Starting phenix.real_space_refine on Thu Jul 2 09:19:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvi_42621/07_2026/8uvi_42621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvi_42621/07_2026/8uvi_42621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uvi_42621/07_2026/8uvi_42621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvi_42621/07_2026/8uvi_42621.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvi_42621/07_2026/8uvi_42621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvi_42621/07_2026/8uvi_42621.cif" } resolution = 2.53 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 Na 2 4.78 5 C 5634 2.51 5 N 1226 2.21 5 O 1300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 8212 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3887 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 33, 'TRANS': 463} Chain breaks: 2 Chain: "B" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3887 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 33, 'TRANS': 463} Chain breaks: 2 Chain: "A" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 218 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'C14': 3, 'CLR': 6, 'SIN': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 1 Chain: "B" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 218 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'C14': 3, 'CLR': 6, 'SIN': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 1 Time building chain proxies: 1.65, per 1000 atoms: 0.20 Number of scatterers: 8212 At special positions: 0 Unit cell: (87.45, 97.35, 90.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 Na 2 11.00 O 1300 8.00 N 1226 7.00 C 5634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 271.6 milliseconds 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 83.7% alpha, 0.0% 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 7 through 14 Processing helix chain 'A' and resid 14 through 34 Proline residue: A 24 - end of helix Proline residue: A 29 - end of helix removed outlier: 3.906A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.902A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.940A pdb=" N PHE A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.605A pdb=" N ARG A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 143 through 163 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 225 through 246 removed outlier: 4.543A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.828A pdb=" N LEU A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 301 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.539A pdb=" N GLY A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 359 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.612A pdb=" N THR A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 4.013A pdb=" N PHE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 426 through 446 removed outlier: 3.653A pdb=" N ILE A 430 " --> pdb=" O PRO A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 483 through 502 Proline residue: A 493 - end of helix removed outlier: 3.552A pdb=" N ILE A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 518 Proline residue: A 512 - end of helix removed outlier: 3.963A pdb=" N SER A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 540 through 566 removed outlier: 4.071A pdb=" N LEU A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 removed outlier: 3.558A pdb=" N ILE A 570 " --> pdb=" O TRP A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 14 Processing helix chain 'B' and resid 14 through 34 Proline residue: B 24 - end of helix Proline residue: B 29 - end of helix removed outlier: 3.906A pdb=" N PHE B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.902A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 87 through 106 removed outlier: 3.807A pdb=" N PHE B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.605A pdb=" N ARG B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 143 through 163 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 225 through 246 removed outlier: 4.544A pdb=" N ILE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.829A pdb=" N LEU B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 301 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 320 through 336 removed outlier: 3.539A pdb=" N GLY