Starting phenix.real_space_refine on Fri Feb 16 20:43:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcp_33125/02_2024/7xcp_33125.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcp_33125/02_2024/7xcp_33125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcp_33125/02_2024/7xcp_33125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcp_33125/02_2024/7xcp_33125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcp_33125/02_2024/7xcp_33125.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcp_33125/02_2024/7xcp_33125.pdb" } resolution = 3.05 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= -0.002 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8261 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 44 5.16 5 C 5274 2.51 5 N 1362 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8261 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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 Time building chain proxies: 6.53, per 1000 atoms: 0.79 Number of scatterers: 8261 At special positions: 0 Unit cell: (73.59, 89.646, 117.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 44 16.00 O 1580 8.00 N 1362 7.00 C 5274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 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 H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 705 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 704 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 374 " 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 44.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.637A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 104 removed outlier: 3.811A pdb=" N GLY A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.536A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.811A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.788A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.056A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.758A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.836A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 445 through 466 removed outlier: 3.624A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.609A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.822A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.802A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.830A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.837A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.615A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.614A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.955A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.641A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.948A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.971A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.940A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.964A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.713A pdb=" N TYR H 109 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP H 99 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE H 107 " --> pdb=" O ASP H 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.587A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.587A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2611 1.34 - 1.46: 1645 1.46 - 1.58: 4164 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8488 Sorted by residual: bond pdb=" N LYS B 386 " pdb=" CA LYS B 386 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.13e+00 bond pdb=" N ASP H 33 " pdb=" CA ASP H 33 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.22e-02 6.72e+03 5.35e+00 bond pdb=" N SER H 31 " pdb=" CA SER H 31 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.61e+00 bond pdb=" CA SER H 31 " pdb=" CB SER H 31 " ideal model delta sigma weight residual 1.530 1.496 0.035 1.69e-02 3.50e+03 4.17e+00 bond pdb=" CA SER H 30 " pdb=" CB SER H 30 " ideal model delta sigma weight residual 1.525 1.497 0.028 1.36e-02 5.41e+03 4.15e+00 ... (remaining 8483 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.64: 177 105.64 - 112.74: 4356 112.74 - 119.84: 2814 119.84 - 126.95: 4060 126.95 - 134.05: 130 Bond angle restraints: 11537 Sorted by residual: angle pdb=" N PHE B 375 " pdb=" CA PHE B 375 " pdb=" C PHE B 375 " ideal model delta sigma weight residual 114.75 106.54 8.21 1.26e+00 6.30e-01 4.25e+01 angle pdb=" C TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta sigma weight residual 109.50 119.51 -10.01 1.69e+00 3.50e-01 3.51e+01 angle pdb=" N LEU B 368 " pdb=" CA LEU B 368 " pdb=" C LEU B 368 " ideal model delta sigma weight residual 114.09 106.60 7.49 1.55e+00 4.16e-01 2.33e+01 angle pdb=" C ASN B 388 " pdb=" CA ASN B 388 " pdb=" CB ASN B 388 " ideal model delta sigma weight residual 110.42 117.25 -6.83 1.99e+00 2.53e-01 