), 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 175 PHE 0.026 0.002 PHE A 548 TRP 0.012 0.001 TRP A 103 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 6442) covalent geometry : angle 0.51768 / 0.27 ( 8712) SS BOND : bond 0.00136 / 0.07 ( 3) SS BOND : angle 0.49553 / 0.27 ( 6) hydrogen bonds : bond 0.04116 / 2.67 ( 341) hydrogen bonds : angle 4.55146 / 3.26 ( 996) link_BETA1-4 : bond 0.00453 / 0.24 ( 1) link_BETA1-4 : angle 0.90955 / 0.46 ( 3) link_NAG-ASN : bond 0.00933 / 0.49 ( 1) link_NAG-ASN : angle 3.96320 / 2.01 ( 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 69 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 127 PHE cc_start: 0.7299 (m-10) cc_final: 0.6649 (m-80) REVERT: A 212 TYR cc_start: 0.4685 (OUTLIER) cc_final: 0.4401 (m-80) REVERT: A 538 ARG cc_start: 0.8306 (mtp180) cc_final: 0.8068 (mtt-85) outliers start: 21 outliers final: 15 residues processed: 66 average time/residue: 0.0654 time to fit residues: 6.1716 Evaluate side-chains 64 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.155334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.143306 restraints weight = 6521.540| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 0.76 r_work: 0.3204 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6447 Z= 0.152 Angle : 0.509 8.403 8724 Z= 0.260 Chirality : 0.041 0.257 951 Planarity : 0.004 0.040 1051 Dihedral : 6.640 84.824 948 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.57 % Allowed : 15.37 % 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: -0.02 (0.31), residues: 761 helix: 1.13 (0.26), residues: 380 sheet: -0.36 (0.52), residues: 102 loop : -1.46 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 44 TYR 0.011 0.001 TYR A 175 PHE 0.026 0.002 PHE A 548 TRP 0.020 0.001 TRP A 306 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 6442) covalent geometry : angle 0.50322 / 0.26 ( 8712) SS BOND : bond 0.00076 / 0.04 ( 3) SS BOND : angle 0.41531 / 0.22 ( 6) hydrogen bonds : bond 0.04072 / 2.64 ( 341) hydrogen bonds : angle 4.51603 / 3.25 ( 996) link_BETA1-4 : bond 0.00297 / 0.16 ( 1) link_BETA1-4 : angle 1.06215 / 0.55 ( 3) link_NAG-ASN : bond 0.00938 / 0.49 ( 1) link_NAG-ASN : angle 3.88336 / 2.01 ( 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 74 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 127 PHE cc_start: 0.7565 (m-10) cc_final: 0.7170 (m-10) REVERT: A 212 TYR cc_start: 0.5131 (OUTLIER) cc_final: 0.4681 (m-80) REVERT: A 306 TRP cc_start: 0.7720 (p-90) cc_final: 0.7309 (t-100) REVERT: A 416 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.7580 (t0) REVERT: A 538 ARG cc_start: 0.8386 (mtp180) cc_final: 0.8080 (mtt-85) REVERT: B 29 GLU cc_start: 0.7970 (mp0) cc_final: 0.7698 (mp0) outliers start: 23 outliers final: 18 residues processed: 71 average time/residue: 0.0646 time to fit residues: 6.5219 Evaluate side-chains 69 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 9 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.155969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.144222 restraints weight = 6437.330| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 0.74 r_work: 0.3213 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6447 Z= 0.129 Angle : 0.486 8.176 8724 Z= 0.249 Chirality : 0.040 0.252 951 Planarity : 0.003 0.039 1051 Dihedral : 6.568 85.488 948 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.42 % Allowed : 15.99 % Favored : 80.59 % 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: 0.15 (0.31), residues: 761 helix: 1.25 (0.26), residues: 380 sheet: -0.08 (0.52), residues: 102 loop : -1.43 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 A 103 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6442) covalent geometry : angle 0.48107 / 0.25 ( 8712) SS BOND : bond 0.00098 / 0.05 ( 3) SS BOND : angle 0.30068 / 