Starting phenix.real_space_refine on Wed Mar 12 16:22:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvi_42621/03_2025/8uvi_42621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvi_42621/03_2025/8uvi_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_42621/03_2025/8uvi_42621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvi_42621/03_2025/8uvi_42621.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvi_42621/03_2025/8uvi_42621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvi_42621/03_2025/8uvi_42621.cif" } resolution = 2.53 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= 0.033 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 219 Unusual residues: {' NA': 1, 'C14': 3, 'CLR': 6, 'SIN': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 219 Unusual residues: {' NA': 1, 'C14': 3, 'CLR': 6, 'SIN': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 5.82, per 1000 atoms: 0.71 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.62 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: 2.72 Time building geometry restraints manager: 3.15 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 2.470 nonbonded pdb=" O THR A 479 " pdb="NA NA A 701 " model vdw 2.209 2.470 nonbonded pdb=" OD1 ASN B 484 " pdb="NA NA B 701 " model vdw 2.209 2.470 nonbonded pdb=" O THR B 479 " pdb="NA NA B 701 " model vdw 2.242 2.470 nonbonded pdb=" OG1 THR A 479 " pdb="NA NA A 701 " model vdw 2.256 2.470 ... (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: 0.05 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: 14.420 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.110 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:19.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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= 0.282 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 (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: 1.41 (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 TRP 0.039 0.002 TRP A 231 HIS 0.001 0.000 HIS B 538 PHE 0.025 0.002 PHE A 234 TYR 0.022 0.003 TYR B 85 ARG 0.007 0.001 ARG A 227 *********************** 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 : 0.936 Fit side-chains revert: symmetry clash REVERT: A 251 THR cc_start: 0.7592 (p) cc_final: 0.7385 (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: 1.4374 time to fit residues: 289.2149 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 : 1.294 ------------------------------------------------------------------------------- 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 82 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.0170 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4053 r_free = 0.4053 target = 0.178472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137502 restraints weight = 9298.729| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.66 r_work: 0.3491 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1771 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= 0.224 Angle : 0.639 7.628 11580 Z= 0.306 Chirality : 0.042 0.170 1382 Planarity : 0.006 0.076 1334 Dihedral : 8.017 59.861 1894 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.75 % Allowed : 10.17 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.28), residues: 982 helix: 1.65 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.40 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 418 HIS 0.002 0.001 HIS B 538 PHE 0.014 0.001 PHE A 478 TYR 0.014 0.001 TYR B 508 ARG 0.006 0.001 ARG A 329 *********************** 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 161 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.881 Fit side-chains REVERT: A 73 MET cc_start: 0.9025 (mtt) cc_final: 0.8747 (mtt) REVERT: A 86 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.7714 (t80) REVERT: A 131 MET cc_start: 0.7493 (mtp) cc_final: 0.7122 (mtm) REVERT: A 140 MET cc_start: 0.7190 (mtm) cc_final: 0.6987 (mtp) REVERT: A 299 PHE cc_start: 0.8095 (t80) cc_final: 0.7893 (t80) REVERT: A 510 MET cc_start: 0.7386 (mmt) cc_final: 0.7054 (mpt) REVERT: A 534 PHE cc_start: 0.6814 (m-80) cc_final: 0.6074 (m-80) REVERT: A 546 ARG cc_start: 0.7245 (mtm110) cc_final: 0.5483 (mmm160) REVERT: B 73 MET cc_start: 0.9032 (mtt) cc_final: 0.8799 (mtt) REVERT: B 86 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.7775 (t80) REVERT: B 259 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6907 (tp) REVERT: B 444 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: B 510 MET cc_start: 0.7493 (mmt) cc_final: 0.7246 (mpt) REVERT: B 540 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.7019 (mp) outliers start: 23 outliers final: 8 residues processed: 147 average time/residue: 1.0142 time to fit residues: 160.6716 Evaluate side-chains 135 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 444 GLU 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 82 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4023 r_free = 0.4023 target = 0.175629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134911 restraints weight = 9469.387| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.67 r_work: 0.3458 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2253 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= 0.229 Angle : 0.625 9.805 11580 Z= 0.300 Chirality : 0.042 0.179 1382 Planarity : 0.006 0.075 1334 Dihedral : 8.053 59.703 1894 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.87 % Allowed : 12.56 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.22 (0.28), residues: 982 helix: 1.79 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.56 (0.49), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 418 HIS 0.002 0.000 HIS B 538 PHE 0.014 0.001 PHE A 478 TYR 0.014 0.001 TYR B 508 ARG 0.007 0.001 ARG B 227 *********************** 