Starting phenix.real_space_refine on Fri Dec 27 20:32:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dv1_27730/12_2024/8dv1_27730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dv1_27730/12_2024/8dv1_27730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dv1_27730/12_2024/8dv1_27730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dv1_27730/12_2024/8dv1_27730.map" model { file = "/net/cci-nas-00/data/ceres_data/8dv1_27730/12_2024/8dv1_27730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dv1_27730/12_2024/8dv1_27730.cif" } resolution = 3.4 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= 0.038 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4183 2.51 5 N 1074 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 6543 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1590 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "D" Number of atoms: 4855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4855 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.44, per 1000 atoms: 0.83 Number of scatterers: 6543 At special positions: 0 Unit cell: (76.311, 87.57, 126.351, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1249 8.00 N 1074 7.00 C 4183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D1001 " - " ASN D 322 " " NAG D1002 " - " ASN D 103 " " NAG D1003 " - " ASN D 432 " " NAG D1004 " - " ASN D 546 " " NAG D1005 " - " ASN D 90 " " NAG D1006 " - " ASN D 53 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 941.3 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 58.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.677A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.589A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.108A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.969A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.736A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 4.486A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 Proline residue: D 235 - end of helix removed outlier: 3.996A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.078A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.881A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.915A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.072A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 350 323 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1266 1.32 - 1.45: 2072 1.45 - 1.58: 3320 1.58 - 1.71: 9 1.71 - 1.84: 58 Bond restraints: 6725 Sorted by residual: bond pdb=" CD2 TRP D 477 " pdb=" CE3 TRP D 477 " ideal model delta sigma weight residual 1.398 1.306 0.092 1.60e-02 3.91e+03 3.28e+01 bond pdb=" CB SER D 44 " pdb=" OG SER D 44 " ideal model delta sigma weight residual 1.417 1.313 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CB TYR A 421 " pdb=" CG TYR A 421 " ideal model delta sigma weight residual 1.512 1.402 0.110 2.20e-02 2.07e+03 2.48e+01 bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.392 0.124 2.50e-02 1.60e+03 2.45e+01 bond pdb=" CB HIS D 540 " pdb=" CG HIS D 540 " ideal model delta sigma weight residual 1.497 1.430 0.067 1.40e-02 5.10e+03 2.29e+01 ... (remaining 6720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 7553 2.16 - 4.32: 1363 4.32 - 6.47: 181 6.47 - 8.63: 35 8.63 - 10.79: 8 Bond angle restraints: 9140 Sorted by residual: angle pdb=" C GLY D 537 " pdb=" N PRO D 538 " pdb=" CA PRO D 538 " ideal model delta sigma weight residual 119.78 128.55 -8.77 1.03e+00 9.43e-01 7.24e+01 angle pdb=" C ALA A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.47 129.12 -9.65 1.16e+00 7.43e-01 6.93e+01 angle pdb=" C ASN D 137 " pdb=" N PRO D 138 " pdb=" CA PRO D 138 " ideal model delta sigma weight residual 119.56 127.64 -8.08 1.02e+00 9.61e-01 6.28e+01 angle pdb=" C VAL D 283 " pdb=" N PRO D 284 " pdb=" CA PRO D 284 " ideal model delta sigma weight residual 119.24 127.24 -8.00 1.04e+00 9.25e-01 5.91e+01 angle pdb=" C SER D 611 " pdb=" N PRO D 612 " pdb=" CA PRO D 612 " ideal model delta sigma weight residual 119.82 127.13 -7.31 9.80e-01 1.04e+00 5.57e+01 ... (remaining 9135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3870 17.80 - 35.59: 146 35.59 - 53.39: 29 53.39 - 71.19: 12 71.19 - 88.98: 5 Dihedral angle restraints: 4062 sinusoidal: 1727 harmonic: 2335 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -140.80 54.80 1 1.00e+01 1.00e-02 4.07e+01 dihedral pdb=" C TYR A 421 " pdb=" N TYR A 421 " pdb=" CA TYR A 421 " pdb=" CB TYR A 421 " ideal model delta harmonic sigma weight residual -122.60 -135.05 12.45 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA ALA D 153 " pdb=" C ALA D 153 " pdb=" N ASN D 154 " pdb=" CA ASN D 154 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 4059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 838 0.137 - 0.274: 124 0.274 - 0.412: 10 0.412 - 0.549: 3 0.549 - 0.686: 1 Chirality restraints: 976 Sorted by residual: chirality pdb=" CA TYR A 421 " pdb=" N TYR A 421 " pdb=" C TYR A 421 " pdb=" CB TYR A 421 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.93 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" C2 NAG D1002 " pdb=" C1 NAG D1002 " pdb=" C3 NAG D1002 " pdb=" N2 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.49 -3.00 0.50 2.00e-01 2.50e+01 6.35e+00 ... (remaining 973 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 90 " 0.217 2.00e-02 2.50e+03 2.54e-01 8.05e+02 pdb=" CG ASN D 90 " -0.123 2.00e-02 2.50e+03 pdb=" OD1 ASN D 90 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN D 90 " -0.403 2.00e-02 2.50e+03 pdb=" C1 NAG D1005 " 0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 163 " 0.287 2.00e-02 2.50e+03 1.39e-01 4.80e+02 pdb=" CG TRP D 163 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP D 163 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP D 163 " -0.148 2.00e-02 2.50e+03 pdb=" NE1 TRP D 163 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TRP D 163 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP D 163 " -0.174 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 163 " 0.148 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 163 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP D 163 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.135 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" CG ASN A 343 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.171 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1716 2.80 - 3.33: 6477 3.33 - 3.85: 11592 3.85 - 4.38: 14234 4.38 - 4.90: 22417 Nonbonded interactions: 56436 Sorted by model distance: nonbonded pdb=" O4 NAG D1004 " pdb=" O6 NAG D1004 " model vdw 2.277 3.040 nonbonded pdb=" N ASN D 103 " pdb=" OD1 ASN D 103 " model vdw 2.318 3.120 nonbonded pdb=" N ASN D 432 " pdb=" OD1 ASN D 432 " model vdw 2.327 3.120 nonbonded pdb=" N ASN D 546 " pdb=" OD1 ASN D 546 " model vdw 2.356 3.120 nonbonded pdb=" N ASN D 322 " pdb=" OD1 ASN D 322 " model vdw 2.411 3.120 ... (remaining 56431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.018 0.125 6725 Z= 1.160 Angle : 1.709 10.789 9140 Z= 1.169 Chirality : 0.101 0.686 976 Planarity : 0.011 0.139 1177 Dihedral : 10.891 88.982 2543 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.43 % Allowed : 1.57 % Favored : 98.00 % Cbeta Deviations : 0.27 % 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: -0.24 (0.28), residues: 792 helix: -0.33 (0.23), residues: 378 sheet: 0.33 (0.67), residues: 58 loop : 0.18 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.287 0.015 TRP D 163 HIS 0.010 0.002 HIS D 241 PHE 0.069 0.008 PHE D 32 TYR 0.070 0.011 TYR D 180 ARG 0.016 0.001 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.7661 (m-40) cc_final: 0.7098 (p0) REVERT: A 472 ILE cc_start: 0.7249 (mm) cc_final: 0.7040 (mm) REVERT: A 500 THR cc_start: 0.8413 (p) cc_final: 0.8103 (p) REVERT: D 476 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8347 (mptt) outliers start: 3 outliers final: 1 residues processed: 200 average time/residue: 0.2308 time to fit residues: 58.0532 Evaluate side-chains 