Starting phenix.real_space_refine on Sat Dec 28 07:55:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvi_42621/12_2024/8uvi_42621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvi_42621/12_2024/8uvi_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_42621/12_2024/8uvi_42621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvi_42621/12_2024/8uvi_42621.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvi_42621/12_2024/8uvi_42621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvi_42621/12_2024/8uvi_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.88, per 1000 atoms: 0.72 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: 2.46 Conformation dependent library (CDL) restraints added in 960.3 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: 0.79 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: 2.29 Time building geometry restraints manager: 2.71 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: 0.00 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: 1.570 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 22.340 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- 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 : 0.885 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: 1.1078 time to fit residues: 222.5996 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 : 0.881 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.902 Fit side-chains REVERT: A 73 MET cc_start: 0.8542 (mtt) cc_final: 0.8246 (mtt) REVERT: A 86 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.7607 (t80) REVERT: A 131 MET cc_start: 0.7073 (mtp) cc_final: 0.6843 (mtm) REVERT: A 510 MET cc_start: 0.7275 (mmt) cc_final: 0.6962 (mpt) REVERT: A 534 PHE cc_start: 0.6686 (m-80) cc_final: 0.5819 (m-80) REVERT: A 546 ARG cc_start: 0.6950 (mtm110) cc_final: 0.5569 (mmm160) REVERT: B 73 MET cc_start: 0.8508 (mtt) cc_final: 0.8280 (mtt) REVERT: B 86 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.7699 (t80) REVERT: B 259 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6911 (tp) REVERT: B 444 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: B 510 MET cc_start: 0.7363 (mmt) cc_final: 0.7132 (mpt) REVERT: B 540 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7427 (mp) outliers start: 23 outliers final: 8 residues processed: 147 average time/residue: 1.0495 time to fit residues: 166.3108 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 : 0.922 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2197 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= 0.214 Angle : 0.611 9.710 11580 Z= 0.293 Chirality : 0.042 0.177 1382 Planarity : 0.006 0.075 1334 Dihedral : 7.943 59.455 1894 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.11 % Allowed : 12.08 % Favored : 84.81 % 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: 2.20 (0.28), residues: 982 helix: 1.80 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.46 (0.49), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 418 HIS 0.001 0.000 HIS B 538 PHE 0.013 0.001 PHE B 391 TYR 0.013 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 160 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.854 Fit side-chains REVERT: A 131 MET cc_start: 0.7022 (mtp) cc_final: 0.6737 (mtm) REVERT: A 227 ARG cc_start: 0.7336 (mtt180) cc_final: 0.7008 (mtt90) REVERT: A 228 ARG cc_start: 0.6907 (mtm-85) cc_final: 0.6571 (mpp80) REVERT: A 546 ARG cc_start: 0.6829 (mtm110) cc_final: 0.5382 (mmm160) REVERT: B 105 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7840 (tp30) REVERT: B 259 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7002 (tp) REVERT: B 444 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6755 (pm20) REVERT: B 510 MET cc_start: 0.7141 (mmt) cc_final: 0.6736 (mpt) outliers start: 26 outliers final: 10 residues processed: 144 average time/residue: 0.9858 time to fit residues: 153.9951 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 : 0.873 ------------------------------------------------------------------------------- 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 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 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 88 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 46 optimal weight: 0.0270 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2491 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= 0.220 Angle : 0.613 9.804 11580 Z= 0.293 Chirality : 0.042 0.186 1382 Planarity : 0.006 0.074 1334 Dihedral : 7.958 59.547 1894 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.63 % Allowed : 14.11 % Favored : 83.25 % 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: 762 sheet: None (None), residues: 0 loop : 0.56 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 418 HIS 0.001 0.000 HIS B 538 PHE 0.024 0.001 PHE B 234 TYR 0.012 0.001 TYR B 508 ARG 0.008 0.001 ARG B 227 *********************** 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 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.861 Fit side-chains REVERT: A 105 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: A 118 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.6252 (mpp) REVERT: A 131 MET cc_start: 0.7185 (mtp) cc_final: 0.6781 (mtm) REVERT: A 227 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6952 (mtt90) REVERT: A 510 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.6414 (mpt) REVERT: A 546 ARG cc_start: 0.7197 (mtm110) cc_final: 0.5744 (mmm160) REVERT: B 105 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: B 259 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6937 (tp) REVERT: B 444 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6741 (pm20) REVERT: B 544 MET cc_start: 0.6465 (ptm) cc_final: 0.6140 (ptp) REVERT: B 546 ARG cc_start: 0.6708 (mtm110) cc_final: 0.5445 (mmm160) outliers start: 22 outliers final: 10 residues processed: 141 average