Starting phenix.real_space_refine on Tue Mar 11 20:56:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lia_23365/03_2025/7lia_23365.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lia_23365/03_2025/7lia_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_2025/7lia_23365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lia_23365/03_2025/7lia_23365.map" model { file = "/net/cci-nas-00/data/ceres_data/7lia_23365/03_2025/7lia_23365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lia_23365/03_2025/7lia_23365.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.068 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.61, per 1000 atoms: 0.73 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: 2.29 Conformation dependent library (CDL) restraints added in 930.3 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: 0.64 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: 1.83 Time building geometry restraints manager: 2.17 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.130 Find NCS groups from input model: 0.070 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- 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 0.054 6442 Z= 0.164 Angle : 0.633 5.928 8712 Z= 0.299 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 : 8.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (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 TRP 0.011 0.001 TRP A 220 HIS 0.001 0.000 HIS A 223 PHE 0.020 0.001 PHE A 548 TYR 0.008 0.001 TYR A 175 ARG 0.001 0.000 ARG A 152 *********************** 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 : 0.629 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: 0.2380 time to fit residues: 21.8532 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 : 0.879 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.0370 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 0.0070 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 177 ASN A 223 HIS A 316 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN C 26 GLN C 77 ASN C 78 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.213943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.176885 restraints weight = 61419.085| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 9.66 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6442 Z= 0.149 Angle : 0.473 12.360 8712 Z= 0.234 Chirality : 0.039 0.172 951 Planarity : 0.003 0.023 1051 Dihedral : 7.200 82.452 1054 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.55 % Allowed : 12.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.30), residues: 761 helix: 0.88 (0.26), residues: 374 sheet: -1.87 (0.47), residues: 101 loop : -2.33 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 103 HIS 0.006 0.001 HIS A 223 PHE 0.021 0.001 PHE A 548 TYR 0.009 0.001 TYR C 73 ARG 0.002 0.000 ARG C 44 *********************** 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: 10 poor density : 59 time to evaluate : 0.596 Fit side-chains REVERT: B 88 THR cc_start: 0.8611 (m) cc_final: 0.8115 (p) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.1760 time to fit residues: 16.3078 Evaluate side-chains 57 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 223 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN C 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.159450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.146212 restraints weight = 6292.882| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 0.82 r_work: 0.3217 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6442 Z= 0.262 Angle : 0.540 9.586 8712 Z= 0.279 Chirality : 0.042 0.221 951 Planarity : 0.004 0.069 1051 Dihedral : 6.372 81.427 1045 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.17 % Allowed : 13.82 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.30), residues: 761 helix: 0.94 (0.26), residues: 373 sheet: -1.45 (0.47), residues: 102 loop : -2.02 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 103 HIS 0.004 0.001 HIS A 235 PHE 0.026 0.002 PHE A 548 TYR 0.015 0.002 TYR A 312 ARG 0.004 0.000 ARG C 44 *********************** 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 72 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.684 Fit side-chains REVERT: B 88 THR cc_start: 0.8840 (m) cc_final: 0.8575 (p) outliers start: 14 outliers final: 12 residues processed: 70 average time/residue: 0.1874 time to fit residues: 18.1054 Evaluate side-chains 62 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN 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 = 0.3605 r_free = 0.3605 target = 0.155275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.142769 restraints weight = 6393.497| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 0.80 r_work: 0.3182 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6442 Z= 0.269 Angle : 0.533 9.318 8712 Z= 0.274 Chirality : 0.043 0.377 951 Planarity : 0.004 0.051 1051 Dihedral : 6.531 83.263 1045 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.95 % Allowed : 13.82 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.30), residues: 761 helix: 0.93 (0.26), residues: 378 sheet: -0.97 (0.49), residues: 102 loop : -1.75 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 103 HIS 0.002 0.001 HIS A 223 PHE 0.027 0.002 PHE A 548 TYR 0.011 0.001 TYR C 73 ARG 0.004 0.000 ARG C 44 *********************** 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 72 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.667 Fit side-chains REVERT: A 127 PHE cc_start: 0.7300 (m-10) cc_final: 0.6652 (m-80) REVERT: A 416 ASN cc_start: 0.8314 (t160) cc_final: 0.7575 (t0) outliers start: 19 outliers final: 12 residues processed: 70 average time/residue: 0.1633 time to fit residues: 16.1718 Evaluate side-chains 63 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.154595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.140947 restraints weight = 6492.096| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 0.82 r_work: 0.3150 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6442 Z= 0.248 Angle : 0.519 8.643 8712 Z= 0.268 Chirality : 0.042 0.275 951 Planarity : 0.004 0.045 1051 Dihedral : 6.490 84.159 1045 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.95 % Allowed : 15.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.31), residues: 761 helix: 0.99 (0.26), residues: 380 sheet: -0.59 (0.50), residues: 102 loop : -1.64 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 306 HIS 0.002 0.001 HIS A 235 PHE 0.027 0.002 PHE A 548 TYR 0.012 0.001 TYR A 175 ARG 0.003 0.000 ARG C 44 *********************** 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 71 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.628 Fit side-chains REVERT: A 127 PHE cc_start: 0.7468 (m-10) cc_final: 0.7014 (m-10) REVERT: A 212 TYR cc_start: 0.4770 (OUTLIER) cc_final: 0.4457 (m-80) REVERT: A 416 ASN cc_start: 0.8288 (t160) cc_final: 0.7536 (t0) outliers start: 19 outliers final: 16 residues processed: 69 average time/residue: 0.1576 time to fit residues: 15.3378 Evaluate side-chains 67 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 50 ASP 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 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.152987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.140363 restraints weight = 6432.812| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 0.81 r_work: 0.3152 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6442 Z= 0.258 Angle : 0.517 8.512 8712 Z= 0.267 Chirality : 0.042 0.276 951 Planarity : 0.004 0.042 1051 Dihedral : 6.540 84.844 1045 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.31), residues: 761 helix: 0.96 (0.26), residues: 384 sheet: -0.37 (0.50), residues: 102 loop : -1.55 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.002 0.001 HIS A 235 PHE 0.027 0.002 PHE A 548 TYR 0.012 0.001 TYR A 175 ARG 0.003 0.000 ARG C 44 *********************** 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 75 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.596 Fit side-chains REVERT: A 127 PHE cc_start: 0.7488 (m-10) cc_final: 0.7024 (m-10) REVERT: A 212 TYR cc_start: 0.4966 (OUTLIER) cc_final: 0.4627 (m-80) REVERT: A 306 TRP cc_start: 0.7812 (t-100) cc_final: 0.7194 (p-90) REVERT: A 416 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7591 (t0) outliers start: 23 outliers final: 17 residues processed: 70 average time/residue: 0.1481 time to fit residues: 14.9823 Evaluate side-chains 70 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 82 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.152479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.138773 restraints weight = 6367.234| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 0.83 r_work: 0.3117 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6442 Z= 0.259 Angle : 0.522 8.400 8712 Z= 0.271 Chirality : 0.042 0.272 951 Planarity : 0.004 0.041 1051 Dihedral : 6.601 85.332 1045 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.19 % Allowed : 15.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.31), residues: 761 helix: 1.02 (0.26), residues: 384 sheet: -0.19 (0.51), residues: 102 loop : -1.54 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.002 0.001 HIS A 235 PHE 0.026 0.002 PHE A 548 TYR 0.012 0.001 TYR A 175 ARG 0.002 0.000 ARG C 44 *********************** 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 77 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 0.634 Fit side-chains REVERT: A 127 PHE cc_start: 0.7602 (m-10) cc_final: 0.7190 (m-10) REVERT: A 212 TYR cc_start: 0.5027 (OUTLIER) cc_final: 0.4639 (m-80) REVERT: A 306 TRP cc_start: 0.7825 (t-100) cc_final: 0.7167 (p-90) REVERT: A 416 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7631 (t0) outliers start: 27 outliers final: 20 residues processed: 71 average time/residue: 0.1508 time to fit residues: 15.4246 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 : 0.589 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.153361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.141329 restraints weight = 6440.035| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 0.75 r_work: 0.3177 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6442 Z= 