1.18e+01 angle pdb=" CA PHE B 375 " pdb=" C PHE B 375 " pdb=" N THR B 376 " ideal model delta sigma weight residual 119.80 115.34 4.46 1.34e+00 5.57e-01 1.11e+01 ... (remaining 11532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4559 17.43 - 34.85: 413 34.85 - 52.28: 86 52.28 - 69.71: 19 69.71 - 87.13: 11 Dihedral angle restraints: 5088 sinusoidal: 2114 harmonic: 2974 Sorted by residual: dihedral pdb=" CA PHE B 374 " pdb=" C PHE B 374 " pdb=" N PHE B 375 " pdb=" CA PHE B 375 " ideal model delta harmonic sigma weight residual 180.00 148.95 31.05 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 55.26 37.74 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" C TYR H 32 " pdb=" N TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta harmonic sigma weight residual -122.60 -132.83 10.23 0 2.50e+00 1.60e-01 1.68e+01 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1063 0.057 - 0.113: 152 0.113 - 0.170: 16 0.170 - 0.227: 2 0.227 - 0.284: 1 Chirality restraints: 1234 Sorted by residual: chirality pdb=" CA TYR H 32 " pdb=" N TYR H 32 " pdb=" C TYR H 32 " pdb=" CB TYR H 32 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ASN B 388 " pdb=" N ASN B 388 " pdb=" C ASN B 388 " pdb=" CB ASN B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CB ILE A 446 " pdb=" CA ILE A 446 " pdb=" CG1 ILE A 446 " pdb=" CG2 ILE A 446 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1231 not shown) Planarity restraints: 1487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE H 29 " 0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C PHE H 29 " -0.068 2.00e-02 2.50e+03 pdb=" O PHE H 29 " 0.026 2.00e-02 2.50e+03 pdb=" N SER H 30 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 32 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C TYR H 32 " -0.055 2.00e-02 2.50e+03 pdb=" O TYR H 32 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP H 33 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO B 373 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.041 5.00e-02 4.00e+02 ... (remaining 1484 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 338 2.73 - 3.27: 8302 3.27 - 3.81: 14303 3.81 - 4.36: 17338 4.36 - 4.90: 29648 Nonbonded interactions: 69929 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 704 " model vdw 2.182 2.230 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.246 2.440 nonbonded pdb=" O ILE A 151 " pdb=" OG SER A 155 " model vdw 2.255 2.440 nonbonded pdb=" O PHE B 490 " pdb=" NH1 ARG B 493 " model vdw 2.258 2.520 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.274 2.440 ... (remaining 69924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 7.160 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 30.090 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 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 : 0.003 0.036 8488 Z= 0.178 Angle : 0.576 10.012 11537 Z= 0.311 Chirality : 0.041 0.284 1234 Planarity : 0.005 0.073 1481 Dihedral : 14.238 87.133 3163 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 0.23 % Allowed : 0.45 % Favored : 99.32 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.72 (0.27), residues: 1010 helix: 1.24 (0.27), residues: 387 sheet: 0.30 (0.44), residues: 147 loop : 0.02 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 110 HIS 0.005 0.001 HIS A 374 PHE 0.010 0.001 PHE A 369 TYR 0.036 0.001 TYR H 32 ARG 0.004 0.000 ARG B 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 TYR cc_start: 0.7527 (t80) cc_final: 0.7282 (t80) REVERT: A 474 MET cc_start: 0.5467 (mmp) cc_final: 0.4811 (tpp) REVERT: B 374 PHE cc_start: 0.4238 (m-80) cc_final: 0.3977 (m-80) REVERT: B 503 VAL cc_start: 0.8213 (t) cc_final: 0.7828 (m) outliers start: 2 outliers final: 2 residues processed: 129 average time/residue: 0.1827 time to fit residues: 33.7094 Evaluate side-chains 119 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 33 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN H 39 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8488 Z= 0.206 Angle : 0.518 8.863 11537 Z= 0.270 Chirality : 0.041 0.278 1234 Planarity : 0.005 0.071 1481 Dihedral : 5.392 52.234 1264 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 1.47 % Allowed : 6.11 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.90 (0.27), residues: 1010 helix: 1.30 (0.26), residues: 396 sheet: 0.68 (0.45), residues: 145 loop : 0.06 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 PHE 0.021 0.002 PHE A 230 TYR 0.017 0.001 TYR B 495 ARG 0.006 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 243 TYR cc_start: 0.7791 (t80) cc_final: 0.7551 (t80) REVERT: A 474 MET cc_start: 0.5328 (mmp) cc_final: 0.4742 (tpp) REVERT: B 374 PHE cc_start: 0.4264 (m-80) cc_final: 0.4061 (m-80) outliers start: 13 outliers final: 8 residues processed: 122 