time/residue: 1.0039 time to fit residues: 152.3775 Evaluate side-chains 140 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 53 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 80 optimal weight: 0.0170 chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2571 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= 0.198 Angle : 0.592 9.356 11580 Z= 0.284 Chirality : 0.041 0.153 1382 Planarity : 0.006 0.073 1334 Dihedral : 7.811 59.909 1894 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.11 % Allowed : 14.71 % Favored : 82.18 % 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: 2.42 (0.28), residues: 982 helix: 1.94 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.59 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 418 HIS 0.001 0.000 HIS B 538 PHE 0.019 0.001 PHE B 234 TYR 0.010 0.001 TYR B 508 ARG 0.010 0.001 ARG A 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 160 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.820 Fit side-chains REVERT: A 118 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.6182 (mpp) REVERT: A 131 MET cc_start: 0.7172 (mtp) cc_final: 0.6745 (mtm) REVERT: A 227 ARG cc_start: 0.7325 (mtt180) cc_final: 0.6961 (mtt90) REVERT: A 510 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6452 (mpt) REVERT: A 546 ARG cc_start: 0.7181 (mtm110) cc_final: 0.5817 (mmm160) REVERT: B 9 LYS cc_start: 0.7586 (mmmt) cc_final: 0.7118 (mtmt) REVERT: B 444 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: B 487 THR cc_start: 0.7452 (t) cc_final: 0.7130 (m) REVERT: B 510 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6203 (mpt) REVERT: B 546 ARG cc_start: 0.6625 (mtm110) cc_final: 0.5429 (mmm160) outliers start: 26 outliers final: 11 residues processed: 145 average time/residue: 0.9422 time to fit residues: 148.4439 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 : 0.868 ------------------------------------------------------------------------------- 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 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 550 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2816 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= 0.264 Angle : 0.671 10.738 11580 Z= 0.319 Chirality : 0.044 0.176 1382 Planarity : 0.006 0.073 1334 Dihedral : 8.205 59.709 1894 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.87 % Allowed : 15.43 % 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: 2.31 (0.28), residues: 982 helix: 1.85 (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 A 418 HIS 0.001 0.000 HIS A 538 PHE 0.025 0.002 PHE B 234 TYR 0.012 0.001 TYR B 508 ARG 0.011 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 158 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.814 Fit side-chains REVERT: A 118 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.6384 (mpp) REVERT: A 131 MET cc_start: 0.7192 (mtp) cc_final: 0.6752 (mtm) REVERT: A 227 ARG cc_start: 0.7293 (mtt180) cc_final: 0.6943 (mtt90) REVERT: A 510 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6418 (mpt) REVERT: A 546 ARG cc_start: 0.7258 (mtm110) cc_final: 0.5853 (mmm160) REVERT: B 9 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7111 (mppt) REVERT: B 444 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6918 (pm20) REVERT: B 546 ARG cc_start: 0.6746 (mtm110) cc_final: 0.5412 (mmm160) outliers start: 24 outliers final: 13 residues processed: 144 average time/residue: 0.9432 time to fit residues: 147.1819 Evaluate side-chains 141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 522 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 10 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2868 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= 0.229 Angle : 0.637 9.682 11580 Z= 0.303 Chirality : 0.042 0.140 1382 Planarity : 0.006 0.072 1334 Dihedral : 8.100 59.125 1894 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.11 % Allowed : 16.03 % Favored : 80.86 % 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: 1.86 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.56 (0.48), residues: 222 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 0.024 0.001 PHE B 234 TYR 0.015 0.001 TYR A 508 ARG 0.009 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 151 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.880 Fit side-chains REVERT: A 118 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.6342 (mpp) REVERT: A 131 MET cc_start: 0.7076 (mtp) cc_final: 0.6523 (mtm) REVERT: A 227 ARG cc_start: 0.7299 (mtt180) cc_final: 0.6950 (mtt90) REVERT: A 234 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7751 (t80) REVERT: A 510 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6573 (mpt) REVERT: A 544 MET cc_start: 0.6326 (ptm) cc_final: 0.6037 (ptm) REVERT: A 546 ARG cc_start: 0.7330 (mtm110) cc_final: 0.5962 (mmm160) REVERT: B 444 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6881 (pm20) REVERT: B 510 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6028 (mpt) REVERT: B 546 ARG cc_start: 0.6818 (mtm110) cc_final: 0.5545 (mmm160) outliers start: 26 outliers final: 13 residues processed: 139 average time/residue: 0.9025 time to fit residues: 136.9827 Evaluate side-chains 143 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 234 PHE 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 444 GLU Chi-restraints excluded: chain B residue 510 MET 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: 0.4980 chunk 56 optimal weight: 0.0970 chunk 28 optimal weight: 0.2980 chunk 18 optimal weight: 0.0000 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 74 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.2582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8464 Z= 0.182 Angle : 0.602 10.132 11580 Z= 0.288 Chirality : 0.041 0.220 1382 Planarity : 0.006 0.073 1334 Dihedral : 7.818 59.008 1894 