Starting phenix.real_space_refine on Fri Nov 15 09:32:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/11_2024/8ext_28662.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/11_2024/8ext_28662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/11_2024/8ext_28662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/11_2024/8ext_28662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/11_2024/8ext_28662.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ext_28662/11_2024/8ext_28662.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 2 6.06 5 S 38 5.16 5 C 5806 2.51 5 N 1460 2.21 5 O 1540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8846 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4422 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 520} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 7.89, per 1000 atoms: 0.89 Number of scatterers: 8846 At special positions: 0 Unit cell: (88.395, 92.655, 116.085, 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 2 29.99 S 38 16.00 O 1540 8.00 N 1460 7.00 C 5806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 997.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 201 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 205 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 201 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 205 " 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 60.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 1 through 31 Processing helix chain 'A' and resid 36 through 48 removed outlier: 4.044A pdb=" N TYR A 40 " --> pdb=" O TYR A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 99 through 134 removed outlier: 3.846A pdb=" N ASP A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 removed outlier: 5.172A pdb=" N LYS A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 193 through 208 Processing helix chain 'A' and resid 209 through 225 Processing helix chain 'A' and resid 228 through 252 Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.808A pdb=" N LEU A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.530A pdb=" N THR A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 497 Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.617A pdb=" N SER A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 579 Processing helix chain 'B' and resid 2 through 31 Processing helix chain 'B' and resid 36 through 48 removed outlier: 4.044A pdb=" N TYR B 40 " --> pdb=" O TYR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 99 through 134 removed outlier: 3.846A pdb=" N ASP B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 152 removed outlier: 5.173A pdb=" N LYS B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 193 through 208 Processing helix chain 'B' and resid 209 through 225 Processing helix chain 'B' and resid 228 through 252 Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.808A pdb=" N LEU B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 450 through 461 removed outlier: 3.530A pdb=" N THR B 454 " --> pdb=" O PRO B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 497 Processing helix chain 'B' and resid 502 through 513 removed outlier: 3.616A pdb=" N SER B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.645A pdb=" N VAL A 160 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE A 182 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG A 162 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.615A pdb=" N ASP A 346 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 375 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN A 348 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY A 530 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY A 539 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY A 528 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 541 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS A 526 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 543 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR A 524 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A 545 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A 522 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A 517 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 523 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164 removed outlier: 6.645A pdb=" N VAL B 160 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B 182 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG B 162 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.615A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY B 530 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY B 539 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY B 528 