Starting phenix.real_space_refine on Tue Sep 24 09:26:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/09_2024/8et9_28589_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/09_2024/8et9_28589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/09_2024/8et9_28589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/09_2024/8et9_28589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/09_2024/8et9_28589_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et9_28589/09_2024/8et9_28589_trim.cif" } resolution = 3.61 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= 0.003 sd= 0.047 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 26 5.16 5 C 2570 2.51 5 N 638 2.21 5 O 655 1.98 5 H 3796 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7685 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 7672 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 27, 'TRANS': 489} Chain breaks: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'WRF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.28, per 1000 atoms: 0.56 Number of scatterers: 7685 At special positions: 0 Unit cell: (118.8, 58.32, 68.04, 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 26 16.00 O 655 8.00 N 638 7.00 C 2570 6.00 H 3796 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 143 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 845.4 milliseconds 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 1 sheets defined 78.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 16 through 39 removed outlier: 4.094A pdb=" N LEU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 31 " --> pdb=" O CYS A 27 " (cutoff:3.500A) Proline residue: A 35 - end of helix removed outlier: 3.879A pdb=" N VAL A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.544A pdb=" N GLU A 58 " --> pdb=" O PRO A 54 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 74 removed outlier: 4.058A pdb=" N ASN A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.541A pdb=" N CYS A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 145 through 175 removed outlier: 3.998A pdb=" N LEU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR A 169 " --> pdb=" O MET A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 removed outlier: 4.256A pdb=" N CYS A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 229 removed outlier: 3.704A pdb=" N VAL A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLY A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 233 through 259 removed outlier: 3.568A pdb=" N VAL A 237 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.507A pdb=" N LEU A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 286 through 293 removed outlier: 3.708A pdb=" N LEU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.636A pdb=" N LYS A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 removed outlier: 4.176A pdb=" N THR A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 368 removed outlier: 3.936A pdb=" N LEU A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 402 removed outlier: 3.684A pdb=" N ASP A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Proline residue: A 389 - end of helix removed outlier: 4.912A pdb=" N ASP A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 Processing helix chain 'A' and resid 429 through 458 removed outlier: 3.965A pdb=" N THR A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 455 " --> pdb=" O CYS A 451 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 492 removed outlier: 4.506A pdb=" N ASN A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 465 " --> pdb=" O PHE A 461 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N CYS A 474 " --> pdb=" O CYS A 470 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) Proline residue: A 482 - end of helix removed outlier: 4.247A pdb=" N TYR A 486 " --> pdb=" O PRO A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 3.707A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.533A pdb=" N ALA A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 246 hydrogen bonds defined for protein. 