Starting phenix.real_space_refine on Tue Feb 11 21:41:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mjn_23879/02_2025/7mjn_23879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjn_23879/02_2025/7mjn_23879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mjn_23879/02_2025/7mjn_23879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjn_23879/02_2025/7mjn_23879.map" model { file = "/net/cci-nas-00/data/ceres_data/7mjn_23879/02_2025/7mjn_23879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjn_23879/02_2025/7mjn_23879.cif" } resolution = 3.29 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= 0.000 sd= 0.019 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 4175 2.51 5 N 1075 2.21 5 O 1239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6526 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1594 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" 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: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.59, per 1000 atoms: 0.70 Number of scatterers: 6526 At special positions: 0 Unit cell: (100, 72, 121, 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 1239 8.00 N 1075 7.00 C 4175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 322 " " NAG E 704 " - " ASN E 546 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 906.8 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 56.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.587A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.924A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.622A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.519A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 52 removed outlier: 3.807A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.721A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.871A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 4.017A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.639A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 158 through 194 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 221 through 249 removed outlier: 3.953A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.721A pdb=" N MET E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 294 through 300 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.636A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.538A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.707A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 4.328A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 4.122A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.564A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 4.282A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.631A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 564 removed outlier: 4.247A pdb=" N GLU E 564 " --> pdb=" O GLY E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 removed outlier: 3.726A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.757A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.932A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.070A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 891 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: 1.76 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.47: 1755 1.47 - 1.59: 2816 1.59 - 1.71: 0 1.71 - 1.83: 58 Bond restraints: 6709 Sorted by residual: bond pdb=" C GLU E 145 " pdb=" N PRO E 146 " ideal model delta sigma weight residual 1.337 1.369 -0.033 1.06e-02 8.90e+03 9.53e+00 bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 ... (remaining 6704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 8752 1.89 - 3.77: 297 3.77 - 5.66: 47 5.66 - 7.55: 16 7.55 - 9.43: 6 Bond angle restraints: 9118 Sorted by residual: angle pdb=" N GLY E 147 " pdb=" CA GLY E 147 " pdb=" C GLY E 147 " ideal model delta sigma weight residual 110.21 114.42 -4.21 9.10e-01 1.21e+00 2.14e+01 angle pdb=" C ASP E 292 " pdb=" N VAL E 293 " pdb=" CA VAL E 293 " ideal model delta sigma weight residual 121.97 130.09 -8.12 1.80e+00 3.09e-01 2.04e+01 angle pdb=" O GLY E 147 " pdb=" C GLY E 147 " pdb=" N LEU E 148 " ideal model delta sigma weight residual 121.85 124.37 -2.52 5.60e-01 3.19e+00 2.02e+01 angle pdb=" CG ARG B 346 " pdb=" CD