0.16 ( 6) hydrogen bonds : bond 0.03910 / 2.55 ( 341) hydrogen bonds : angle 4.41741 / 3.18 ( 996) link_BETA1-4 : bond 0.00324 / 0.17 ( 1) link_BETA1-4 : angle 1.12496 / 0.59 ( 3) link_NAG-ASN : bond 0.00913 / 0.48 ( 1) link_NAG-ASN : angle 3.61309 / 1.86 ( 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 69 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.218 Fit side-chains REVERT: A 212 TYR cc_start: 0.4851 (OUTLIER) cc_final: 0.4542 (m-80) REVERT: A 416 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7843 (t0) outliers start: 22 outliers final: 17 residues processed: 65 average time/residue: 0.0602 time to fit residues: 5.7399 Evaluate side-chains 65 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.153423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.140824 restraints weight = 6404.241| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 0.82 r_work: 0.3184 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6447 Z= 0.140 Angle : 0.497 7.829 8724 Z= 0.255 Chirality : 0.040 0.249 951 Planarity : 0.003 0.038 1051 Dihedral : 6.622 85.967 948 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.57 % Allowed : 16.15 % Favored : 80.28 % 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: 0.22 (0.31), residues: 761 helix: 1.28 (0.26), residues: 379 sheet: 0.06 (0.53), residues: 102 loop : -1.40 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.012 0.001 TYR A 175 PHE 0.025 0.001 PHE A 548 TRP 0.019 0.001 TRP A 306 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6442) covalent geometry : angle 0.49259 / 0.25 ( 8712) SS BOND : bond 0.00087 / 0.04 ( 3) SS BOND : angle 0.30298 / 0.16 ( 6) hydrogen bonds : bond 0.03957 / 2.57 ( 341) hydrogen bonds : angle 4.43845 / 3.20 ( 996) link_BETA1-4 : bond 0.00297 / 0.16 ( 1) link_BETA1-4 : angle 1.12034 / 0.59 ( 3) link_NAG-ASN : bond 0.00848 / 0.45 ( 1) link_NAG-ASN : angle 3.63718 / 1.88 ( 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 66 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.179 Fit side-chains REVERT: A 212 TYR cc_start: 0.4878 (OUTLIER) cc_final: 0.4549 (m-80) REVERT: A 416 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7903 (t0) outliers start: 23 outliers final: 19 residues processed: 63 average time/residue: 0.0612 time to fit residues: 5.6331 Evaluate side-chains 64 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.155109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.143156 restraints weight = 6481.179| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 0.76 r_work: 0.3202 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3111 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= 0.139 Angle : 0.499 7.618 8724 Z= 0.256 Chirality : 0.041 0.248 951 Planarity : 0.003 0.038 1051 Dihedral : 6.627 86.042 948 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.42 % Allowed : 15.99 % Favored : 80.59 % 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: 0.29 (0.31), residues: 761 helix: 1.33 (0.26), residues: 378 sheet: 0.18 (0.53), residues: 102 loop : -1.37 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.012 0.001 TYR A 175 PHE 0.027 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/Z covalent geometry : bond 0.00325 / 0.14 ( 6442) covalent geometry : angle 0.49431 / 0.26 ( 8712) SS BOND : bond 0.00077 / 0.04 ( 3) SS BOND : angle 0.33403 / 0.18 ( 6) hydrogen bonds : bond 0.03971 / 2.59 ( 341) hydrogen bonds : angle 4.43099 / 3.20 ( 996) link_BETA1-4 : bond 0.00355 / 0.19 ( 1) link_BETA1-4 : angle 1.14646 / 0.60 ( 3) link_NAG-ASN : bond 0.00856 / 0.45 ( 1) link_NAG-ASN : angle 3.63567 / 1.88 ( 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 69 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.220 Fit side-chains REVERT: A 127 PHE cc_start: 0.7616 (m-10) cc_final: 0.7180 (m-10) REVERT: A 212 TYR cc_start: 