B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 359 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 377 through 390 removed outlier: 3.612A pdb=" N THR B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 4.012A pdb=" N PHE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 426 through 446 removed outlier: 3.653A pdb=" N ILE B 430 " --> pdb=" O PRO B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 483 through 502 Proline residue: B 493 - end of helix removed outlier: 3.552A pdb=" N ILE B 500 " --> pdb=" O ALA B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 518 Proline residue: B 512 - end of helix removed outlier: 3.963A pdb=" N SER B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 526 Processing helix chain 'B' and resid 527 through 535 Processing helix chain 'B' and resid 540 through 566 removed outlier: 4.071A pdb=" N LEU B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.559A pdb=" N ILE B 570 " --> pdb=" O TRP B 566 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1536 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: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1160 1.30 - 1.43: 2123 1.43 - 1.55: 5074 1.55 - 1.68: 21 1.68 - 1.81: 86 Bond restraints: 8464 Sorted by residual: bond pdb=" C CYS A 82 " pdb=" O CYS A 82 " ideal model delta sigma weight residual 1.244 1.189 0.055 1.00e-02 1.00e+04 2.97e+01 bond pdb=" C PRO A 83 " pdb=" O PRO A 83 " ideal model delta sigma weight residual 1.237 1.173 0.064 1.32e-02 5.74e+03 2.34e+01 bond pdb=" C GLN B 84 " pdb=" O GLN B 84 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.28e-02 6.10e+03 2.27e+01 bond pdb=" C PHE B 86 " pdb=" O PHE B 86 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.41e-02 5.03e+03 1.99e+01 bond pdb=" C ASP B 88 " pdb=" O ASP B 88 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.25e-02 6.40e+03 1.70e+01 ... (remaining 8459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 11380 2.53 - 5.07: 169 5.07 - 7.60: 24 7.60 - 10.14: 6 10.14 - 12.67: 1 Bond angle restraints: 11580 Sorted by residual: angle pdb=" C THR A 89 " pdb=" CA THR A 89 " pdb=" CB THR A 89 " ideal model delta sigma weight residual 110.68 123.35 -12.67 1.70e+00 3.46e-01 5.56e+01 angle pdb=" C LYS A 80 " pdb=" CA LYS A 80 " pdb=" CB LYS A 80 " ideal model delta sigma weight residual 109.02 118.32 -9.30 1.68e+00 3.54e-01 3.06e+01 angle pdb=" C ASP A 88 " pdb=" CA ASP A 88 " pdb=" CB ASP A 88 " ideal model delta sigma weight residual 110.63 119.94 -9.31 1.85e+00 2.92e-01 2.53e+01 angle pdb=" CA ASP A 88 " pdb=" CB ASP A 88 " pdb=" CG ASP A 88 " ideal model delta sigma weight residual 112.60 117.17 -4.57 1.00e+00 1.00e+00 2.09e+01 angle pdb=" C LEU A 87 " pdb=" N ASP A 88 " pdb=" CA ASP A 88 " ideal model delta sigma weight residual 120.28 126.80 -6.52 1.44e+00 4.82e-01 2.05e+01 ... (remaining 11575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 5228 24.62 - 49.24: 230 49.24 - 73.85: 42 73.85 - 98.47: 8 98.47 - 123.09: 8 Dihedral angle restraints: 5516 sinusoidal: 2654 harmonic: 2862 Sorted by residual: dihedral pdb=" C THR A 89 " pdb=" N THR A 89 " pdb=" CA THR A 89 " pdb=" CB THR A 89 " ideal model delta harmonic sigma weight residual -122.00 -137.51 15.51 0 2.50e+00 1.60e-01 3.85e+01 dihedral pdb=" C PHE A 86 " pdb=" N PHE A 86 " pdb=" CA PHE A 86 " pdb=" CB PHE A 86 " ideal model delta harmonic sigma weight residual -122.60 -135.34 12.74 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" N PHE A 86 " pdb=" C PHE A 86 " pdb=" CA PHE A 86 " pdb=" CB PHE A 86 " ideal model delta harmonic sigma weight residual 122.80 133.98 -11.18 0 2.50e+00 1.60e-01 2.00e+01 ... (remaining 5513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1314 0.093 - 0.187: 57 0.187 - 0.280: 7 0.280 - 0.373: 1 0.373 - 0.467: 3 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA PHE A 86 " pdb=" N PHE A 86 " pdb=" C PHE A 86 " pdb=" CB PHE A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CA PHE B 86 " pdb=" N PHE B 86 " pdb=" C PHE B 86 " pdb=" CB PHE B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA THR A 89 " pdb=" N THR A 89 " pdb=" C THR A 89 " pdb=" CB THR A 89 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 1379 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 88 " 0.014 2.00e-02 2.50e+03 2.98e-02 8.87e+00 pdb=" C