ARG B 346 " pdb=" NE ARG B 346 " ideal model delta sigma weight residual 112.00 120.75 -8.75 2.20e+00 2.07e-01 1.58e+01 angle pdb=" N LYS E 234 " pdb=" CA LYS E 234 " pdb=" C LYS E 234 " ideal model delta sigma weight residual 113.16 117.91 -4.75 1.42e+00 4.96e-01 1.12e+01 ... (remaining 9113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3652 17.64 - 35.27: 302 35.27 - 52.91: 57 52.91 - 70.54: 8 70.54 - 88.18: 5 Dihedral angle restraints: 4024 sinusoidal: 1685 harmonic: 2339 Sorted by residual: dihedral pdb=" CA ALA E 396 " pdb=" C ALA E 396 " pdb=" N ASN E 397 " pdb=" CA ASN E 397 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TRP E 606 " pdb=" C TRP E 606 " pdb=" N SER E 607 " pdb=" CA SER E 607 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE E 233 " pdb=" C ILE E 233 " pdb=" N LYS E 234 " pdb=" CA LYS E 234 " ideal model delta harmonic sigma weight residual -180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 4021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 710 0.049 - 0.097: 176 0.097 - 0.146: 67 0.146 - 0.195: 10 0.195 - 0.243: 5 Chirality restraints: 968 Sorted by residual: chirality pdb=" CB VAL E 581 " pdb=" CA VAL E 581 " pdb=" CG1 VAL E 581 " pdb=" CG2 VAL E 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL E 447 " pdb=" CA VAL E 447 " pdb=" CG1 VAL E 447 " pdb=" CG2 VAL E 447 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU E 520 " pdb=" CB LEU E 520 " pdb=" CD1 LEU E 520 " pdb=" CD2 LEU E 520 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 965 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 463 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 467 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" CG ASP B 467 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP B 467 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP B 467 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 134 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO E 135 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 135 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 135 " -0.026 5.00e-02 4.00e+02 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1922 2.82 - 3.34: 6061 3.34 - 3.86: 10993 3.86 - 4.38: 12649 4.38 - 4.90: 21926 Nonbonded interactions: 53551 Sorted by model distance: nonbonded pdb=" OH TYR E 183 " pdb=" OD1 ASP E 509 " model vdw 2.295 3.040 nonbonded pdb=" OD1 ASP E 494 " pdb=" OG1 THR E 496 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR E 215 " pdb=" OE1 GLU E 571 " model vdw 2.352 3.040 nonbonded pdb=" OG SER B 383 " pdb=" OG1 THR B 385 " model vdw 2.354 3.040 nonbonded pdb=" O PHE E 314 " pdb=" OG SER E 317 " model vdw 2.378 3.040 ... (remaining 53546 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: 3.830 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: 0.060 Process input model: 18.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 0.053 6709 Z= 0.285 Angle : 0.844 9.434 9118 Z= 0.462 Chirality : 0.053 0.243 968 Planarity : 0.007 0.054 1175 Dihedral : 13.379 88.178 2506 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.27), residues: 793 helix: -0.80 (0.23), residues: 374 sheet: 0.98 (0.78), residues: 51 loop : -1.07 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 165 HIS 0.006 0.002 HIS E 378 PHE 0.016 0.002 PHE E 369 TYR 0.015 0.002 TYR E 237 ARG 0.013 0.001 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.726 Fit side-chains REVERT: B 506 GLN cc_start: 0.8870 (mt0) cc_final: 0.8656 (mt0) REVERT: E 123 MET cc_start: 0.9504 (mmt) cc_final: 0.9287 (mmt) REVERT: E 190 MET cc_start: 0.9238 (tmm) cc_final: 0.9036 (tmm) REVERT: E 249 MET cc_start: 0.9160 (mmm) cc_final: 0.8745 (mmt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1888 time to fit residues: 15.0721 Evaluate side-chains 41 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.041973 restraints weight = 27601.690| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.98 r_work: 0.2591 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6709 Z= 0.243 Angle : 0.560 8.286 9118 Z= 0.290 Chirality : 0.041 0.164 968 Planarity : 0.004 0.036 1175 Dihedral : 5.728 58.233 971 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.43 % Allowed : 4.57 % Favored : 95.00 % 