average time/residue: 0.1919 time to fit residues: 32.8657 Evaluate side-chains 123 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 110 TRP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8488 Z= 0.166 Angle : 0.487 8.117 11537 Z= 0.253 Chirality : 0.040 0.189 1234 Planarity : 0.004 0.061 1481 Dihedral : 4.838 41.476 1263 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 0.79 % Allowed : 8.48 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.27), residues: 1010 helix: 1.36 (0.26), residues: 396 sheet: 0.52 (0.44), residues: 147 loop : 0.10 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 165 HIS 0.003 0.001 HIS A 241 PHE 0.022 0.001 PHE A 230 TYR 0.018 0.001 TYR L 49 ARG 0.004 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 0.903 Fit side-chains REVERT: A 243 TYR cc_start: 0.7812 (t80) cc_final: 0.7538 (t80) REVERT: B 374 PHE cc_start: 0.4188 (m-80) cc_final: 0.3964 (m-80) REVERT: H 46 GLU cc_start: 0.7328 (tt0) cc_final: 0.6994 (tt0) outliers start: 7 outliers final: 5 residues processed: 124 average time/residue: 0.1891 time to fit residues: 33.1653 Evaluate side-chains 119 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 47 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8488 Z= 0.168 Angle : 0.490 9.088 11537 Z= 0.253 Chirality : 0.040 0.169 1234 Planarity : 0.004 0.057 1481 Dihedral : 4.558 38.893 1263 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 1.24 % Allowed : 10.07 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.93 (0.27), residues: 1010 helix: 1.46 (0.26), residues: 390 sheet: 0.43 (0.44), residues: 147 loop : 0.06 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 165 HIS 0.003 0.001 HIS A 378 PHE 0.023 0.001 PHE A 230 TYR 0.017 0.001 TYR B 351 ARG 0.003 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.387 Fit side-chains REVERT: A 243 TYR cc_start: 0.7784 (t80) cc_final: 0.7528 (t80) REVERT: B 374 PHE cc_start: 0.4248 (m-80) cc_final: 0.3993 (m-80) REVERT: H 46 GLU cc_start: 0.7260 (tt0) cc_final: 0.7027 (tt0) outliers start: 11 outliers final: 9 residues processed: 124 average time/residue: 0.1984 time to fit residues: 34.9780 Evaluate side-chains 125 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.3980 chunk 54 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8488 Z= 0.150 Angle : 0.481 8.760 11537 Z= 0.247 Chirality : 0.039 0.164 1234 Planarity : 0.004 0.054 1481 Dihedral : 4.354 37.173 1263 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.24 % Allowed : 10.86 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 1010 helix: 1.50 (0.26), residues: 396 sheet: 0.38 (0.43), residues: 147 loop : 0.13 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 165 HIS 0.002 0.001 HIS A 241 PHE 0.022 0.001 PHE A 230 TYR 0.020 0.001 TYR L 49 ARG 0.003 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.931 Fit side-chains REVERT: A 243 TYR cc_start: 0.7796 (t80) cc_final: 0.7549 (t80) REVERT: B 374 PHE cc_start: 0.4266 (m-80) cc_final: 0.4022 (m-80) REVERT: H 46 GLU cc_start: 0.7230 (tt0) cc_final: 0.6999 (tt0) outliers start: 11 outliers final: 9 residues processed: 121 average time/residue: 0.2022 time to fit residues: 34.6521 Evaluate side-chains 121 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8488 Z= 0.171 Angle : 0.491 9.812 11537 Z= 0.251 Chirality : 0.040 0.162 1234 Planarity : 0.004 0.052 1481 Dihedral : 4.343 38.043 1263 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.47 % Allowed : 11.43 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.97 (0.27), residues: 1010 helix: 1.47 (0.26), residues: 397 sheet: 0.31 (0.42), residues: 155 loop : 0.16 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 165 HIS 0.003 0.001 HIS A 378 PHE 0.022 0.001 PHE A 230 TYR 0.020 0.001 TYR L 49 ARG 0.002 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.888 Fit side-chains REVERT: A 243 TYR cc_start: 0.7789 (t80) cc_final: 0.7528 (t80) REVERT: B 374 PHE cc_start: 0.4252 (m-80) cc_final: 0.3996 (m-80) REVERT: B 390 LEU cc_start: 0.5661 (OUTLIER) cc_final: 0.5339 (tt) outliers start: 13 outliers final: 11 residues processed: 123 average time/residue: 0.1908 time to fit residues: 33.2540 Evaluate side-chains 124 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8488 Z= 0.190 Angle : 0.519 11.020 11537 Z= 0.263 Chirality : 0.040 0.164 1234 Planarity : 0.004 0.074 1481 Dihedral : 4.398 39.304 1263 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.58 % Allowed : 11.65 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.94 (0.27), residues: 1010 helix: 1.42 (0.26), residues: 397 sheet: 0.30 (0.41), residues: 155 loop : 0.15 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 165 HIS 0.003 0.001 HIS A 241 PHE 0.023 0.001 PHE A 230 TYR 0.021 0.001 TYR L 49 ARG 0.003 