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 156 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.916 Fit side-chains REVERT: A 131 MET cc_start: 0.7597 (mtp) cc_final: 0.7028 (mtm) REVERT: A 140 MET cc_start: 0.7320 (mtm) cc_final: 0.7119 (mtp) REVERT: A 227 ARG cc_start: 0.7290 (mtt180) cc_final: 0.6907 (mtt90) REVERT: A 228 ARG cc_start: 0.7151 (mtm-85) cc_final: 0.6636 (mpp80) REVERT: A 299 PHE cc_start: 0.7943 (t80) cc_final: 0.7615 (t80) REVERT: A 546 ARG cc_start: 0.7279 (mtm110) cc_final: 0.5402 (mmm160) REVERT: B 259 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6947 (tp) REVERT: B 444 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7112 (pm20) REVERT: B 510 MET cc_start: 0.7272 (mmt) cc_final: 0.6843 (mpt) outliers start: 24 outliers final: 10 residues processed: 142 average time/residue: 0.9199 time to fit residues: 141.5023 Evaluate side-chains 133 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 287 LEU Chi-restraints excluded: chain B residue 444 GLU 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 66 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 3 optimal weight: 0.0470 chunk 67 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3997 r_free = 0.3997 target = 0.173186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132135 restraints weight = 9381.231| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.67 r_work: 0.3418 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8464 Z= 0.251 Angle : 0.635 9.842 11580 Z= 0.304 Chirality : 0.043 0.167 1382 Planarity : 0.006 0.074 1334 Dihedral : 8.174 58.712 1894 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.75 % Allowed : 14.23 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.24 (0.28), residues: 982 helix: 1.80 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.59 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 418 HIS 0.001 0.000 HIS A 109 PHE 0.027 0.002 PHE B 234 TYR 0.013 0.001 TYR B 508 ARG 0.008 0.001 ARG B 329 *********************** 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 152 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.801 Fit side-chains REVERT: A 34 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7928 (pt) REVERT: A 105 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: A 118 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.6744 (mpp) REVERT: A 131 MET cc_start: 0.7707 (mtp) cc_final: 0.7128 (mtm) REVERT: A 227 ARG cc_start: 0.7313 (mtt180) cc_final: 0.6864 (mtt90) REVERT: A 228 ARG cc_start: 0.7069 (mtm-85) cc_final: 0.6804 (mtm110) REVERT: A 299 PHE cc_start: 0.7939 (t80) cc_final: 0.7670 (t80) REVERT: A 510 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6610 (mpt) REVERT: A 546 ARG cc_start: 0.7596 (mtm110) cc_final: 0.5927 (mmm160) REVERT: B 86 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.7399 (t80) REVERT: B 105 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8256 (tp30) REVERT: B 259 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6809 (tp) REVERT: B 444 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7142 (pm20) REVERT: B 544 MET cc_start: 0.6630 (ptm) cc_final: 0.6086 (ptm) REVERT: B 546 ARG cc_start: 0.7145 (mtm110) cc_final: 0.5484 (mmm160) outliers start: 23 outliers final: 10 residues processed: 140 average time/residue: 0.9659 time to fit residues: 146.0268 Evaluate side-chains 141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 105 GLU 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 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 Chi-restraints excluded: chain B residue 444 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.172566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131321 restraints weight = 9334.276| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.67 r_work: 0.3426 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8464 Z= 0.241 Angle : 0.631 10.784 11580 Z= 0.301 Chirality : 0.043 0.170 1382 Planarity : 0.006 0.074 1334 Dihedral : 8.142 58.569 1894 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.11 % Allowed : 15.07 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 982 helix: 1.87 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.62 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 418 HIS 0.002 0.000 HIS B 538 PHE 0.022 0.001 PHE B 234 TYR 0.012 0.001 TYR A 508 ARG 0.011 0.001 ARG B 329 *********************** 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 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.805 Fit side-chains REVERT: A 118 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.6774 (mpp) REVERT: A 131 MET cc_start: 0.7677 (mtp) cc_final: 0.7103 (mtm) REVERT: A 227 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6873 (mtt90) REVERT: A 299 PHE cc_start: 0.7967 (t80) cc_final: 0.7704 (t80) REVERT: A 510 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.6573 (mpt) REVERT: A 546 ARG cc_start: 0.7499 (mtm110) cc_final: 0.5691 (mmm160) REVERT: B 259 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6838 (tp) REVERT: B 444 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: B 546 ARG cc_start: 0.7176 (mtm110) cc_final: 0.5524 (mmm160) outliers start: 26 outliers final: 11 residues processed: 138 average time/residue: 0.9426 time to fit residues: 141.3434 Evaluate side-chains 134 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 287 LEU 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 444 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.172607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131680 restraints weight = 9370.817| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.67 r_work: 0.3422 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8464 Z= 0.248 Angle : 0.639 9.229 11580 Z= 0.306 Chirality : 0.043 0.154 1382 Planarity : 0.006 0.073 1334 Dihedral : 8.219 58.578 1894 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.99 % Allowed : 15.31 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.30 (0.28), residues: 982 helix: 1.84 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.62 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 418 HIS 0.001 0.000 HIS B 538 PHE 0.025 0.001 PHE B 234 TYR 0.020 0.002 TYR A 508 ARG 0.010 0.001 ARG B 329 *********************** 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 150 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.808 Fit side-chains REVERT: A 118 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.6797 (mpp) REVERT: A 131 MET cc_start: 0.7737 (mtp) cc_final: 0.6975 (mtm) REVERT: A 227 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6785 (mtt90) REVERT: A 234 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7841 (t80) REVERT: A 299 PHE cc_start: 0.7937 (t80) cc_final: 0.7704 (t80) REVERT: A 510 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6561 (mpt) REVERT: A 546 ARG cc_start: 0.7713 (mtm110) cc_final: 0.6002 (mmm160) REVERT: B 86 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.7350 (t80) REVERT: B 259 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6821 (tp) REVERT: B 280 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.7097 (tp) REVERT: B 444 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: B 510 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6918 (mpt) REVERT: B 544 MET cc_start: 0.6719 (ptm) cc_final: 0.6514 (ptm) REVERT: B 546 ARG cc_start: 0.7252 (mtm110) cc_final: 0.5660 (mmm160) outliers start: 25 outliers final: 11 residues processed: 137 average time/residue: 0.8971 time to fit residues: 133.4416 Evaluate side-chains 142 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 287 LEU 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 280 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 550 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.173740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133275 restraints weight = 9412.135| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.66 r_work: 0.3436 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2898 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= 0.226 Angle : 0.627 9.436 11580 Z= 0.301 Chirality : 0.042 0.145 1382 Planarity : 0.006 0.072 1334 Dihedral : 8.151 58.818 1894 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.47 % Allowed : 15.91 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.28), residues: 982 helix: 1.91 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.53 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 418 HIS 0.001 0.000 HIS B 538 PHE 0.024 0.001 PHE B 234 TYR 0.014 0.001 TYR A 508 ARG 0.013 0.001 ARG A 329 *********************** 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 157 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.789 Fit side-chains REVERT: A 118 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.6800 (mpp) REVERT: A 131 MET cc_start: 0.7634 (mtp) cc_final: 0.6877 (mtm) REVERT: A 227 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6784 (mtt90) REVERT: A 299 PHE cc_start: 0.7923 (t80) cc_final: 0.7675 (t80) REVERT: A 329 ARG cc_start: 0.7196 (mtm110) cc_final: 0.6922 (mtm110) REVERT: A 503 ARG cc_start: 0.7285 (pmt-80) cc_final: 0.7005 (pmt-80) REVERT: A 546 ARG cc_start: 0.7557 (mtm110) cc_final: 0.5716 (mmm160) REVERT: B 259 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6806 (tp) REVERT: B 444 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7228 (pm20) REVERT: B 510 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6216 (mpt) REVERT: B 544 MET cc_start: 0.6433 (ptm) cc_final: 0.6076 (ptm) REVERT: B 546 ARG cc_start: 0.7177 (mtm110) cc_final: 0.5601 (mmm160) outliers start: 29 outliers final: 16 residues processed: 146 average time/residue: 0.9388 time to fit residues: 148.3696 Evaluate side-chains 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 287 LEU 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 444 GLU Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 550 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.0470 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 56 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.175365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134629 restraints weight = 9469.466| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.69 r_work: 0.3459 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2924 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= 0.201 Angle : 0.619 10.263 11580 Z= 0.298 Chirality : 0.042 0.245 1382 Planarity : 0.006 0.073 1334 Dihedral : 8.035 59.929 1894 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.11 % Allowed : 16.39 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.40 (0.28), residues: 982 helix: 1.93 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.54 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 418 HIS 0.001 0.000 HIS A 538 PHE 0.024 0.001 PHE B 234 TYR 0.013 0.001 TYR A 508 ARG 0.011 0.001 ARG A 329 *********************** 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 152 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.815 Fit side-chains REVERT: A 118 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.6744 (mpp) REVERT: A 227 ARG cc_start: 0.7313 (mtt180) cc_final: 0.6902 (mtt90) REVERT: A 299 PHE cc_start: 0.7895 (t80) cc_final: 0.7596 (t80) REVERT: A 444 GLU cc_start: 0.7992 (tt0) cc_final: 0.7241 (mt-10) REVERT: A 503 ARG cc_start: 0.7244 (pmt-80) cc_final: 0.6972 (pmt-80) REVERT: A 546 ARG cc_start: 0.7553 (mtm110) cc_final: 0.5699 (mmm160) REVERT: B 9 LYS cc_start: 0.7524 (mmmt) cc_final: 0.6973 (mtmt) REVERT: B 444 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: B 510 