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 541 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS B 526 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY B 543 " --> pdb=" O TYR B 524 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR B 524 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 545 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU B 522 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 521 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS B 517 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 523 " --> pdb=" O ILE B 515 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1461 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: 2.75 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1815 1.31 - 1.44: 2726 1.44 - 1.58: 4399 1.58 - 1.71: 38 1.71 - 1.84: 68 Bond restraints: 9046 Sorted by residual: bond pdb=" CB HIS A 282 " pdb=" CG HIS A 282 " ideal model delta sigma weight residual 1.497 1.335 0.162 1.40e-02 5.10e+03 1.34e+02 bond pdb=" CB HIS B 282 " pdb=" CG HIS B 282 " ideal model delta sigma weight residual 1.497 1.335 0.162 1.40e-02 5.10e+03 1.34e+02 bond pdb=" CB HIS B 153 " pdb=" CG HIS B 153 " ideal model delta sigma weight residual 1.497 1.349 0.148 1.40e-02 5.10e+03 1.11e+02 bond pdb=" CB HIS A 153 " pdb=" CG HIS A 153 " ideal model delta sigma weight residual 1.497 1.349 0.148 1.40e-02 5.10e+03 1.11e+02 bond pdb=" CB PHE A 220 " pdb=" CG PHE A 220 " ideal model delta sigma weight residual 1.502 1.312 0.190 2.30e-02 1.89e+03 6.83e+01 ... (remaining 9041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.92: 12014 5.92 - 11.84: 144 11.84 - 17.77: 6 17.77 - 23.69: 2 23.69 - 29.61: 6 Bond angle restraints: 12172 Sorted by residual: angle pdb=" O ASP B 346 " pdb=" C ASP B 346 " pdb=" N TYR B 347 " ideal model delta sigma weight residual 122.79 148.72 -25.93 1.14e+00 7.69e-01 5.17e+02 angle pdb=" O ASP A 346 " pdb=" C ASP A 346 " pdb=" N TYR A 347 " ideal model delta sigma weight residual 122.79 148.72 -25.93 1.14e+00 7.69e-01 5.17e+02 angle pdb=" CA ASP A 346 " pdb=" C ASP A 346 " pdb=" N TYR A 347 " ideal model delta sigma weight residual 115.27 85.66 29.61 1.34e+00 5.57e-01 4.88e+02 angle pdb=" CA ASP B 346 " pdb=" C ASP B 346 " pdb=" N TYR B 347 " ideal model delta sigma weight residual 115.27 85.66 29.61 1.34e+00 5.57e-01 4.88e+02 angle pdb=" O ILE A 51 " pdb=" C ILE A 51 " pdb=" N PRO A 52 " ideal model delta sigma weight residual 121.10 136.04 -14.94 1.14e+00 7.69e-01 1.72e+02 ... (remaining 12167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 5016 14.03 - 28.05: 308 28.05 - 42.08: 70 42.08 - 56.10: 28 56.10 - 70.13: 10 Dihedral angle restraints: 5432 sinusoidal: 2256 harmonic: 3176 Sorted by residual: dihedral pdb=" C LEU B 18 " pdb=" N LEU B 18 " pdb=" CA LEU B 18 " pdb=" CB LEU B 18 " ideal model delta harmonic sigma weight residual -122.60 -112.59 -10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" C LEU A 18 " pdb=" N LEU A 18 " pdb=" CA LEU A 18 " pdb=" CB LEU A 18 " ideal model delta harmonic sigma weight residual -122.60 -112.59 -10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" C ASN B 406 " pdb=" N ASN B 406 " pdb=" CA ASN B 406 " pdb=" CB ASN B 406 " ideal model delta harmonic sigma weight residual -122.60 -132.21 9.61 0 2.50e+00 1.60e-01 1.48e+01 ... (remaining 5429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 716 0.085 - 0.171: 414 0.171 - 0.256: 156 0.256 - 0.341: 36 0.341 - 0.426: 14 Chirality restraints: 1336 Sorted by residual: chirality pdb=" CA TYR A 178 " pdb=" N TYR A 178 " pdb=" C TYR A 178 " pdb=" CB TYR A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CA TYR B 178 " pdb=" N TYR B 178 " pdb=" C TYR B 178 " pdb=" CB TYR B 178 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA PHE B 151 " pdb=" N PHE B 151 " pdb=" C PHE B 151 " pdb=" CB PHE B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 1333 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 346 " 0.022 2.00e-02 2.50e+03 7.33e-02 5.37e+01 pdb=" C ASP A 346 " -0.125 2.00e-02 2.50e+03 pdb=" O ASP A 346 " 0.058 2.00e-02 2.50e+03 pdb=" N TYR A 347 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 346 " -0.022 2.00e-02 2.50e+03 7.33e-02 5.37e+01 pdb=" C ASP B 346 " 0.125 2.00e-02 2.50e+03 pdb=" O ASP B 346 " -0.058 2.00e-02 2.50e+03 pdb=" N TYR B 347 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 51 " 0.024 2.00e-02 2.50e+03 6.08e-02 3.70e+01 pdb=" C ILE A 51 " -0.105 2.00e-02 2.50e+03 pdb=" O ILE A 51 " 0.044 2.00e-02 2.50e+03 pdb=" N PRO A 52 " 0.036 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 174 2.59 - 3.17: 9050 3.17 - 3.75: 15210 3.75 - 4.32: 22367 4.32 - 4.90: 32315 Nonbonded interactions: 79116 