0.228 Angle : 0.503 8.146 8712 Z= 0.261 Chirality : 0.041 0.266 951 Planarity : 0.004 0.041 1051 Dihedral : 6.527 86.152 1045 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.31), residues: 761 helix: 1.14 (0.26), residues: 384 sheet: -0.08 (0.51), residues: 102 loop : -1.50 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 66 HIS 0.002 0.001 HIS A 143 PHE 0.026 0.001 PHE A 548 TYR 0.012 0.001 TYR A 175 ARG 0.002 0.000 ARG C 44 *********************** 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 74 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.596 Fit side-chains REVERT: A 127 PHE cc_start: 0.7591 (m-10) cc_final: 0.7175 (m-10) REVERT: A 212 TYR cc_start: 0.4952 (OUTLIER) cc_final: 0.4577 (m-80) REVERT: A 306 TRP cc_start: 0.7755 (t-100) cc_final: 0.7225 (p-90) REVERT: A 416 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7901 (t0) outliers start: 23 outliers final: 20 residues processed: 71 average time/residue: 0.1525 time to fit residues: 15.7955 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 : 0.659 ------------------------------------------------------------------------------- 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 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 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 11 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.154397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.138723 restraints weight = 6382.902| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 0.67 r_work: 0.3132 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6442 Z= 0.202 Angle : 0.493 8.010 8712 Z= 0.254 Chirality : 0.041 0.257 951 Planarity : 0.004 0.041 1051 Dihedral : 6.432 86.387 1045 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.42 % Allowed : 16.77 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.31), residues: 761 helix: 1.32 (0.26), residues: 379 sheet: 0.03 (0.52), residues: 102 loop : -1.42 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 66 HIS 0.002 0.001 HIS A 143 PHE 0.025 0.001 PHE A 548 TYR 0.013 0.001 TYR A 175 ARG 0.002 0.000 ARG C 44 *********************** 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 70 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.657 Fit side-chains REVERT: A 212 TYR cc_start: 0.5014 (OUTLIER) cc_final: 0.4625 (m-80) REVERT: A 306 TRP cc_start: 0.7823 (t-100) cc_final: 0.7162 (p-90) REVERT: A 416 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.7948 (t0) outliers start: 22 outliers final: 19 residues processed: 67 average time/residue: 0.1500 time to fit residues: 14.6079 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 : 0.672 ------------------------------------------------------------------------------- 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 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 chunk 64 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.155111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.141806 restraints weight = 6427.995| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 0.80 r_work: 0.3165 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6442 Z= 0.193 Angle : 0.481 7.690 8712 Z= 0.249 Chirality : 0.040 0.253 951 Planarity : 0.003 0.041 1051 Dihedral : 6.329 86.827 1045 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.73 % Allowed : 16.46 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.31), residues: 761 helix: 1.52 (0.26), residues: 373 sheet: 0.16 (0.52), residues: 103 loop : -1.41 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 66 HIS 0.002 0.001 HIS A 143 PHE 0.025 0.001 PHE A 548 TYR 0.013 0.001 TYR A 175 ARG 0.002 0.000 ARG C 44 ********************** 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 72 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.658 Fit side-chains REVERT: A 212 TYR cc_start: 0.4935 (OUTLIER) cc_final: 0.4497 (m-80) REVERT: A 306 TRP cc_start: 0.7789 (t-100) cc_final: 0.7126 (p-90) REVERT: A 416 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7892 (t0) outliers start: 24 outliers final: 20 residues processed: 67 average time/residue: 0.1621 time to fit residues: 15.8128 Evaluate side-chains 70 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.153802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.138238 restraints weight = 6496.245| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 0.71 r_work: 0.3073 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6442 Z= 0.222 Angle : 0.498 7.641 8712 Z= 0.257 Chirality : 0.041 0.256 951 Planarity : 0.004 0.040 1051 Dihedral : 6.399 86.652 1045 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.57 % Allowed : 16.30 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.31), residues: 761 helix: 1.48 (0.26), residues: 373 sheet: 0.19 (0.52), residues: 103 loop : -1.38 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 66 HIS 0.002 0.001 HIS A 143 PHE 0.026 0.001 PHE A 548 TYR 0.013 0.001 TYR A 175 ARG 0.002 0.000 ARG C 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2716.71 seconds wall clock time: 47 minutes 57.39 seconds (2877.39 seconds total)