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6109 (mpt) REVERT: B 544 MET cc_start: 0.6663 (ptm) cc_final: 0.6355 (ptm) outliers start: 26 outliers final: 14 residues processed: 141 average time/residue: 0.9066 time to fit residues: 138.6735 Evaluate side-chains 141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 287 LEU 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 286 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 550 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.173544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132654 restraints weight = 9571.404| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.68 r_work: 0.3428 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8464 Z= 0.240 Angle : 0.658 8.989 11580 Z= 0.317 Chirality : 0.043 0.150 1382 Planarity : 0.006 0.074 1334 Dihedral : 8.245 59.410 1894 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.63 % Allowed : 17.34 % 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 (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: 2.31 (0.28), residues: 982 helix: 1.86 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.58 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 418 HIS 0.002 0.000 HIS A 538 PHE 0.053 0.002 PHE B 234 TYR 0.015 0.001 TYR A 508 ARG 0.014 0.001 ARG B 329 *********************** 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 146 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.996 Fit side-chains REVERT: A 118 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.6815 (mpp) REVERT: A 227 ARG cc_start: 0.7314 (mtt180) cc_final: 0.6822 (mtt90) REVERT: A 299 PHE cc_start: 0.7934 (t80) cc_final: 0.7643 (t80) REVERT: A 329 ARG cc_start: 0.7267 (mtm110) cc_final: 0.6988 (mtm110) REVERT: A 546 ARG cc_start: 0.7553 (mtm110) cc_final: 0.5829 (mmm160) REVERT: B 9 LYS cc_start: 0.7584 (mmmt) cc_final: 0.7003 (mppt) REVERT: B 444 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7264 (pm20) REVERT: B 510 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6251 (mpt) REVERT: B 546 ARG cc_start: 0.7077 (mtm110) cc_final: 0.5473 (mmm160) outliers start: 22 outliers final: 15 residues processed: 135 average time/residue: 1.0216 time to fit residues: 149.2261 Evaluate side-chains 140 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 60 SER 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 287 LEU 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 286 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 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 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 = 0.174090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133180 restraints weight = 9408.551| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.68 r_work: 0.3436 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3021 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= 0.226 Angle : 0.656 10.953 11580 Z= 0.315 Chirality : 0.043 0.251 1382 Planarity : 0.006 0.074 1334 Dihedral : 8.236 59.505 1894 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.75 % Allowed : 17.22 % 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 (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: 2.32 (0.28), residues: 982 helix: 1.84 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.67 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 418 HIS 0.001 0.000 HIS B 538 PHE 0.038 0.001 PHE B 234 TYR 0.014 0.001 TYR A 508 ARG 0.013 0.001 ARG B 329 ********************** 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 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.926 Fit side-chains REVERT: A 118 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.6795 (mpp) REVERT: A 227 ARG cc_start: 0.7305 (mtt180) cc_final: 0.6825 (mtt90) REVERT: A 299 PHE cc_start: 0.7942 (t80) cc_final: 0.7655 (t80) REVERT: A 329 ARG cc_start: 0.7276 (mtm110) cc_final: 0.6982 (mtm110) REVERT: A 503 ARG cc_start: 0.7364 (pmt-80) cc_final: 0.7046 (pmt-80) REVERT: A 546 ARG cc_start: 0.7616 (mtm110) cc_final: 0.5872 (mmm160) REVERT: B 9 LYS cc_start: 0.7547 (mmmt) cc_final: 0.6977 (mppt) REVERT: B 329 ARG cc_start: 0.7172 (mtm110) cc_final: 0.6971 (mtm110) REVERT: B 444 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7252 (pm20) REVERT: B 510 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6211 (mpt) REVERT: B 546 ARG cc_start: 0.7174 (mtm110) cc_final: 0.5613 (mmm160) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 0.9409 time to fit residues: 135.4532 Evaluate side-chains 142 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 60 SER 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 287 LEU 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 444 GLU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 5.9990 chunk 53 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 0.0470 chunk 84 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.176265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135585 restraints weight = 9530.609| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.70 r_work: 0.3470 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3061 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= 0.196 Angle : 0.628 8.405 11580 Z= 0.302 Chirality : 0.041 0.138 1382 Planarity : 0.006 0.074 1334 Dihedral : 8.092 59.805 1894 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.63 % Allowed : 17.94 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.28), residues: 982 helix: 1.89 (0.19), residues: 764 sheet: None (None), residues: 0 loop : 0.57 (0.49), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 418 HIS 0.001 0.000 HIS B 538 PHE 0.032 0.001 PHE B 478 TYR 0.013 0.001 TYR A 508 ARG 0.013 0.001 ARG B 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7442.27 seconds wall clock time: 129 minutes 33.28 seconds (7773.28 seconds total)