Starting phenix.real_space_refine on Tue Feb 13 12:55:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/02_2024/8woz_37703.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/02_2024/8woz_37703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/02_2024/8woz_37703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/02_2024/8woz_37703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/02_2024/8woz_37703.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/02_2024/8woz_37703.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 3994 2.51 5 N 1032 2.21 5 O 1181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 38": "OD1" <-> "OD2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6244 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4858 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1385 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 160} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.88, per 1000 atoms: 0.62 Number of scatterers: 6244 At special positions: 0 Unit cell: (77.28, 97.98, 107.64, 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 36 16.00 O 1181 8.00 N 1032 7.00 C 3994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " 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 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 54.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.876A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 78 removed outlier: 3.612A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.224A pdb=" N THR A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.868A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.783A pdb=" N ALA A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.712A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.841A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) 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 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 247 removed outlier: 3.516A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.659A pdb=" N PHE A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 4.059A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.841A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.762A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.838A 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 405 removed outlier: 3.927A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 4.188A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.778A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.512A pdb=" N THR A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) 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: 3.679A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.832A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.524A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.613A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.606A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.616A pdb=" N LEU B 355 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 356' Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.358A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.323A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.610A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.143A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 441 276 hydrogen bonds defined for protein. 774 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: 1.63 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1261 1.33 - 1.45: 1667 1.45 - 1.57: 3434 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6420 Sorted by residual: bond pdb=" N ASP A 292 " pdb=" CA ASP A 292 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.29e-02 6.01e+03 1.19e+01 bond pdb=" N HIS A 378 " pdb=" CA HIS A 378 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.43e+00 bond pdb=" N ASN A 90 " pdb=" CA ASN A 90 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.78e+00 bond pdb=" N VAL A 293 " pdb=" CA VAL A 293 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.38e+00 bond pdb=" C ASP A 292 " pdb=" O ASP A 292 " ideal model delta sigma weight residual 1.235 1.208 0.028 1.26e-02 6.30e+03 4.78e+00 ... (remaining 6415 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.13: 101 104.13 - 111.61: 2725 111.61 - 119.08: 2376 119.08 - 126.56: 3382 126.56 - 134.03: 140 Bond angle restraints: 8724 Sorted by residual: angle pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " pdb=" CG HIS A 378 " ideal model delta sigma weight residual 113.80 119.10 -5.30 1.00e+00 1.00e+00 2.81e+01 angle pdb=" C ASP A 292 " pdb=" CA ASP A 292 " pdb=" CB ASP A 292 " ideal model delta sigma weight residual 110.42 99.96 10.46 1.99e+00 2.53e-01 2.76e+01 angle pdb=" C HIS A 378 " pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " ideal model delta sigma weight residual 110.79 102.59 8.20 1.66e+00 3.63e-01 2.44e+01 angle pdb=" O GLY A 377 " pdb=" C GLY A 377 " pdb=" N HIS A 378 " ideal model delta sigma weight residual 122.19 117.62 4.57 9.60e-01 1.09e+00 2.27e+01 angle pdb=" CA GLY A 377 " pdb=" C GLY A 377 " pdb=" N HIS A 378 " ideal model delta sigma weight residual 117.04 121.49 -4.45 9.90e-01 1.02e+00 2.02e+01 ... (remaining 8719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 3262 17.74 - 35.49: 398 35.49 - 53.23: 113 53.23 - 70.97: 9 70.97 - 88.71: 8 Dihedral angle restraints: 3790 sinusoidal: 1530 harmonic: 2260 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -126.19 40.19 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA TRP A 473 " pdb=" C TRP A 473 " pdb=" N MET A 474 " pdb=" CA MET A 474 " ideal model delta harmonic sigma weight residual 180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CB CYS B 467 " pdb=" SG CYS B 467 " pdb=" SG CYS B 474 " pdb=" CB CYS B 474 " ideal model delta sinusoidal sigma weight residual -86.00 -55.24 -30.76 1 1.00e+01 1.00e-02 1.35e+01 ... (remaining 3787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 578 0.035 - 0.071: 246 0.071 - 0.106: 65 0.106 - 0.141: 18 0.141 - 0.176: 3 Chirality restraints: 910 Sorted by residual: chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CB VAL A 581 " pdb=" CA VAL A 581 " pdb=" CG1 VAL A 581 " pdb=" CG2 VAL A 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA HIS A 378 " pdb=" N HIS A 378 " pdb=" C HIS A 378 " pdb=" CB HIS A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 907 not shown) Planarity restraints: 1127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO A 258 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 398 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO B 399 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 399 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 399 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 378 " -0.025 2.00e-02 2.50e+03 2.04e-02 6.24e+00 pdb=" CG HIS A 378 " 0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS A 378 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 378 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 378 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 378 " -0.015 2.00e-02 2.50e+03 ... (remaining 1124 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 143 2.70 - 3.25: 6140 3.25 - 3.80: 9376 3.80 - 4.35: 11814 4.35 - 4.90: 19566 Nonbonded interactions: 47039 Sorted by model distance: nonbonded pdb=" O VAL A 293 " pdb=" OG1 THR A 294 " model vdw 2.147 2.440 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.241 2.520 nonbonded pdb=" OG SER B 362 " pdb=" O ALA B 422 " model vdw 2.243 2.440 nonbonded pdb=" ND2 ASN A 137 " pdb=" OE1 GLN A 139 " model vdw 2.249 2.520 nonbonded pdb=" OD1 ASP A 198 " pdb=" N ASP A 201 " model vdw 2.314 2.520 ... (remaining 47034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.010 Extract box with map and model: 6.760 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.660 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 0.052 6420 Z= 0.215 Angle : 0.704 12.263 8724 Z= 0.395 Chirality : 0.042 0.176 910 Planarity : 0.006 0.107 1127 Dihedral : 16.315 88.714 2328 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.15 % Allowed : 22.88 % Favored : 76.97 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.70 % 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 (0.32), residues: 764 helix: 0.44 (0.28), residues: 381 sheet: 0.84 (0.81), residues: 40 loop : -1.48 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 594 HIS 0.012 0.001 HIS A 378 PHE 0.018 0.001 PHE A 72 TYR 0.015 0.001 TYR A 183 ARG 0.002 0.000 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.635 Fit side-chains REVERT: A 207 TYR cc_start: 0.7010 (m-10) cc_final: 0.6729 (m-10) REVERT: A 247 LYS cc_start: 0.6663 (tptt) cc_final: 0.6414 (mmtt) REVERT: A 539 LEU cc_start: 0.8697 (tp) cc_final: 0.8487 (tt) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.1740 time to fit residues: 27.3213 Evaluate side-chains 114 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 0.0010 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6420 Z= 0.194 Angle : 0.573 11.894 8724 Z= 0.294 Chirality : 0.041 0.161 910 Planarity : 0.005 0.074 1127 Dihedral : 4.621 54.468 843 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.78 % Allowed : 21.40 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.40 (0.31), residues: 764 helix: 0.66 (0.27), residues: 389 sheet: 0.87 (0.81), residues: 42 loop : -1.54 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 PHE 0.016 0.001 PHE A 603 TYR 0.017 0.001 TYR A 183 ARG 0.003 0.000 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.707 Fit side-chains REVERT: A 247 LYS cc_start: 0.6981 (tptt) cc_final: 0.6662 (mmtt) REVERT: A 471 GLU cc_start: 0.7683 (pm20) cc_final: 0.7374 (pm20) REVERT: A 539 LEU cc_start: 0.8705 (tp) cc_final: 0.8488 (tt) outliers start: 12 outliers final: 5 residues processed: 129 average