738 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: 2.43 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 3788 1.02 - 1.22: 23 1.22 - 1.41: 1637 1.41 - 1.61: 2304 1.61 - 1.81: 38 Bond restraints: 7790 Sorted by residual: bond pdb=" CA THR A 444 " pdb=" C THR A 444 " ideal model delta sigma weight residual 1.524 1.445 0.079 1.32e-02 5.74e+03 3.56e+01 bond pdb=" NE ARG A 440 " pdb=" HE ARG A 440 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C TYR A 362 " pdb=" O TYR A 362 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.15e-02 7.56e+03 2.72e+01 bond pdb=" CA GLN A 242 " pdb=" C GLN A 242 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" C GLN A 242 " pdb=" O GLN A 242 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.17e-02 7.31e+03 1.11e+01 ... (remaining 7785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 13791 1.57 - 3.14: 241 3.14 - 4.72: 38 4.72 - 6.29: 4 6.29 - 7.86: 4 Bond angle restraints: 14078 Sorted by residual: angle pdb=" N THR A 444 " pdb=" CA THR A 444 " pdb=" C THR A 444 " ideal model delta sigma weight residual 111.69 104.82 6.87 1.23e+00 6.61e-01 3.12e+01 angle pdb=" C MET A 441 " pdb=" N GLY A 442 " pdb=" CA GLY A 442 " ideal model delta sigma weight residual 120.03 126.10 -6.07 1.12e+00 7.97e-01 2.94e+01 angle pdb=" O ILE A 443 " pdb=" C ILE A 443 " pdb=" N THR A 444 " ideal model delta sigma weight residual 121.87 116.41 5.46 1.01e+00 9.80e-01 2.92e+01 angle pdb=" O GLY A 439 " pdb=" C GLY A 439 " pdb=" N ARG A 440 " ideal model delta sigma weight residual 122.19 126.68 -4.49 9.60e-01 1.09e+00 2.19e+01 angle pdb=" CA GLY A 439 " pdb=" C GLY A 439 " pdb=" N ARG A 440 " ideal model delta sigma weight residual 117.04 112.46 4.58 9.90e-01 1.02e+00 2.14e+01 ... (remaining 14073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 3405 16.75 - 33.49: 188 33.49 - 50.24: 66 50.24 - 66.99: 44 66.99 - 83.74: 2 Dihedral angle restraints: 3705 sinusoidal: 1905 harmonic: 1800 Sorted by residual: dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS A 122 " pdb=" CB CYS A 122 " ideal model delta sinusoidal sigma weight residual -86.00 -125.26 39.26 1 1.00e+01 1.00e-02 2.17e+01 dihedral pdb=" CB CYS A 89 " pdb=" SG CYS A 89 " pdb=" SG CYS A 143 " pdb=" CB CYS A 143 " ideal model delta sinusoidal sigma weight residual 93.00 60.10 32.90 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" CA LYS A 518 " pdb=" CB LYS A 518 " pdb=" CG LYS A 518 " pdb=" CD LYS A 518 " ideal model delta sinusoidal sigma weight residual -180.00 -126.26 -53.74 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 3702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 541 0.055 - 0.110: 85 0.110 - 0.165: 6 0.165 - 0.220: 1 0.220 - 0.275: 1 Chirality restraints: 634 Sorted by residual: chirality pdb=" CA PHE A 388 " pdb=" N PHE A 388 " pdb=" C PHE A 388 " pdb=" CB PHE A 388 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA TYR A 362 " pdb=" N TYR A 362 " pdb=" C TYR A 362 " pdb=" CB TYR A 362 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA LEU A 385 " pdb=" N LEU A 385 " pdb=" C LEU A 385 " pdb=" CB LEU A 385 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 631 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 388 " 0.065 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO A 389 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 443 " -0.020 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ILE A 443 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE A 443 " -0.024 2.00e-02 2.50e+03 pdb=" N THR A 444 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 443 " 0.017 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" N THR A 444 " -0.056 2.00e-02 2.50e+03 pdb=" CA THR A 444 " 0.014 2.00e-02 2.50e+03 pdb=" H THR A 444 " 0.025 2.00e-02 2.50e+03 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 253 2.17 - 2.78: 14676 2.78 - 3.38: 21373 3.38 - 3.99: 25388 3.99 - 4.60: 40814 Nonbonded interactions: 102504 Sorted by model distance: nonbonded pdb="HD11 ILE A 398 " pdb=" HE2 PHE A 452 " model vdw 1.560 2.270 nonbonded pdb=" O LEU A 43 " pdb=" HG SER A 134 " model vdw 1.592 2.450 nonbonded pdb=" O ILE A 350 " pdb="HD22 ASN A 354 " model vdw 1.637 2.450 nonbonded pdb=" OD1 ASN A 72 " pdb=" H TYR A 73 " model vdw 1.663 2.450 nonbonded pdb="HD13 ILE A 398 " pdb=" HE2 PHE A 452 " model vdw 1.688 2.270 ... (remaining 102499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.290 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: 0.140 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.570 Find NCS groups from input model: 0.050 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 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 : 0.005 0.079 3994 Z= 0.329 Angle : 0.612 6.868 5456 Z= 0.400 Chirality : 0.039 0.275 634 Planarity : 0.006 0.099 678 Dihedral : 10.837 83.735 1346 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.52 % Allowed : 4.97 % Favored : 94.50 % 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: 1.38 (0.36), residues: 511 helix: 1.78 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.01 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.001 0.000 HIS A 49 PHE 0.015 0.001 PHE A 388 TYR 0.010 0.001 TYR A 73 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ILE cc_start: 0.9083 (mp) cc_final: 0.8832 (mt) REVERT: A 173 ARG cc_start: 0.7502 (ttt180) cc_final: 0.7000 (ttt-90) REVERT: A 203 MET cc_start: 0.7721 (tmm) cc_final: 0.7465 (tmm) REVERT: A 264 TRP cc_start: 0.7457 (m-90) cc_final: 0.7152 (m-10) REVERT: A 276 PHE cc_start: 0.7787 (m-10) cc_final: 0.7268 (m-80) REVERT: A 301 LYS cc_start: 0.8411 (ttpt) cc_final: 0.7965 (tptp) REVERT: A 367 MET cc_start: 0.5771 (mmt) cc_final: 0.4503 (mmt) REVERT: A 389 PRO cc_start: 0.8302 (Cg_exo) cc_final: 0.8050 (Cg_endo) outliers start: 2 outliers final: 2 residues processed: 131 average time/residue: 0.3586 time to fit residues: 58.3330 Evaluate side-chains 93 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 246 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 0.0050 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3994 Z= 0.193 Angle : 0.539 4.156 5456 Z= 0.290 Chirality : 0.035 0.130 634 Planarity : 0.004 0.056 678 Dihedral : 4.503 44.120 553 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.40 % Allowed : 12.57 % Favored : 84.03 % 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: 1.63 (0.37), residues: 511 helix: 1.97 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.93 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 262 HIS 0.008 0.001 HIS A 368 PHE 0.009 0.001 PHE A 447 TYR 0.012 0.001 TYR A 200 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7619 (ttm) cc_final: 0.7361 (ttp) REVERT: A 164 SER cc_start: 0.8159 (m) cc_final: 0.7916 (p) REVERT: A 173 ARG cc_start: 0.7538 (ttt180) cc_final: 0.7131 (ttt-90) REVERT: A 203 MET cc_start: 0.7760 (tmm) cc_final: 0.7435 (tmm) REVERT: A 264 TRP cc_start: 0.7447 (m-90) cc_final: 0.7143 (m-10) REVERT: A 353 TYR cc_start: 0.8307 (t80) cc_final: 0.8057 (t80) REVERT: A 367 MET cc_start: 0.5689 (mmt) cc_final: 0.4556 (mmt) REVERT: A 445 MET cc_start: 0.7646 (mtp) cc_final: 0.7414 (mtm) outliers start: 13 outliers final: 8 residues processed: 106 average time/residue: 0.2700 time to fit residues: 36.9012 Evaluate side-chains 98 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 490 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3994 Z= 0.229 Angle : 0.537 4.399 5456 Z= 0.291 Chirality : 0.035 0.143 634 Planarity : 0.004 0.047 678 Dihedral : 4.378 43.861 552 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.66 % Allowed : 14.92 % Favored : 81.41 % 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: 1.41 (0.37), residues: 511 helix: 1.81 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.08 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 262 HIS 0.007 0.001 HIS A 368 PHE 0.011 0.001 PHE A 23 TYR 0.011 0.001 TYR A 73 ARG 0.002 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7697 (ttm) cc_final: 0.7431 (ttp) REVERT: A 173 ARG cc_start: 0.7599 (ttt180) cc_final: 0.7194 (ttt-90) REVERT: A 203 MET cc_start: 0.7827 (tmm) cc_final: 0.7557 (tmm) REVERT: A 264 TRP cc_start: 0.7537 (m-90) cc_final: 0.7222 (m-10) REVERT: A 353 TYR cc_start: 0.8343 (t80) cc_final: 0.8107 (t80) REVERT: A 367 MET cc_start: 0.5556 (mmt) cc_final: 0.4462 (mmt) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.2629 time to fit residues: 35.1267 Evaluate side-chains 103 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 490 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3994 Z= 0.247 Angle : 0.540 4.564 5456 Z= 0.293 Chirality : 0.036 0.132 634 Planarity : 0.004 0.042 678 Dihedral : 4.434 43.340 552 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.66 % Allowed : 16.49 % Favored : 79.84 % 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: 1.20 (0.37), residues: 511 helix: 1.66 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.18 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.006 0.002 HIS A 368 PHE 0.012 0.001 PHE A 23 TYR 0.011 0.001 TYR A 73 ARG 0.003 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.7740 (ttm) cc_final: 0.7507 (ttm) REVERT: A 173 ARG cc_start: 0.7590 (ttt180) cc_final: 0.7191 (ttt-90) REVERT: A 203 MET cc_start: 0.7849 (tmm) cc_final: 0.7578 (tmm) REVERT: A 264 TRP cc_start: 0.7644 (m-90) cc_final: 0.7317 (m-10) REVERT: A 345 ARG cc_start: 0.7340 (ttp-170) cc_final: 0.7138 (ttm170) REVERT: A 353 TYR cc_start: 0.8366 (t80) cc_final: 0.8161 (t80) REVERT: A 367 MET cc_start: 0.5550 (mmt) cc_final: 0.4549 (mmt) outliers start: 14 outliers final: 10 residues processed: 99 average time/residue: 0.2775 time to fit residues: 36.1321 Evaluate side-chains 99 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 490 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 50.0000 chunk 28 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3994 Z= 0.264 Angle : 0.552 4.615 5456 Z= 0.302 Chirality : 0.036 0.135 634 Planarity : 0.004 0.040 678 Dihedral : 4.477 43.399 552 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.71 % Allowed : 17.54 % Favored : 77.75 % 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: 0.99 (0.37), residues: 511 helix: 1.49 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.22 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.006 0.002 HIS A 368 PHE 0.013 0.001 PHE A 23 TYR 0.011 0.002 TYR A 73 ARG 0.003 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7591 (ttt180) cc_final: 0.7173 (ttt-90) REVERT: A 203 MET cc_start: 0.7890 (tmm) cc_final: 0.7655 (tmm) REVERT: A 264 TRP cc_start: 0.7640 (m-90) cc_final: 0.7149 (m-10) REVERT: A 345 ARG cc_start: 0.7279 (ttp-170) cc_final: 0.7033 (ttm170) REVERT: A 367 MET cc_start: 0.5610 (mmt) cc_final: 0.4630 (mmt) outliers start: 18 outliers final: 12 residues processed: 104 average time/residue: 0.2745 time to fit residues: 38.1622 Evaluate side-chains 103 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 490 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3994 Z= 0.173 Angle : 0.522 4.348 5456 Z= 0.273 Chirality : 0.035 0.133 634 Planarity : 0.004 0.040 678 Dihedral : 4.377 44.348 552 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.62 % Allowed : 18.59 % Favored : 78.80 % 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: 1.24 (0.37), residues: 511 helix: 1.71 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.20 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 407 HIS 0.005 0.001 HIS A 368 PHE 0.014 0.001 PHE A 276 TYR 0.012 0.001 TYR A 200 ARG 0.001 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7483 (ttt180) cc_final: 0.7099 (ttt-90) REVERT: A 194 MET cc_start: 0.8771 (ttt) cc_final: 0.8459 (ttt) REVERT: A 203 MET cc_start: 0.7824 (tmm) cc_final: 0.7601 (tmm) REVERT: A 264 TRP cc_start: 0.7632 (m-90) cc_final: 0.7242 (m-10) REVERT: A 345 ARG cc_start: 0.7177 (ttp-170) cc_final: 0.6923 (ttm170) REVERT: A 367 MET cc_start: 0.5384 (mmt) cc_final: 0.4446 (mmt) outliers start: 10 outliers final: 9 residues processed: 99 average time/residue: 0.2789 time to fit residues: 36.3744 Evaluate side-chains 98 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 522 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.0770 chunk 9 optimal weight: 50.0000 chunk 31 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3994 Z= 0.185 Angle : 0.517 4.665 5456 Z= 0.274 Chirality : 0.035 0.134 634 Planarity : 0.004 0.044 678 Dihedral : 4.336 44.015 552 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.83 % Allowed : 20.42 % Favored : 77.75 % 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: 1.25 (0.38), residues: 511 helix: 1.76 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.28 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 281 HIS 0.005 0.001 HIS A 368 PHE 0.022 0.001 PHE A 276 TYR 0.010 0.001 TYR A 73 ARG 0.002 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7464 (ttt180) cc_final: 0.7115 (ttt-90) REVERT: A 194 MET cc_start: 0.8783 (ttt) cc_final: 0.8477 (ttt) REVERT: A 264 TRP cc_start: 0.7652 (m-90) cc_final: 0.7248 (m-10) REVERT: A 353 TYR cc_start: 0.8372 (t80) cc_final: 0.7962 (t80) REVERT: A 367 MET cc_start: 0.5251 (mmt) cc_final: 0.4477 (mmt) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.2683 time to fit residues: 33.5054 Evaluate side-chains 92 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 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 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3994 Z= 0.184 Angle : 0.530 5.873 5456 Z= 0.279 Chirality : 0.035 0.137 634 Planarity : 0.004 