121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 322 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 0.0570 chunk 71 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 ASN D 96 GLN D 401 HIS D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6725 Z= 0.237 Angle : 0.685 11.810 9140 Z= 0.354 Chirality : 0.054 0.662 976 Planarity : 0.005 0.040 1177 Dihedral : 7.471 89.057 1013 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.72 % Allowed : 9.44 % Favored : 88.84 % 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: 1.13 (0.30), residues: 792 helix: 1.32 (0.27), residues: 375 sheet: 0.07 (0.66), residues: 60 loop : 0.41 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 165 HIS 0.006 0.001 HIS D 374 PHE 0.018 0.002 PHE D 369 TYR 0.022 0.002 TYR D 183 ARG 0.004 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7992 (pt) cc_final: 0.7545 (pt) REVERT: A 355 ARG cc_start: 0.8464 (tpt170) cc_final: 0.8138 (tpt170) REVERT: A 409 GLN cc_start: 0.8772 (mt0) cc_final: 0.8522 (mt0) REVERT: A 469 SER cc_start: 0.8746 (t) cc_final: 0.8544 (p) REVERT: D 26 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8201 (ttmt) REVERT: D 56 GLU cc_start: 0.8022 (pm20) cc_final: 0.7576 (pm20) REVERT: D 115 ARG cc_start: 0.7942 (mmm-85) cc_final: 0.7622 (mmm-85) REVERT: D 168 TRP cc_start: 0.7199 (t-100) cc_final: 0.6822 (t-100) REVERT: D 206 ASP cc_start: 0.8825 (t70) cc_final: 0.8591 (t0) outliers start: 12 outliers final: 6 residues processed: 157 average time/residue: 0.2157 time to fit residues: 44.0586 Evaluate side-chains 130 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 233 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 0.0060 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 ASN D 210 ASN D 373 HIS D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6725 Z= 0.264 Angle : 0.674 13.805 9140 Z= 0.339 Chirality : 0.052 0.607 976 Planarity : 0.004 0.029 1177 Dihedral : 7.061 79.372 1011 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.29 % Allowed : 9.73 % Favored : 86.98 % 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: 1.05 (0.30), residues: 792 helix: 1.35 (0.27), residues: 380 sheet: -0.40 (0.65), residues: 61 loop : 0.31 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 165 HIS 0.007 0.001 HIS D 378 PHE 0.015 0.002 PHE A 374 TYR 0.019 0.001 TYR D 385 ARG 0.004 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 423 TYR cc_start: 0.8528 (t80) cc_final: 0.8221 (t80) REVERT: A 498 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: D 26 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8405 (ttmt) REVERT: D 56 GLU cc_start: 0.8050 (pm20) cc_final: 0.7572 (pm20) REVERT: D 115 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7739 (mmm-85) REVERT: D 168 TRP cc_start: 0.7248 (t-100) cc_final: 0.6684 (t-100) REVERT: D 206 ASP cc_start: 0.8833 (t70) cc_final: 0.8607 (t0) REVERT: D 401 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.7534 (t-90) REVERT: D 494 ASP cc_start: 0.8221 (t70) cc_final: 0.8006 (t0) outliers start: 23 outliers final: 11 residues processed: 132 average time/residue: 0.2471 time to fit residues: 42.5360 Evaluate side-chains 126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6725 Z= 0.264 Angle : 0.645 10.964 9140 Z= 0.324 Chirality : 0.051 0.596 976 Planarity : 0.004 0.027 1177 Dihedral : 6.250 50.971 1011 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.43 % Allowed : 11.87 % Favored : 85.69 % 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: 0.95 (0.30), residues: 792 helix: 1.39 (0.26), residues: 380 sheet: -0.44 (0.65), residues: 61 loop : 0.10 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 165 HIS 0.005 0.001 HIS D 378 PHE 0.014 0.002 PHE A 374 TYR 0.018 0.001 TYR D 385 ARG 0.004 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.782 Fit side-chains REVERT: A 498 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: D 56 GLU cc_start: 0.8020 (pm20) cc_final: 0.7576 (pm20) REVERT: D 63 ASN cc_start: 0.7999 (m-40) cc_final: 