ASP B 88 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP B 88 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 89 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 528 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO B 529 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 529 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 529 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 528 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO A 529 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 529 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 529 " -0.039 5.00e-02 4.00e+02 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 70 2.65 - 3.22: 7838 3.22 - 3.78: 13014 3.78 - 4.34: 18417 4.34 - 4.90: 29602 Nonbonded interactions: 68941 Sorted by model distance: nonbonded pdb=" OG1 THR B 479 " pdb="NA NA B 701 " model vdw 2.093 3.210 nonbonded pdb=" O THR A 479 " pdb="NA NA A 701 " model vdw 2.209 3.210 nonbonded pdb=" OD1 ASN B 484 " pdb="NA NA B 701 " model vdw 2.209 3.210 nonbonded pdb=" O THR B 479 " pdb="NA NA B 701 " model vdw 2.242 3.210 nonbonded pdb=" OG1 THR A 479 " pdb="NA NA A 701 " model vdw 2.256 3.210 ... (remaining 68936 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.510 Find NCS groups from input model: 0.050 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.004 0.064 8464 Z= 0.253 Angle : 0.745 12.674 11580 Z= 0.393 Chirality : 0.051 0.467 1382 Planarity : 0.007 0.069 1334 Dihedral : 14.601 123.090 3656 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.72 % Allowed : 0.36 % Favored : 98.92 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % 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: 1.41 (0.28), residues: 982 helix: 1.26 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.09 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 227 TYR 0.022 0.003 TYR B 85 PHE 0.025 0.002 PHE A 234 TRP 0.039 0.002 TRP A 231 HIS 0.001 0.000 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.25 ( 8464) covalent geometry : angle 0.74544 / 0.39 (11580) hydrogen bonds : bond 0.12876 / 8.51 ( 522) hydrogen bonds : angle 5.39806 / 3.94 ( 1536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 185 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 251 THR cc_start: 0.7592 (p) cc_final: 0.7384 (p) REVERT: A 299 PHE cc_start: 0.8115 (t80) cc_final: 0.7776 (t80) REVERT: A 510 MET cc_start: 0.7254 (mmt) cc_final: 0.5813 (mmt) REVERT: B 510 MET cc_start: 0.7396 (mmt) cc_final: 0.7044 (mpt) outliers start: 6 outliers final: 2 residues processed: 188 average time/residue: 0.4316 time to fit residues: 87.0361 Evaluate side-chains 141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 86 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN A 422 GLN B 422 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.179102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138182 restraints weight = 9380.716| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.68 r_work: 0.3499 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8464 Z= 0.139 Angle : 0.634 7.837 11580 Z= 0.304 Chirality : 0.042 0.168 1382 Planarity : 0.006 0.076 1334 Dihedral : 7.975 59.845 1894 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.75 % Allowed : 9.93 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.28), residues: 982 helix: 1.64 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.38 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 329 TYR 0.014 0.001 TYR B 508 PHE 0.015 0.001 PHE A 478 TRP 0.016 0.002 TRP B 418 HIS 0.002 0.001 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8464) covalent geometry : angle 0.63378 / 0.30 (11580) hydrogen bonds : bond 0.03858 / 2.55 ( 522) hydrogen bonds : angle 4.14862 / 3.04 ( 1536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.258 Fit side-chains REVERT: A 73 MET cc_start: 0.9028 (mtt) cc_final: 0.8782 (mtt) REVERT: A 86 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.7850 (t80) REVERT: A 131 MET cc_start: 0.7440 (mtp) cc_final: 0.7068 (mtm) REVERT: A 510 MET cc_start: 0.7378 (mmt) cc_final: 0.7042 (mpt) REVERT: A 534 PHE cc_start: 0.6824 (m-80) cc_final: 0.6235 (m-80) REVERT: A 546 ARG cc_start: 0.7216 (mtm110) cc_final: 0.5459 (mmm160) REVERT: B 73 MET cc_start: 0.9016 (mtt) cc_final: 0.8808 (mtt) REVERT: B 86 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.7766 (t80) REVERT: B 227 ARG cc_start: 0.7211 (mtt90) cc_final: 0.6764 (mtt-85) REVERT: B 259 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6891 (tp) REVERT: B 540 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7016 (mp) outliers start: 23 outliers final: 8 residues processed: 153 average time/residue: 0.4194 time to fit residues: 69.1502 Evaluate side-chains 137 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 540 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 395 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.175130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134414 restraints weight = 9386.182| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.67 r_work: 0.3453 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8464 Z= 0.151 Angle : 0.639 10.770 11580 Z= 0.305 Chirality : 0.043 0.179 1382 Planarity : 0.006 0.075 1334 Dihedral : 8.156 59.788 1894 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.47 % Allowed : 12.32 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.13 (0.28), residues: 982 helix: 1.74 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.47 (0.48), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 329 TYR 0.011 0.001 TYR A 508 PHE 0.014 0.001 PHE B 391 TRP 0.018 0.002 TRP B 418 HIS 0.002 0.000 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 ( 8464) covalent geometry : angle 0.63853 / 0.30 (11580) hydrogen bonds : bond 0.03917 / 2.61 ( 522) hydrogen bonds : angle 4.03610 / 2.95 ( 1536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.196 Fit side-chains REVERT: A 118 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.6703 (mpp) REVERT: A 131 MET cc_start: 0.7496 (mtp) cc_final: 0.6976 (mtm) REVERT: A 140 MET cc_start: 0.7333 (mtm) cc_final: 0.7133 (mtp) REVERT: A 228 ARG cc_start: 0.7127 (mtm-85) cc_final: 0.6626 (mpp80) REVERT: A 546 ARG cc_start: 0.7346 (mtm110) cc_final: 0.5571 (mmm160) REVERT: B 86 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.7532 (t80) REVERT: B 259 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6898 (tp) REVERT: B 280 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6926 (tp) outliers start: 29 outliers final: 9 residues processed: 146 average time/residue: 0.3729 time to fit residues: 58.9997 Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 461 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 395 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.175608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134892 restraints weight = 9545.683| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.69 r_work: 0.3458 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8464 Z= 0.131 Angle : 0.605 9.851 11580 Z= 0.290 Chirality : 0.041 0.165 1382 Planarity : 0.006 0.074 1334 Dihedral : 8.029 59.853 1894 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.75 % Allowed : 14.47 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.27 (0.28), residues: 982 helix: 1.84 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.49 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 329 TYR 0.009 0.001 TYR B 508 PHE 0.022 0.001 PHE B 234 TRP 0.018 0.002 TRP B 418 HIS 0.001 0.000 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 8464) covalent geometry : angle 0.60543 / 0.29 (11580) hydrogen bonds : bond 0.03585 / 2.40 ( 522) hydrogen bonds : angle 3.89941 / 2.86 ( 1536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.365 Fit side-chains REVERT: A 118 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.6763 (mpp) REVERT: A 131 MET cc_start: 0.7677 (mtp) cc_final: 0.7176 (mtm) REVERT: A 227 ARG cc_start: 0.7306 (mtt180) cc_final: 0.6980 (mtt90) REVERT: A 228 ARG cc_start: 0.7014 (mtm-85) cc_final: 0.6534 (mpp80) REVERT: A 510 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6542 (mpt) REVERT: A 546 ARG cc_start: 0.7457 (mtm110) cc_final: 0.5713 (mmm160) REVERT: B 9 LYS cc_start: 0.7540 (mmmt) cc_final: 0.7031 (mtmt) REVERT: B 259 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6903 (tp) REVERT: B 487 THR cc_start: 0.7377 (t) cc_final: 0.7162 (m) REVERT: B 563 MET cc_start: 0.7171 (mmm) cc_final: 0.6937 (mpp) outliers start: 23 outliers final: 10 residues processed: 141 average time/residue: 0.3614 time to fit