0.5140 (OUTLIER) cc_final: 0.4664 (m-80) REVERT: A 306 TRP cc_start: 0.7966 (t-100) cc_final: 0.6839 (p-90) REVERT: A 416 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7980 (t0) outliers start: 22 outliers final: 19 residues processed: 65 average time/residue: 0.0561 time to fit residues: 5.2885 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 : 0.207 ------------------------------------------------------------------------------- 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 82 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.154337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.142119 restraints weight = 6494.814| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 0.79 r_work: 0.3176 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6447 Z= 0.148 Angle : 0.507 7.565 8724 Z= 0.260 Chirality : 0.041 0.250 951 Planarity : 0.003 0.037 1051 Dihedral : 6.724 86.441 948 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.57 % Allowed : 15.99 % Favored : 80.43 % 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: 0.24 (0.54), residues: 102 loop : -1.35 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.012 0.001 TYR A 175 PHE 0.026 0.001 PHE A 548 TRP 0.010 0.001 TRP A 103 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 6442) covalent geometry : angle 0.50203 / 0.26 ( 8712) SS BOND : bond 0.00079 / 0.04 ( 3) SS BOND : angle 0.31872 / 0.18 ( 6) hydrogen bonds : bond 0.04050 / 2.64 ( 341) hydrogen bonds : angle 4.46456 / 3.22 ( 996) link_BETA1-4 : bond 0.00276 / 0.15 ( 1) link_BETA1-4 : angle 1.14356 / 0.60 ( 3) link_NAG-ASN : bond 0.00834 / 0.44 ( 1) link_NAG-ASN : angle 3.70946 / 1.92 ( 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 69 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.201 Fit side-chains REVERT: A 127 PHE cc_start: 0.7540 (m-10) cc_final: 0.7153 (m-10) REVERT: A 212 TYR cc_start: 0.4931 (OUTLIER) cc_final: 0.4584 (m-80) REVERT: A 416 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7910 (t0) outliers start: 23 outliers final: 20 residues processed: 65 average time/residue: 0.0593 time to fit residues: 5.6429 Evaluate side-chains 69 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 B residue 127 MET Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 82 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.0970 chunk 72 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 0.0040 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.156569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.144673 restraints weight = 6384.167| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 0.76 r_work: 0.3218 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3116 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= 0.115 Angle : 0.476 7.739 8724 Z= 0.245 Chirality : 0.040 0.240 951 Planarity : 0.003 0.038 1051 Dihedral : 6.532 86.541 948 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.26 % Allowed : 16.46 % Favored : 80.28 % 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: 0.47 (0.31), residues: 761 helix: 1.46 (0.26), residues: 379 sheet: 0.34 (0.53), residues: 103 loop : -1.32 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 44 TYR 0.012 0.001 TYR A 175 PHE 0.025 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/Z covalent geometry : bond 0.00261 / 0.12 ( 6442) covalent geometry : angle 0.47187 / 0.24 ( 8712) SS BOND : bond 0.00076 / 0.04 ( 3) SS BOND : angle 0.30695 / 0.16 ( 6) hydrogen bonds : bond 0.03771 / 2.46 ( 341) hydrogen bonds : angle 4.34020 / 3.13 ( 996) link_BETA1-4 : bond 0.00348 / 0.18 ( 1) link_BETA1-4 : angle 1.23405 / 0.65 ( 3) link_NAG-ASN : bond 0.00922 / 0.49 ( 1) link_NAG-ASN : angle 3.43424 / 1.77 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1338.49 seconds wall clock time: 23 minutes 51.24 seconds (1431.24 seconds total)