Sorted by model distance: nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.014 2.230 nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.014 2.230 nonbonded pdb=" OE1 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.021 2.230 nonbonded pdb=" OE1 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.022 2.230 nonbonded pdb=" O MET A 33 " pdb=" CD1 LEU B 311 " model vdw 2.281 3.460 ... (remaining 79111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.940 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4877 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 : 0.026 0.190 9046 Z= 1.677 Angle : 2.042 29.611 12172 Z= 1.432 Chirality : 0.123 0.426 1336 Planarity : 0.010 0.073 1488 Dihedral : 10.968 70.129 3384 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.33 % Favored : 93.90 % Rotamer: Outliers : 2.03 % Allowed : 1.01 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1050 helix: -0.09 (0.19), residues: 550 sheet: -0.87 (0.47), residues: 118 loop : -0.57 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.011 TRP B 540 HIS 0.014 0.003 HIS B 213 PHE 0.045 0.006 PHE B 151 TYR 0.056 0.010 TYR B 203 ARG 0.004 0.001 ARG B 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8475 (mt) cc_final: 0.8015 (mm) REVERT: A 20 LEU cc_start: 0.8877 (mt) cc_final: 0.8629 (mt) REVERT: A 37 LYS cc_start: 0.8324 (mttt) cc_final: 0.8005 (mttt) REVERT: A 119 PHE cc_start: 0.7232 (m-10) cc_final: 0.6999 (m-80) REVERT: A 260 THR cc_start: 0.7838 (t) cc_final: 0.7605 (t) REVERT: A 314 ILE cc_start: 0.8847 (mt) cc_final: 0.8631 (mt) REVERT: A 341 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5324 (tppt) outliers start: 10 outliers final: 4 residues processed: 167 average time/residue: 0.1996 time to fit residues: 40.5807 Evaluate side-chains 101 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 HIS ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN B 487 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4696 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9046 Z= 0.236 Angle : 0.749 7.072 12172 Z= 0.408 Chirality : 0.047 0.220 1336 Planarity : 0.005 0.050 1488 Dihedral : 5.382 20.345 1156 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.20 % Allowed : 2.64 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1050 helix: 0.70 (0.19), residues: 584 sheet: -0.49 (0.48), residues: 120 loop : -0.55 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 39 HIS 0.015 0.002 HIS A 213 PHE 0.023 0.003 PHE B 248 TYR 0.038 0.002 TYR B 203 ARG 0.005 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 TYR cc_start: 0.6601 (p90) cc_final: 0.5938 (p90) REVERT: B 37 LYS cc_start: 0.8046 (mttt) cc_final: 0.7355 (mmtp) REVERT: B 152 ASN cc_start: 0.7165 (m-40) cc_final: 0.6596 (t0) REVERT: B 181 LEU cc_start: 0.7465 (mp) cc_final: 0.7073 (mp) REVERT: B 209 ARG cc_start: 0.7641 (mtt180) cc_final: 0.7261 (mtt180) REVERT: B 218 ASN cc_start: 0.8651 (m110) cc_final: 0.8359 (m110) REVERT: B 220 PHE cc_start: 0.5992 (m-80) cc_final: 0.5703 (m-80) REVERT: B 221 SER cc_start: 0.8264 (m) cc_final: 0.8029 (p) REVERT: B 316 ILE cc_start: 0.7600 (tp) cc_final: 0.7350 (tp) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1723 time to fit residues: 29.1541 Evaluate side-chains 102 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 96 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 0.0010 chunk 95 optimal weight: 4.9990 chunk 32 optimal weight: 0.0010 chunk 77 optimal weight: 1.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4685 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9046 Z= 0.189 Angle : 0.624 7.820 12172 Z= 0.344 Chirality : 0.042 0.145 1336 Planarity : 0.004 0.038 1488 Dihedral : 5.135 21.881 1156 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.20 % Allowed : 2.84 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1050 helix: 0.21 (0.20), residues: 592 sheet: -0.87 (0.49), residues: 120 loop : -0.82 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 475 HIS 0.027 0.003 HIS B 239 PHE 0.029 0.002 PHE B 442 TYR 0.043 0.002 TYR B 203 ARG 0.004 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3465 (ttt) cc_final: 0.1720 (mmt) REVERT: B 107 THR cc_start: 0.7017 (p) cc_final: 0.6684 (p) REVERT: B 152 ASN cc_start: 0.7138 (m-40) cc_final: 0.6611 (t0) REVERT: B 179 ILE cc_start: 0.7389 (mt) cc_final: 0.6983 (mt) REVERT: B 209 ARG cc_start: 0.7742 (mtt180) cc_final: 0.7302 (mtt180) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1515 time to fit residues: 23.8209 Evaluate side-chains 97 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 HIS B 271 ASN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 557 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4787 