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.11 % Allowed : 16.63 % Favored : 80.26 % 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: 2.42 (0.28), residues: 982 helix: 1.95 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.53 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 418 HIS 0.002 0.000 HIS A 538 PHE 0.018 0.001 PHE B 234 TYR 0.014 0.001 TYR A 508 ARG 0.010 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 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.897 Fit side-chains REVERT: A 118 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.6110 (mpp) REVERT: A 131 MET cc_start: 0.7048 (mtp) cc_final: 0.6602 (mtm) REVERT: A 227 ARG cc_start: 0.7336 (mtt180) cc_final: 0.6979 (mtt90) REVERT: A 503 ARG cc_start: 0.7289 (pmt-80) cc_final: 0.7048 (pmt-80) REVERT: A 546 ARG cc_start: 0.6939 (mtm110) cc_final: 0.5461 (mmp-170) REVERT: B 9 LYS cc_start: 0.7512 (mmmt) cc_final: 0.7049 (mtmt) REVERT: B 510 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6104 (mpt) outliers start: 26 outliers final: 10 residues processed: 141 average time/residue: 0.9117 time to fit residues: 139.6802 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 : 0.865 ------------------------------------------------------------------------------- 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 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 259 LEU Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 510 MET 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 82 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8464 Z= 0.236 Angle : 0.644 9.386 11580 Z= 0.309 Chirality : 0.043 0.203 1382 Planarity : 0.006 0.074 1334 Dihedral : 8.138 59.911 1894 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.51 % Allowed : 17.82 % Favored : 79.67 % 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: 2.39 (0.28), residues: 982 helix: 1.90 (0.19), residues: 760 sheet: None (None), residues: 0 loop : 0.66 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 418 HIS 0.002 0.000 HIS B 538 PHE 0.047 0.001 PHE B 234 TYR 0.013 0.001 TYR A 508 ARG 0.009 0.001 ARG B 227 *********************** 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: 21 poor density : 125 time to evaluate : 0.889 Fit side-chains REVERT: A 118 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.6327 (mpp) REVERT: A 131 MET cc_start: 0.7196 (mtp) cc_final: 0.6611 (mtm) REVERT: A 227 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6969 (mtt90) REVERT: A 546 ARG cc_start: 0.7314 (mtm110) cc_final: 0.5904 (mmm160) REVERT: B 510 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6108 (mpt) REVERT: B 544 MET cc_start: 0.6569 (ptm) cc_final: 0.6240 (ptm) REVERT: B 546 ARG cc_start: 0.6708 (mtm110) cc_final: 0.5484 (mmm160) outliers start: 21 outliers final: 12 residues processed: 138 average time/residue: 0.8732 time to fit residues: 131.2515 Evaluate side-chains 136 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 510 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 93 optimal weight: 0.0770 chunk 56 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 0.0000 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 60 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.1742 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2984 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= 0.181 Angle : 0.623 10.968 11580 Z= 0.296 Chirality : 0.042 0.283 1382 Planarity : 0.006 0.073 1334 Dihedral : 7.818 59.143 1894 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.15 % Allowed : 18.42 % 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: 2.49 (0.28), residues: 982 helix: 1.99 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.61 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 418 HIS 0.001 0.000 HIS A 505 PHE 0.033 0.001 PHE B 478 TYR 0.009 0.001 TYR A 508 ARG 0.014 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 141 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.932 Fit side-chains REVERT: A 131 MET cc_start: 0.7098 (mtp) cc_final: 0.6542 (mtm) REVERT: A 227 ARG cc_start: 0.7307 (mtt180) cc_final: 0.6970 (mtt90) REVERT: A 503 ARG cc_start: 0.7275 (pmt-80) cc_final: 0.7051 (pmt-80) REVERT: A 546 ARG cc_start: 0.7161 (mtm110) cc_final: 0.5728 (mmm160) REVERT: B 9 LYS cc_start: 0.7487 (mmmt) cc_final: 0.7025 (mppt) REVERT: B 510 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6069 (mpt) REVERT: B 557 LEU cc_start: 0.7939 (mt) cc_final: 0.7570 (mp) outliers start: 18 outliers final: 9 residues processed: 134 average time/residue: 0.9366 time to fit residues: 136.1020 Evaluate side-chains 130 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 461 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 86 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 510 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 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 = 0.4011 r_free = 0.4011 target = 0.174847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133806 restraints weight = 9380.563| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.69 r_work: 0.3445 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3028 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= 0.224 Angle : 0.652 10.332 11580 Z= 0.313 Chirality : 0.043 0.237 1382 Planarity : 0.006 0.074 1334 Dihedral : 8.091 59.976 1894 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.03 % Allowed : 18.78 % Favored : 79.19 % 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: 2.39 (0.28), residues: 982 helix: 1.90 (0.19), residues: 762 sheet: None (None), residues: 0 loop : 0.62 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 418 HIS 0.003 0.000 HIS B 538 PHE 0.030 0.001 PHE B 478 TYR 0.011 0.001 TYR A 508 ARG 0.012 0.001 ARG B 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3143.96 seconds wall clock time: 57 minutes 18.53 seconds (3438.53 seconds total)