residues: 55.1692 Evaluate side-chains 136 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 0.0040 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.176296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135619 restraints weight = 9465.630| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.68 r_work: 0.3465 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8464 Z= 0.124 Angle : 0.588 9.330 11580 Z= 0.283 Chirality : 0.041 0.153 1382 Planarity : 0.006 0.073 1334 Dihedral : 7.950 59.892 1894 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.27 % Allowed : 15.79 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.28), residues: 982 helix: 1.91 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.51 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 329 TYR 0.009 0.001 TYR B 508 PHE 0.019 0.001 PHE B 234 TRP 0.018 0.002 TRP B 418 HIS 0.001 0.000 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 ( 8464) covalent geometry : angle 0.58828 / 0.28 (11580) hydrogen bonds : bond 0.03461 / 2.33 ( 522) hydrogen bonds : angle 3.82521 / 2.80 ( 1536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.169 Fit side-chains REVERT: A 131 MET cc_start: 0.7662 (mtp) cc_final: 0.7137 (mtm) REVERT: A 227 ARG cc_start: 0.7320 (mtt180) cc_final: 0.6963 (mtt90) REVERT: A 510 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6591 (mpt) REVERT: A 546 ARG cc_start: 0.7495 (mtm110) cc_final: 0.5809 (mmm160) REVERT: B 9 LYS cc_start: 0.7553 (mmmt) cc_final: 0.7006 (mtmt) REVERT: B 487 THR cc_start: 0.7385 (t) cc_final: 0.7175 (m) REVERT: B 544 MET cc_start: 0.5845 (ptm) cc_final: 0.5440 (ptm) REVERT: B 546 ARG cc_start: 0.6900 (mtm110) cc_final: 0.5388 (mmm160) REVERT: B 563 MET cc_start: 0.7138 (mmm) cc_final: 0.6904 (mpp) outliers start: 19 outliers final: 11 residues processed: 143 average time/residue: 0.3333 time to fit residues: 51.7173 Evaluate side-chains 138 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 550 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 15 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.173915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132954 restraints weight = 9333.333| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.66 r_work: 0.3425 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8464 Z= 0.148 Angle : 0.632 9.417 11580 Z= 0.303 Chirality : 0.043 0.175 1382 Planarity : 0.006 0.073 1334 Dihedral : 8.195 59.201 1894 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.99 % Allowed : 15.79 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.32 (0.28), residues: 982 helix: 1.85 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.62 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 329 TYR 0.009 0.001 TYR B 508 PHE 0.023 0.001 PHE B 234 TRP 0.019 0.002 TRP B 418 HIS 0.002 0.000 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 8464) covalent geometry : angle 0.63248 / 0.30 (11580) hydrogen bonds : bond 0.03766 / 2.55 ( 522) hydrogen bonds : angle 3.88797 / 2.84 ( 1536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.220 Fit side-chains REVERT: A 118 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.6729 (mpp) REVERT: A 131 MET cc_start: 0.7697 (mtp) cc_final: 0.7111 (mtm) REVERT: A 227 ARG cc_start: 0.7290 (mtt180) cc_final: 0.6869 (mtt90) REVERT: A 411 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: A 510 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.6547 (mpt) REVERT: A 546 ARG cc_start: 0.7737 (mtm110) cc_final: 0.6087 (mmm160) REVERT: B 105 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8192 (tp30) REVERT: B 487 THR cc_start: 0.7388 (t) cc_final: 0.7186 (m) REVERT: B 534 PHE cc_start: 0.6326 (m-80) cc_final: 0.6104 (m-80) REVERT: B 546 ARG cc_start: 0.7133 (mtm110) cc_final: 0.5462 (mmm160) outliers start: 25 outliers final: 11 residues processed: 145 average time/residue: 0.3444 time to fit residues: 54.0629 Evaluate side-chains 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 83 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 56 optimal weight: 0.0770 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.175789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.135169 restraints weight = 9442.641| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.67 r_work: 0.3462 