0.7737 (m-40) REVERT: D 115 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7736 (mmm-85) REVERT: D 168 TRP cc_start: 0.7191 (t-100) cc_final: 0.6666 (t-100) REVERT: D 249 MET cc_start: 0.7986 (tpt) cc_final: 0.7736 (tpt) outliers start: 17 outliers final: 10 residues processed: 132 average time/residue: 0.2041 time to fit residues: 35.4441 Evaluate side-chains 125 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6725 Z= 0.195 Angle : 0.604 9.282 9140 Z= 0.302 Chirality : 0.049 0.561 976 Planarity : 0.003 0.027 1177 Dihedral : 5.647 51.868 1011 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.58 % Allowed : 12.30 % Favored : 85.12 % 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: 1.01 (0.30), residues: 792 helix: 1.52 (0.27), residues: 381 sheet: -0.51 (0.64), residues: 61 loop : 0.04 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 165 HIS 0.004 0.001 HIS D 378 PHE 0.013 0.001 PHE A 374 TYR 0.018 0.001 TYR D 385 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.6494 (t70) cc_final: 0.6057 (m-30) REVERT: A 466 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7571 (ttm-80) REVERT: A 498 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: D 26 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8319 (mttt) REVERT: D 63 ASN cc_start: 0.8040 (m-40) cc_final: 0.7809 (m-40) REVERT: D 163 TRP cc_start: 0.5847 (t60) cc_final: 0.5326 (t60) outliers start: 18 outliers final: 14 residues processed: 128 average time/residue: 0.2151 time to fit residues: 35.8217 Evaluate side-chains 126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 530 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 8 optimal weight: 0.0170 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN D 437 ASN D 493 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6725 Z= 0.188 Angle : 0.578 8.270 9140 Z= 0.293 Chirality : 0.048 0.547 976 Planarity : 0.003 0.027 1177 Dihedral : 5.408 51.435 1011 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.43 % Allowed : 14.16 % Favored : 83.40 % 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: 1.04 (0.31), residues: 792 helix: 1.54 (0.27), residues: 381 sheet: -0.46 (0.65), residues: 61 loop : 0.06 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 165 HIS 0.004 0.001 HIS D 378 PHE 0.012 0.001 PHE A 374 TYR 0.018 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.6655 (t70) cc_final: 0.6096 (m-30) REVERT: A 498 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7867 (mt0) outliers start: 17 outliers final: 12 residues processed: 126 average time/residue: 0.2107 time to fit residues: 35.3230 Evaluate side-chains 120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6725 Z= 0.213 Angle : 0.608 15.607 9140 Z= 0.305 Chirality : 0.049 0.562 976 Planarity : 0.003 0.027 1177 Dihedral : 5.511 51.320 1011 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.29 % Allowed : 14.45 % Favored : 83.26 % 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: 0.96 (0.30), residues: 792 helix: 1.52 (0.26), residues: 381 sheet: -0.42 (0.66), residues: 61 loop : -0.05 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 168 HIS 0.005 0.001 HIS D 378 PHE 0.012 0.001 PHE A 374 TYR 0.018 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.6585 (t70) cc_final: 0.5892 (m-30) REVERT: A 498 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7852 (mt0) outliers start: 16 outliers final: 15 residues processed: 121 average time/residue: 0.1976 time to fit residues: 31.8609 Evaluate side-chains 124 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN D 437 ASN D 493 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6725 Z= 0.237 Angle : 0.606 7.846 9140 Z= 0.310 Chirality : 0.049 0.573 976 Planarity : 0.004 0.028 1177 Dihedral : 5.519 51.231 1011 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.58 % Allowed : 15.02 % Favored : 82.40 % 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: 0.92 (0.30), residues: 792 helix: 1.46 (0.26), residues: 383 sheet: -0.36 (0.65), residues: 62 loop : -0.06 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 168 HIS 0.004 0.001 HIS D 378 PHE 0.013 0.001 PHE A 374 TYR 0.018 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 364 ASP cc_start: 0.6704 (t70) cc_final: 0.5956 (m-30) REVERT: A 498 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: D 249 MET cc_start: 0.8095 (tpt) cc_final: 0.7782 (tpp) REVERT: D 290 ASN cc_start: 0.7719 (t0) cc_final: 0.7435 (t0) REVERT: D 530 CYS cc_start: 0.7207 (t) cc_final: 0.6944 (t) outliers start: 18 outliers final: 15 residues processed: 123 average time/residue: 0.2049 time to fit residues: 34.0345 Evaluate side-chains 123 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN D 437 ASN D 493 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6725 Z= 0.213 Angle : 0.599 7.840 9140 Z= 0.308 Chirality : 0.048 0.552 976 Planarity : 0.003 0.027 1177 Dihedral : 5.505 51.834 1011 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.29 % Allowed : 15.59 % Favored : 82.12 % 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: 0.88 (0.30), residues: 792 helix: 1.43 (0.26), residues: 383 sheet: -0.40 (0.66), residues: 62 loop : -0.09 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 168 HIS 0.005 0.001 HIS D 378 PHE 0.012 0.001 PHE D 369 TYR 0.018 0.001 TYR D 385 ARG 0.003 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7777 (mt0) REVERT: D 134 ASN cc_start: 0.2944 (t0) cc_final: 0.2709 (t0) REVERT: D 163 TRP cc_start: 0.6063 (t60) cc_final: 0.5833 (t60) REVERT: D 249 MET cc_start: 0.8065 (tpt) cc_final: 0.7757 (tpp) REVERT: D 476 LYS cc_start: 0.8603 (tppt) cc_final: 0.8305 (tppt) REVERT: D 530 CYS cc_start: 0.7197 (t) cc_final: 0.6941 (t) outliers start: 16 outliers final: 14 residues processed: 122 average time/residue: 0.2170 time to fit residues: 34.8753 Evaluate side-chains 124 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.0030 chunk 9 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6725 Z= 0.224 Angle : 0.607 7.829 9140 Z= 0.316 Chirality : 0.049 0.557 976 Planarity : 0.004 0.027 1177 Dihedral : 5.524 51.765 1011 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.15 % Allowed : 16.17 % Favored : 81.69 % 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: 0.87 (0.30), residues: 792 helix: 1.44 (0.26), residues: 383 sheet: -0.46 (0.66), residues: 61 loop : -0.12 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 168 HIS 0.005 0.001 HIS D 378 PHE 0.012 0.001 PHE A 374 TYR 0.018 0.001 TYR D 385 ARG 0.003 0.000 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: D 115 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7595 (mmm160) REVERT: D 474 MET cc_start: 0.8006 (mmp) cc_final: 0.7792 (mmm) REVERT: D 476 LYS cc_start: 0.8622 (tppt) cc_final: 0.8328 (tppt) REVERT: D 530 CYS cc_start: 0.7203 (t) cc_final: 0.6954 (t) outliers start: 15 outliers final: 14 residues processed: 115 average time/residue: 0.2014 time to fit residues: 30.9628 Evaluate side-chains 120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS D 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.108453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096011 restraints weight = 15253.028| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.70 r_work: 0.3351 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6725 Z= 0.279 Angle : 0.659 12.972 9140 Z= 0.340 Chirality : 0.050 0.586 976 Planarity : 0.004 0.028 1177 Dihedral : 5.682 51.128 1011 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.00 % Allowed : 16.88 % Favored : 81.12 % 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: 0.70 (0.30), residues: 792 helix: 1.26 (0.26), residues: 383 sheet: -0.34 (0.65), residues: 62 loop : -0.19 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 168 HIS 0.007 0.001 HIS D 378 PHE 0.014 0.002 PHE A 374 TYR 0.017 0.001 TYR D 385 ARG 0.003 0.001 ARG A 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1963.46 seconds wall clock time: 37 minutes 8.27 seconds (2228.27 seconds total)