0.037 678 Dihedral : 4.308 44.700 552 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.88 % Allowed : 20.16 % Favored : 76.96 % 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: 1.22 (0.38), residues: 511 helix: 1.77 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.38 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 355 HIS 0.005 0.001 HIS A 368 PHE 0.027 0.001 PHE A 276 TYR 0.010 0.001 TYR A 73 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7467 (ttt180) cc_final: 0.7087 (ttt-90) REVERT: A 194 MET cc_start: 0.8791 (ttt) cc_final: 0.8477 (ttt) REVERT: A 264 TRP cc_start: 0.7638 (m-90) cc_final: 0.7227 (m-10) REVERT: A 353 TYR cc_start: 0.8327 (t80) cc_final: 0.7900 (t80) REVERT: A 367 MET cc_start: 0.5267 (mmt) cc_final: 0.4565 (mmt) outliers start: 11 outliers final: 10 residues processed: 94 average time/residue: 0.2736 time to fit residues: 33.9553 Evaluate side-chains 96 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3994 Z= 0.193 Angle : 0.536 5.666 5456 Z= 0.283 Chirality : 0.035 0.133 634 Planarity : 0.004 0.036 678 Dihedral : 4.305 44.633 552 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.66 % Allowed : 19.90 % Favored : 76.44 % 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: 1.18 (0.38), residues: 511 helix: 1.70 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 281 HIS 0.005 0.001 HIS A 368 PHE 0.011 0.001 PHE A 23 TYR 0.010 0.001 TYR A 200 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7484 (ttt180) cc_final: 0.7138 (ttt-90) REVERT: A 194 MET cc_start: 0.8783 (ttt) cc_final: 0.8481 (ttt) REVERT: A 264 TRP cc_start: 0.7656 (m-90) cc_final: 0.7232 (m-10) REVERT: A 353 TYR cc_start: 0.8328 (t80) cc_final: 0.7902 (t80) REVERT: A 367 MET cc_start: 0.5230 (mmt) cc_final: 0.4569 (mmt) outliers start: 14 outliers final: 11 residues processed: 97 average time/residue: 0.2493 time to fit residues: 31.6320 Evaluate side-chains 96 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 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 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3994 Z= 0.194 Angle : 0.548 7.159 5456 Z= 0.288 Chirality : 0.035 0.135 634 Planarity : 0.004 0.036 678 Dihedral : 4.306 44.925 552 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.62 % Allowed : 21.99 % Favored : 75.39 % 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: 1.14 (0.38), residues: 511 helix: 1.67 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.31 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 289 HIS 0.005 0.001 HIS A 368 PHE 0.015 0.001 PHE A 276 TYR 0.012 0.001 TYR A 280 ARG 0.001 0.000 ARG A 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 53 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue SER 115 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue MET 369 is missing expected H atoms. Skipping. Residue LEU 428 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7124 (ttt-90) REVERT: A 194 MET cc_start: 0.8773 (ttt) cc_final: 0.8472 (ttt) REVERT: A 264 TRP cc_start: 0.7666 (m-90) cc_final: 0.7236 (m-10) REVERT: A 353 TYR cc_start: 0.8328 (t80) cc_final: 0.7906 (t80) REVERT: A 367 MET cc_start: 0.5198 (mmt) cc_final: 0.3800 (ttp) outliers start: 10 outliers final: 10 residues processed: 90 average time/residue: 0.2902 time to fit residues: 34.4795 Evaluate side-chains 93 residues out of total 435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.0060 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.175214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140206 restraints weight = 15210.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146369 restraints weight = 6394.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150326 restraints weight = 3715.362| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3994 Z= 0.223 Angle : 0.556 6.461 5456 Z= 0.296 Chirality : 0.035 0.131 634 Planarity : 0.004 0.035 678 Dihedral : 4.354 45.390 552 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.88 % Allowed : 21.99 % Favored : 75.13 % 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: 1.02 (0.38), residues: 511 helix: 1.55 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 289 HIS 0.005 0.001 HIS A 368 PHE 0.015 0.001 PHE A 276 TYR 0.011 0.001 TYR A 200 ARG 0.002 0.000 ARG A 463 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2532.04 seconds wall clock time: 44 minutes 38.16 seconds (2678.16 seconds total)