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8464 Z= 0.126 Angle : 0.609 9.542 11580 Z= 0.292 Chirality : 0.042 0.163 1382 Planarity : 0.006 0.073 1334 Dihedral : 8.063 59.765 1894 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.75 % Allowed : 16.87 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 982 helix: 1.90 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.45 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 329 TYR 0.010 0.001 TYR B 508 PHE 0.023 0.001 PHE B 234 TRP 0.018 0.002 TRP A 418 HIS 0.001 0.000 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8464) covalent geometry : angle 0.60857 / 0.29 (11580) hydrogen bonds : bond 0.03518 / 2.36 ( 522) hydrogen bonds : angle 3.88251 / 2.83 ( 1536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.280 Fit side-chains REVERT: A 118 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.6655 (mpp) REVERT: A 131 MET cc_start: 0.7618 (mtp) cc_final: 0.7096 (mtm) REVERT: A 227 ARG cc_start: 0.7268 (mtt180) cc_final: 0.6935 (mtt90) REVERT: A 228 ARG cc_start: 0.6944 (mtm110) cc_final: 0.6604 (mpp80) REVERT: A 503 ARG cc_start: 0.7234 (pmt-80) cc_final: 0.6953 (pmt-80) REVERT: A 510 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6721 (mpt) REVERT: A 534 PHE cc_start: 0.6842 (m-80) cc_final: 0.6629 (m-80) REVERT: A 546 ARG cc_start: 0.7551 (mtm110) cc_final: 0.5885 (mmm160) REVERT: B 487 THR cc_start: 0.7388 (t) cc_final: 0.7169 (m) REVERT: B 510 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6343 (mpt) REVERT: B 546 ARG cc_start: 0.6999 (mtm110) cc_final: 0.5423 (mmm160) outliers start: 23 outliers final: 14 residues processed: 151 average time/residue: 0.3440 time to fit residues: 56.1586 Evaluate side-chains 146 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 522 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 7 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.176442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135951 restraints weight = 9447.288| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.68 r_work: 0.3473 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8464 Z= 0.124 Angle : 0.616 9.986 11580 Z= 0.295 Chirality : 0.042 0.206 1382 Planarity : 0.006 0.073 1334 Dihedral : 8.018 59.893 1894 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.87 % Allowed : 17.11 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.38 (0.28), residues: 982 helix: 1.92 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.51 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 329 TYR 0.009 0.001 TYR B 508 PHE 0.023 0.001 PHE B 234 TRP 0.018 0.002 TRP A 418 HIS 0.001 0.000 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 8464) covalent geometry : angle 0.61556 / 0.30 (11580) hydrogen bonds : bond 0.03521 / 2.36 ( 522) hydrogen bonds : angle 3.92682 / 2.86 ( 1536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.258 Fit side-chains REVERT: A 118 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.6669 (mpp) REVERT: A 131 MET cc_start: 0.7674 (mtp) cc_final: 0.7123 (mtm) REVERT: A 227 ARG cc_start: 0.7304 (mtt180) cc_final: 0.6935 (mtt90) REVERT: A 329 ARG cc_start: 0.7249 (mtm110) cc_final: 0.6970 (mtm110) REVERT: A 503 ARG cc_start: 0.7243 (pmt-80) cc_final: 0.6979 (pmt-80) REVERT: A 522 MET cc_start: 0.6752 (tpp) cc_final: 0.6401 (mmm) REVERT: A 546 ARG cc_start: 0.7410 (mtm110) cc_final: 0.5757 (mmm160) REVERT: B 510 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6394 (mpt) REVERT: B 546 ARG cc_start: 0.6999 (mtm110) cc_final: 0.5454 (mmm160) outliers start: 24 outliers final: 14 residues processed: 142 average time/residue: 0.3314 time to fit residues: 51.2779 Evaluate side-chains 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 522 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132763 restraints weight = 9337.364| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.66 r_work: 0.3427 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8464 Z= 0.153 Angle : 0.656 8.673 11580 Z= 0.316 Chirality : 0.043 0.168 1382 Planarity : 0.006 0.073 1334 Dihedral : 8.310 59.623 1894 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.63 % Allowed : 17.82 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.34 (0.28), residues: 982 helix: 1.88 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.56 