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: 0.05 (0.29), residues: 793 helix: 0.62 (0.25), residues: 392 sheet: 0.09 (0.74), residues: 58 loop : -0.56 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.012 0.001 PHE E 369 TYR 0.016 0.001 TYR B 451 ARG 0.005 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: B 386 LYS cc_start: 0.9408 (mtmm) cc_final: 0.9179 (mtmt) REVERT: E 123 MET cc_start: 0.9447 (mmt) cc_final: 0.9224 (mmt) REVERT: E 190 MET cc_start: 0.9263 (tmm) cc_final: 0.9036 (tmm) REVERT: E 249 MET cc_start: 0.9120 (mmm) cc_final: 0.8672 (mmt) REVERT: E 323 MET cc_start: 0.9450 (mmp) cc_final: 0.9227 (mmp) REVERT: E 332 MET cc_start: 0.8075 (ppp) cc_final: 0.7829 (ppp) outliers start: 3 outliers final: 1 residues processed: 47 average time/residue: 0.1696 time to fit residues: 11.4486 Evaluate side-chains 43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 248 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 75 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.056981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.042927 restraints weight = 28499.816| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 4.03 r_work: 0.2652 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6709 Z= 0.151 Angle : 0.502 9.151 9118 Z= 0.252 Chirality : 0.040 0.179 968 Planarity : 0.004 0.031 1175 Dihedral : 4.730 56.431 971 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.71 % Allowed : 6.29 % Favored : 93.00 % 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: 0.58 (0.29), residues: 793 helix: 1.18 (0.26), residues: 392 sheet: 0.26 (0.79), residues: 48 loop : -0.44 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 165 HIS 0.003 0.001 HIS E 535 PHE 0.011 0.001 PHE E 369 TYR 0.012 0.001 TYR B 369 ARG 0.003 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.711 Fit side-chains REVERT: B 406 GLU cc_start: 0.8899 (pm20) cc_final: 0.8618 (mp0) REVERT: E 249 MET cc_start: 0.9123 (mmm) cc_final: 0.8655 (mmt) REVERT: E 323 MET cc_start: 0.9428 (mmp) cc_final: 0.9078 (mmp) REVERT: E 332 MET cc_start: 0.8196 (ppp) cc_final: 0.7975 (ppp) REVERT: E 462 MET cc_start: 0.9269 (mmm) cc_final: 0.9037 (mtm) REVERT: E 474 MET cc_start: 0.8454 (mmp) cc_final: 0.7769 (mmm) outliers start: 5 outliers final: 0 residues processed: 49 average time/residue: 0.1958 time to fit residues: 13.5913 Evaluate side-chains 40 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 60 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 32 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.057572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.043136 restraints weight = 28099.620| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 4.18 r_work: 0.2627 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6709 Z= 0.135 Angle : 0.477 7.812 9118 Z= 0.240 Chirality : 0.040 0.175 968 Planarity : 0.003 0.034 1175 Dihedral : 4.403 55.973 971 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.57 % Allowed : 7.29 % Favored : 92.14 % 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: 793 helix: 1.47 (0.27), residues: 392 sheet: -0.02 (0.77), residues: 48 loop : -0.29 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.002 0.001 HIS E 505 PHE 0.011 0.001 PHE E 369 TYR 0.010 0.001 TYR B 369 ARG 0.002 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.757 Fit side-chains REVERT: B 406 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: E 249 MET cc_start: 0.9092 (mmm) cc_final: 0.8638 (mmt) REVERT: E 323 MET cc_start: 0.9400 (mmp) cc_final: 0.9146 (mmp) REVERT: E 332 MET cc_start: 0.8317 (ppp) cc_final: 0.8089 (ppp) REVERT: E 411 SER cc_start: 0.9169 (m) cc_final: 0.8650 (p) REVERT: E 446 ILE cc_start: 0.9338 (mm) cc_final: 0.9072 (mp) REVERT: E 462 MET cc_start: 0.9270 (mmm) cc_final: 0.9055 (mtm) outliers start: 4 outliers final: 1 residues processed: 50 average time/residue: 0.1644 time to fit residues: 12.2917 Evaluate side-chains 44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.042360 restraints weight = 28131.293| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 4.15 r_work: 0.2608 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6709 Z= 0.172 Angle : 0.504 8.846 9118 Z= 0.250 Chirality : 0.040 0.164 968 Planarity : 0.003 0.034 1175 Dihedral : 4.318 55.694 971 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.57 % Allowed : 8.57 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.30), residues: 793 helix: 1.57 (0.27), residues: 398 sheet: -0.04 (0.79), residues: 48 loop : -0.16 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 PHE 0.011 0.001 PHE E 369 TYR 0.010 0.001 TYR E 515 ARG 0.002 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.782 Fit side-chains REVERT: B 406 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: E 249 MET cc_start: 0.9091 (mmm) cc_final: 0.8631 (mmt) REVERT: E 332 MET cc_start: 0.8377 (ppp) cc_final: 0.8173 (ppp) REVERT: E 411 SER cc_start: 0.9177 (m) cc_final: 0.8738 (p) REVERT: E 462 MET cc_start: 0.9283 (mmm) cc_final: 0.9056 (mtm) outliers start: 4 outliers final: 1 residues processed: 45 average time/residue: 0.1442 time to fit residues: 9.8538 Evaluate side-chains 44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 0.0060 chunk 33 optimal weight: 5.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.042486 restraints weight = 27970.410| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 4.11 r_work: 0.2610 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6709 Z= 0.162 Angle : 0.493 9.429 9118 Z= 0.245 Chirality : 0.040 0.163 968 Planarity : 0.003 0.037 1175 Dihedral : 4.259 55.476 971 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.29 % Allowed : 9.57 % Favored : 90.14 % 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: 1.12 (0.30), residues: 793 helix: 1.69 (0.27), residues: 394 sheet: -0.05 (0.78), residues: 48 loop : -0.17 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 PHE 0.011 0.001 PHE E 369 TYR 0.016 0.001 TYR B 369 ARG 0.002 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.703 Fit side-chains REVERT: B 378 LYS cc_start: 0.9242 (mmtm) cc_final: 0.9033 (mmtm) REVERT: B 406 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8573 (mp0) REVERT: E 249 MET cc_start: 0.9070 (mmm) cc_final: 0.8634 (mmt) REVERT: E 270 MET cc_start: 0.9315 (tpp) cc_final: 0.8723 (tpp) REVERT: E 332 MET cc_start: 0.8484 (ppp) cc_final: 0.8268 (ppp) REVERT: E 411 SER cc_start: 0.9170 (m) cc_final: 0.8739 (p) REVERT: E 462 MET cc_start: 0.9287 (mmm) cc_final: 0.9055 (mtm) outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.1648 time to fit residues: 11.1603 Evaluate side-chains 43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.042516 restraints weight = 28195.720| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 4.16 r_work: 0.2609 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6709 Z= 0.167 Angle : 0.505 10.161 9118 Z= 0.248 Chirality : 0.040 0.163 968 Planarity : 0.003 0.036 1175 Dihedral : 4.210 55.381 971 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.14 % Allowed : 9.57 % Favored : 89.29 % 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: 1.23 (0.31), residues: 793 helix: 1.69 (0.27), residues: 398 sheet: -0.01 (0.78), residues: 48 loop : -0.02 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 PHE 0.011 0.001 PHE E 369 TYR 0.015 0.001 TYR B 369 ARG 0.002 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: E 249 MET cc_start: 0.9066 (mmm) cc_final: 0.8627 (mmt) REVERT: E 323 MET cc_start: 0.9378 (mmp) cc_final: 0.9154 (mmp) REVERT: E 332 MET cc_start: 0.8542 (ppp) cc_final: 0.8314 (ppp) REVERT: E 462 MET cc_start: 0.9288 (mmm) cc_final: 0.9051 (mtm) outliers start: 8 outliers final: 2 residues processed: 48 average time/residue: 0.1693 time to fit residues: 11.8314 Evaluate side-chains 45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 143 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 28 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.0060 chunk 69 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.042586 restraints weight = 28266.195| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 4.17 r_work: 0.2617 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6709 Z= 0.163 Angle : 0.515 11.350 9118 Z= 0.250 Chirality : 0.040 0.164 968 Planarity : 0.003 0.037 1175 Dihedral : 4.184 55.324 971 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.57 % Allowed : 10.29 % Favored : 89.14 % 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: 