time/residue: 0.1759 time to fit residues: 30.8184 Evaluate side-chains 117 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 337 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6420 Z= 0.215 Angle : 0.574 12.420 8724 Z= 0.295 Chirality : 0.041 0.154 910 Planarity : 0.005 0.064 1127 Dihedral : 4.239 17.290 841 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.42 % Allowed : 21.69 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.36 (0.31), residues: 764 helix: 0.71 (0.27), residues: 388 sheet: 0.98 (0.81), residues: 42 loop : -1.56 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 594 HIS 0.006 0.001 HIS A 378 PHE 0.016 0.001 PHE A 603 TYR 0.019 0.002 TYR A 183 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.674 Fit side-chains REVERT: A 95 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6615 (mtt-85) REVERT: A 207 TYR cc_start: 0.6935 (m-10) cc_final: 0.6668 (m-10) REVERT: A 247 LYS cc_start: 0.7158 (tptt) cc_final: 0.6852 (tptt) REVERT: A 471 GLU cc_start: 0.7731 (pm20) cc_final: 0.7469 (pm20) REVERT: A 594 TRP cc_start: 0.7188 (OUTLIER) cc_final: 0.6832 (t-100) outliers start: 23 outliers final: 10 residues processed: 135 average time/residue: 0.1683 time to fit residues: 30.3946 Evaluate side-chains 125 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.0370 chunk 46 optimal weight: 0.0030 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.3468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6420 Z= 0.165 Angle : 0.562 11.649 8724 Z= 0.284 Chirality : 0.040 0.158 910 Planarity : 0.005 0.057 1127 Dihedral : 4.116 16.153 841 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.23 % Allowed : 22.44 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.11 (0.31), residues: 764 helix: 0.93 (0.27), residues: 379 sheet: 0.71 (0.82), residues: 44 loop : -1.36 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 594 HIS 0.004 0.001 HIS A 241 PHE 0.015 0.001 PHE A 603 TYR 0.015 0.001 TYR A 183 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 247 LYS cc_start: 0.7199 (tptt) cc_final: 0.6876 (tptt) REVERT: A 364 VAL cc_start: 0.6510 (OUTLIER) cc_final: 0.6129 (t) REVERT: A 471 GLU cc_start: 0.7774 (pm20) cc_final: 0.7423 (pm20) outliers start: 15 outliers final: 9 residues processed: 131 average time/residue: 0.1644 time to fit residues: 29.1083 Evaluate side-chains 123 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 30 optimal weight: 0.1980 chunk 62 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6420 Z= 0.265 Angle : 0.607 12.586 8724 Z= 0.312 Chirality : 0.043 0.166 910 Planarity : 0.005 0.058 1127 Dihedral : 4.369 17.921 841 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.57 % Allowed : 21.99 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.38 (0.31), residues: 764 helix: 0.74 (0.27), residues: 381 sheet: 0.87 (0.83), residues: 44 loop : -1.59 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 477 HIS 0.008 0.002 HIS A 378 PHE 0.016 0.002 PHE A 603 TYR 0.021 0.002 TYR A 183 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.7336 (tptt) cc_final: 0.7078 (tptt) REVERT: A 364 VAL cc_start: 0.6802 (OUTLIER) cc_final: 0.6452 (t) REVERT: A 471 GLU cc_start: 0.7860 (pm20) cc_final: 0.7493 (pm20) outliers start: 24 outliers final: 14 residues processed: 140 average time/residue: 0.1711 time to fit residues: 32.0229 Evaluate side-chains 139 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 0.0040 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6420 Z= 0.199 Angle : 0.577 12.163 8724 Z= 0.294 Chirality : 0.041 0.167 910 Planarity : 0.005 0.057 1127 Dihedral : 4.278 17.374 841 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.82 % Allowed : 23.92 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.20 (0.31), residues: 764 helix: 0.85 (0.27), residues: 378 sheet: 0.93 (0.84), residues: 44 loop : -1.42 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.005 0.001 HIS A 378 PHE 0.015 0.001 PHE A 603 TYR 0.017 0.001 TYR A 183 ARG 0.006 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8020 (mttm) cc_final: 0.7784 (mttm) REVERT: A 202 TYR cc_start: 0.7394 (t80) cc_final: 0.7185 (t80) REVERT: A 364 VAL cc_start: 0.6418 (OUTLIER) cc_final: 0.6016 (t) REVERT: A 471 GLU cc_start: 0.7846 (pm20) cc_final: 0.7487 (pm20) outliers start: 19 outliers final: 11 residues processed: 134 average time/residue: 0.1728 time to fit residues: 30.8536 Evaluate side-chains 126 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.0370 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6420 Z= 0.208 Angle : 0.584 11.784 8724 Z= 0.296 Chirality : 0.041 0.154 910 Planarity : 0.005 0.057 1127 Dihedral : 4.250 17.236 841 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.53 % Allowed : 23.92 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.20 (0.31), residues: 764 helix: 0.83 (0.27), residues: 379 sheet: 0.97 (0.84), residues: 44 loop : -1.41 