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 329 TYR 0.010 0.001 TYR B 508 PHE 0.038 0.002 PHE B 234 TRP 0.018 0.002 TRP A 418 HIS 0.002 0.000 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.15 ( 8464) covalent geometry : angle 0.65585 / 0.32 (11580) hydrogen bonds : bond 0.03852 / 2.61 ( 522) hydrogen bonds : angle 4.00145 / 2.93 ( 1536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.228 Fit side-chains REVERT: A 118 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.6675 (mpp) REVERT: A 131 MET cc_start: 0.7630 (mtp) cc_final: 0.6926 (mtm) REVERT: A 227 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6932 (mtt90) REVERT: A 544 MET cc_start: 0.5783 (ptm) cc_final: 0.5372 (ttm) REVERT: A 546 ARG cc_start: 0.7590 (mtm110) cc_final: 0.5945 (mmm160) REVERT: B 234 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7070 (t80) REVERT: B 510 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6381 (mpt) REVERT: B 546 ARG cc_start: 0.7201 (mtm110) cc_final: 0.5620 (mmm160) outliers start: 22 outliers final: 13 residues processed: 139 average time/residue: 0.3134 time to fit residues: 47.4332 Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 522 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.174220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.133378 restraints weight = 9353.128| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.67 r_work: 0.3436 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8464 Z= 0.145 Angle : 0.659 10.646 11580 Z= 0.317 Chirality : 0.044 0.228 1382 Planarity : 0.006 0.073 1334 Dihedral : 8.306 58.922 1894 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.51 % Allowed : 17.94 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.28 (0.28), residues: 982 helix: 1.82 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.59 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 329 TYR 0.015 0.001 TYR A 508 PHE 0.021 0.001 PHE B 234 TRP 0.018 0.002 TRP A 418 HIS 0.002 0.000 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 8464) covalent geometry : angle 0.65885 / 0.32 (11580) hydrogen bonds : bond 0.03794 / 2.58 ( 522) hydrogen bonds : angle 4.03193 / 2.94 ( 1536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.284 Fit side-chains REVERT: A 118 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.6675 (mpp) REVERT: A 131 MET cc_start: 0.7612 (mtp) cc_final: 0.6986 (mtm) REVERT: A 227 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6952 (mtt90) REVERT: A 544 MET cc_start: 0.5411 (ptm) cc_final: 0.5200 (ttm) REVERT: A 546 ARG cc_start: 0.7650 (mtm110) cc_final: 0.5947 (mmm160) REVERT: B 329 ARG cc_start: 0.7106 (mtm110) cc_final: 0.6894 (mtm110) REVERT: B 510 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6315 (mpt) REVERT: B 546 ARG cc_start: 0.7231 (mtm110) cc_final: 0.5580 (mmm160) outliers start: 21 outliers final: 13 residues processed: 139 average time/residue: 0.3169 time to fit residues: 47.8508 Evaluate side-chains 143 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 522 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 28 optimal weight: 0.0070 chunk 69 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 0.0670 chunk 93 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.177233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136807 restraints weight = 9411.907| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.68 r_work: 0.3485 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8464 Z= 0.125 Angle : 0.636 9.202 11580 Z= 0.307 Chirality : 0.042 0.172 1382 Planarity : 0.006 0.074 1334 Dihedral : 8.150 59.909 1894 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.15 % Allowed : 18.54 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.35 (0.28), residues: 982 helix: 1.91 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.47 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 329 TYR 0.015 0.001 TYR A 508 PHE 0.014 0.001 PHE A 478 TRP 0.020 0.002 TRP B 231 HIS 0.002 0.000 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 8464) covalent geometry : angle 0.63597 / 0.31 (11580) hydrogen bonds : bond 0.03557 / 2.40 ( 522) hydrogen bonds : angle 4.01467 / 2.92 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2724.00 seconds wall clock time: 47 minutes 5.54 seconds (2825.54 seconds total)