1.26 (0.31), residues: 793 helix: 1.73 (0.27), residues: 398 sheet: -0.04 (0.78), residues: 48 loop : -0.02 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 PHE 0.010 0.001 PHE E 523 TYR 0.015 0.001 TYR B 369 ARG 0.002 0.000 ARG E 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: E 249 MET cc_start: 0.9067 (mmm) cc_final: 0.8629 (mmt) REVERT: E 270 MET cc_start: 0.9292 (tpp) cc_final: 0.8358 (tpp) REVERT: E 332 MET cc_start: 0.8535 (ppp) cc_final: 0.8325 (ppp) REVERT: E 462 MET cc_start: 0.9281 (mmm) cc_final: 0.9047 (mtm) outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.1763 time to fit residues: 11.6337 Evaluate side-chains 45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 11 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 75 optimal weight: 0.0010 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.057596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.043137 restraints weight = 28561.202| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 4.21 r_work: 0.2630 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6709 Z= 0.159 Angle : 0.534 12.150 9118 Z= 0.257 Chirality : 0.040 0.166 968 Planarity : 0.003 0.037 1175 Dihedral : 4.142 55.278 971 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.57 % Allowed : 11.43 % Favored : 88.00 % 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: 1.28 (0.31), residues: 793 helix: 1.76 (0.27), residues: 398 sheet: -0.06 (0.78), residues: 48 loop : -0.01 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 165 HIS 0.002 0.001 HIS E 374 PHE 0.011 0.001 PHE E 314 TYR 0.014 0.001 TYR B 369 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8578 (mp0) REVERT: E 249 MET cc_start: 0.9095 (mmm) cc_final: 0.8680 (mmt) REVERT: E 270 MET cc_start: 0.9282 (tpp) cc_final: 0.8414 (tpp) REVERT: E 332 MET cc_start: 0.8568 (ppp) cc_final: 0.8358 (ppp) REVERT: E 462 MET cc_start: 0.9270 (mmm) cc_final: 0.9037 (mtm) outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.1707 time to fit residues: 11.2218 Evaluate side-chains 45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.056855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.042349 restraints weight = 28216.721| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 4.15 r_work: 0.2605 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6709 Z= 0.204 Angle : 0.548 12.735 9118 Z= 0.264 Chirality : 0.041 0.159 968 Planarity : 0.003 0.037 1175 Dihedral : 4.200 55.398 971 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.57 % Allowed : 11.14 % Favored : 88.29 % 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: 1.30 (0.31), residues: 793 helix: 1.79 (0.27), residues: 399 sheet: -0.08 (0.78), residues: 48 loop : -0.02 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 165 HIS 0.003 0.001 HIS E 34 PHE 0.011 0.001 PHE E 314 TYR 0.014 0.001 TYR B 369 ARG 0.002 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8574 (mp0) REVERT: E 249 MET cc_start: 0.9076 (mmm) cc_final: 0.8661 (mmt) REVERT: E 270 MET cc_start: 0.9289 (tpp) cc_final: 0.8425 (tpp) REVERT: E 332 MET cc_start: 0.8583 (ppp) cc_final: 0.8358 (ppp) REVERT: E 462 MET cc_start: 0.9275 (mmm) cc_final: 0.9026 (mtm) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.1747 time to fit residues: 11.3110 Evaluate side-chains 45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 366 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.042148 restraints weight = 28235.911| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.95 r_work: 0.2623 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6709 Z= 0.215 Angle : 0.557 12.932 9118 Z= 0.269 Chirality : 0.041 0.154 968 Planarity : 0.003 0.037 1175 Dihedral : 4.261 55.287 971 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.86 % Allowed : 11.14 % Favored : 88.00 % 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 (0.31), residues: 793 helix: 1.87 (0.27), residues: 393 sheet: -0.13 (0.79), residues: 48 loop : 0.04 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 165 HIS 0.004 0.001 HIS E 34 PHE 0.013 0.001 PHE E 314 TYR 0.014 0.001 TYR B 369 ARG 0.002 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3256.90 seconds wall clock time: 58 minutes 58.94 seconds (3538.94 seconds total)