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.005 0.001 HIS A 378 PHE 0.014 0.001 PHE A 603 TYR 0.017 0.001 TYR A 183 ARG 0.005 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8030 (mttm) cc_final: 0.7796 (mttm) REVERT: A 202 TYR cc_start: 0.7428 (t80) cc_final: 0.7189 (t80) REVERT: A 364 VAL cc_start: 0.6457 (OUTLIER) cc_final: 0.6072 (t) REVERT: A 471 GLU cc_start: 0.7862 (pm20) cc_final: 0.7507 (pm20) REVERT: A 485 VAL cc_start: 0.7639 (t) cc_final: 0.7248 (t) outliers start: 17 outliers final: 12 residues processed: 132 average time/residue: 0.1647 time to fit residues: 29.1355 Evaluate side-chains 129 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6420 Z= 0.275 Angle : 0.643 12.464 8724 Z= 0.324 Chirality : 0.043 0.164 910 Planarity : 0.005 0.058 1127 Dihedral : 4.407 18.281 841 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.38 % Allowed : 24.81 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.41 (0.31), residues: 764 helix: 0.66 (0.27), residues: 380 sheet: 1.03 (0.84), residues: 44 loop : -1.55 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 165 HIS 0.007 0.001 HIS A 378 PHE 0.014 0.002 PHE A 603 TYR 0.026 0.002 TYR A 215 ARG 0.005 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8122 (mttm) cc_final: 0.7858 (mttm) REVERT: A 202 TYR cc_start: 0.7509 (t80) cc_final: 0.7283 (t80) REVERT: A 364 VAL cc_start: 0.6528 (OUTLIER) cc_final: 0.6139 (t) REVERT: A 471 GLU cc_start: 0.7873 (pm20) cc_final: 0.7529 (pm20) REVERT: A 485 VAL cc_start: 0.7692 (t) cc_final: 0.7305 (t) outliers start: 16 outliers final: 12 residues processed: 138 average time/residue: 0.1762 time to fit residues: 32.6189 Evaluate side-chains 137 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.0070 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN B 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6420 Z= 0.202 Angle : 0.605 11.777 8724 Z= 0.304 Chirality : 0.041 0.166 910 Planarity : 0.005 0.057 1127 Dihedral : 4.256 17.012 841 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.08 % Allowed : 25.71 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.23 (0.31), residues: 764 helix: 0.83 (0.27), residues: 379 sheet: 0.99 (0.84), residues: 44 loop : -1.46 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.005 0.001 HIS A 378 PHE 0.014 0.001 PHE A 603 TYR 0.019 0.001 TYR A 215 ARG 0.005 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 144 LEU cc_start: 0.7865 (tp) cc_final: 0.7609 (tt) REVERT: A 174 LYS cc_start: 0.8085 (mttm) cc_final: 0.7852 (mttm) REVERT: A 202 TYR cc_start: 0.7403 (t80) cc_final: 0.7163 (t80) REVERT: A 364 VAL cc_start: 0.6336 (OUTLIER) cc_final: 0.5946 (t) REVERT: A 471 GLU cc_start: 0.7847 (pm20) cc_final: 0.7513 (pm20) REVERT: A 485 VAL cc_start: 0.7618 (t) cc_final: 0.7221 (t) outliers start: 14 outliers final: 11 residues processed: 124 average time/residue: 0.1817 time to fit residues: 30.2884 Evaluate side-chains 125 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.2980 chunk 60 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6420 Z= 0.211 Angle : 0.621 12.253 8724 Z= 0.310 Chirality : 0.041 0.159 910 Planarity : 0.005 0.056 1127 Dihedral : 4.239 17.081 841 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.93 % Allowed : 26.60 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.21 (0.31), residues: 764 helix: 0.87 (0.27), residues: 379 sheet: 0.92 (0.84), residues: 42 loop : -1.46 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.006 0.001 HIS A 378 PHE 0.014 0.001 PHE A 72 TYR 0.021 0.001 TYR A 215 ARG 0.005 0.000 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8067 (mttm) cc_final: 0.7832 (mttm) REVERT: A 202 TYR cc_start: 0.7426 (t80) cc_final: 0.7181 (t80) REVERT: A 364 VAL cc_start: 0.6264 (OUTLIER) cc_final: 0.5904 (t) REVERT: A 471 GLU cc_start: 0.7857 (pm20) cc_final: 0.7526 (pm20) outliers start: 13 outliers final: 11 residues processed: 126 average time/residue: 0.1851 time to fit residues: 31.1721 Evaluate side-chains 127 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.160010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139197 restraints weight = 9562.261| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.41 r_work: 0.3672 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6420 Z= 0.221 Angle : 0.633 11.926 8724 Z= 0.316 Chirality : 0.042 0.158 910 Planarity : 0.005 0.056 1127 Dihedral : 4.258 17.159 841 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.23 % Allowed : 26.75 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.20 (0.31), residues: 764 helix: 0.87 (0.27), residues: 379 sheet: 0.93 (0.84), residues: 44 loop : -1.46 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.006 0.001 HIS A 378 PHE 0.014 0.002 PHE A 603 TYR 0.021 0.002 TYR A 215 ARG 0.005 0.000 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1746.96 seconds wall clock time: 32 minutes 23.41 seconds (1943.41 seconds total)