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.824 Fit side-chains REVERT: A 35 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.5571 (mp0) REVERT: A 243 TYR cc_start: 0.7802 (t80) cc_final: 0.7510 (t80) REVERT: A 397 ASN cc_start: 0.7907 (p0) cc_final: 0.7702 (p0) REVERT: B 390 LEU cc_start: 0.5689 (OUTLIER) cc_final: 0.5349 (tt) outliers start: 14 outliers final: 10 residues processed: 122 average time/residue: 0.1989 time to fit residues: 33.9264 Evaluate side-chains 122 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 chunk 47 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 265 HIS A 508 ASN A 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8488 Z= 0.145 Angle : 0.497 10.355 11537 Z= 0.252 Chirality : 0.039 0.160 1234 Planarity : 0.004 0.070 1481 Dihedral : 4.248 37.768 1263 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.47 % Allowed : 12.33 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.97 (0.27), residues: 1010 helix: 1.50 (0.26), residues: 396 sheet: 0.14 (0.41), residues: 157 loop : 0.19 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 165 HIS 0.003 0.001 HIS A 378 PHE 0.022 0.001 PHE A 230 TYR 0.023 0.001 TYR L 49 ARG 0.002 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.911 Fit side-chains REVERT: A 243 TYR cc_start: 0.7763 (t80) cc_final: 0.7502 (t80) REVERT: A 474 MET cc_start: 0.5358 (mmp) cc_final: 0.4901 (tpp) REVERT: B 390 LEU cc_start: 0.5626 (OUTLIER) cc_final: 0.5313 (tt) REVERT: H 46 GLU cc_start: 0.7197 (tt0) cc_final: 0.6996 (tt0) outliers start: 13 outliers final: 10 residues processed: 123 average time/residue: 0.1985 time to fit residues: 34.1668 Evaluate side-chains 123 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8488 Z= 0.233 Angle : 0.535 10.009 11537 Z= 0.273 Chirality : 0.041 0.167 1234 Planarity : 0.004 0.075 1481 Dihedral : 4.470 41.342 1263 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.58 % Allowed : 13.01 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.27), residues: 1010 helix: 1.39 (0.26), residues: 397 sheet: 0.25 (0.41), residues: 161 loop : 0.12 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 PHE 0.024 0.002 PHE A 230 TYR 0.019 0.002 TYR L 49 ARG 0.003 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.858 Fit side-chains REVERT: A 35 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.5552 (mp0) REVERT: B 390 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5347 (tt) outliers start: 14 outliers final: 11 residues processed: 123 average time/residue: 0.1757 time to fit residues: 31.2611 Evaluate side-chains 123 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 8 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.0010 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8488 Z= 0.162 Angle : 0.511 9.951 11537 Z= 0.260 Chirality : 0.041 0.304 1234 Planarity : 0.004 0.073 1481 Dihedral : 4.368 39.402 1263 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.36 % Allowed : 13.12 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.27), residues: 1010 helix: 1.42 (0.26), residues: 400 sheet: 0.13 (0.41), residues: 163 loop : 0.26 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 165 HIS 0.002 0.001 HIS A 378 PHE 0.023 0.001 PHE A 230 TYR 0.021 0.001 TYR L 49 ARG 0.003 0.000 ARG H 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.947 Fit side-chains REVERT: A 35 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.5554 (mp0) REVERT: A 474 MET cc_start: 0.5357 (mmp) cc_final: 0.4895 (tpp) REVERT: B 390 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5411 (tt) outliers start: 12 outliers final: 9 residues processed: 119 average time/residue: 0.1910 time to fit residues: 32.4328 Evaluate side-chains 121 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.215058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.179756 restraints weight = 15232.548| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 3.83 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4035 r_free = 0.4035 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4035 r_free = 0.4035 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8488 Z= 0.197 Angle : 0.522 9.710 11537 Z= 0.265 Chirality : 0.041 0.237 1234 Planarity : 0.004 0.072 1481 Dihedral : 4.381 39.930 1263 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.24 % Allowed : 13.46 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.91 (0.27), residues: 1010 helix: 1.36 (0.26), residues: 403 sheet: 0.19 (0.41), residues: 161 loop : 0.20 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 165 HIS 0.003 0.001 HIS A 378 PHE 0.023 0.001 PHE A 230 TYR 0.020 0.001 TYR L 49 ARG 0.003 0.000 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1952.24 seconds wall clock time: 36 minutes 13.87 seconds (2173.87 seconds total)