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9046 Z= 0.202 Angle : 0.668 12.045 12172 Z= 0.358 Chirality : 0.043 0.194 1336 Planarity : 0.004 0.034 1488 Dihedral : 4.976 20.308 1156 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.20 % Allowed : 2.84 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1050 helix: 0.00 (0.20), residues: 596 sheet: -0.95 (0.52), residues: 112 loop : -1.02 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 475 HIS 0.012 0.001 HIS B 213 PHE 0.019 0.002 PHE B 442 TYR 0.038 0.002 TYR B 203 ARG 0.004 0.001 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3614 (ttt) cc_final: 0.1629 (mmm) REVERT: B 37 LYS cc_start: 0.7934 (mttt) cc_final: 0.7515 (mmtp) REVERT: B 119 PHE cc_start: 0.7127 (m-10) cc_final: 0.6754 (m-80) REVERT: B 152 ASN cc_start: 0.7049 (m-40) cc_final: 0.6540 (t0) REVERT: B 209 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7369 (mtt180) REVERT: B 368 MET cc_start: 0.2390 (mmm) cc_final: 0.1877 (mmt) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1636 time to fit residues: 23.7317 Evaluate side-chains 90 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 0.0870 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 70 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 0.0970 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS B 282 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4610 moved from start: 0.6580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9046 Z= 0.153 Angle : 0.593 7.618 12172 Z= 0.324 Chirality : 0.043 0.166 1336 Planarity : 0.004 0.039 1488 Dihedral : 4.678 18.379 1156 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.20 % Allowed : 1.42 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1050 helix: 0.21 (0.20), residues: 600 sheet: -1.12 (0.51), residues: 112 loop : -1.00 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 39 HIS 0.009 0.001 HIS A 213 PHE 0.023 0.002 PHE A 12 TYR 0.037 0.002 TYR B 203 ARG 0.003 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3762 (ttt) cc_final: 0.2118 (mmm) REVERT: B 119 PHE cc_start: 0.6963 (m-10) cc_final: 0.6631 (m-80) REVERT: B 152 ASN cc_start: 0.6994 (m-40) cc_final: 0.6500 (t0) REVERT: B 187 PHE cc_start: 0.5103 (m-80) cc_final: 0.4080 (m-80) REVERT: B 239 HIS cc_start: 0.6481 (m90) cc_final: 0.5800 (m-70) REVERT: B 412 MET cc_start: 0.0547 (ptt) cc_final: -0.0141 (ptm) REVERT: B 435 GLN cc_start: 0.6330 (OUTLIER) cc_final: 0.5676 (tm-30) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1536 time to fit residues: 22.8440 Evaluate side-chains 94 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 85 optimal weight: 0.0020 chunk 47 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4600 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9046 Z= 0.148 Angle : 0.609 9.162 12172 Z= 0.323 Chirality : 0.043 0.202 1336 Planarity : 0.004 0.039 1488 Dihedral : 4.538 17.864 1156 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1050 helix: 0.39 (0.20), residues: 598 sheet: -1.03 (0.51), residues: 112 loop : -1.21 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 540 HIS 0.009 0.001 HIS B 213 PHE 0.019 0.001 PHE B 22 TYR 0.033 0.001 TYR B 203 ARG 0.001 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3641 (ttt) cc_final: 0.1785 (mmt) REVERT: A 14 PHE cc_start: 0.5143 (t80) cc_final: 0.4883 (t80) REVERT: A 119 PHE cc_start: 0.6874 (m-10) cc_final: 0.6531 (m-80) REVERT: A 152 ASN cc_start: 0.7038 (m-40) cc_final: 0.6432 (t0) REVERT: A 216 ILE cc_start: 0.8285 (mt) cc_final: 0.7978 (mt) REVERT: A 239 HIS cc_start: 0.6233 (m90) cc_final: 0.5995 (m-70) REVERT: A 249 VAL cc_start: 0.8189 (t) cc_final: 0.7923 (t) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1485 time to fit residues: 22.3815 Evaluate side-chains 96 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 57 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4683 moved from start: 0.7074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9046 Z= 0.176 Angle : 0.620 7.529 12172 Z= 0.337 Chirality : 0.043 0.180 1336 Planarity : 0.004 0.038 1488 Dihedral : 4.566 17.648 1156 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1050 helix: 0.21 (0.20), residues: 600 sheet: -1.14 (0.50), residues: 112 loop : -1.30 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 39 HIS 0.007 0.001 HIS A 239 PHE 0.019 0.002 PHE A 22 TYR 0.035 0.002 TYR B 203 ARG 0.002 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4038 (ttt) cc_final: 0.2044 (mmt) REVERT: B 119 PHE cc_start: 0.6889 (m-10) cc_final: 0.6630 (m-80) REVERT: B 152 ASN cc_start: 0.7037 (m-40) cc_final: 0.6631 (t0) REVERT: B 239 HIS cc_start: 0.6621 (m90) cc_final: 0.6417 (m-70) REVERT: B 240 ASP cc_start: 0.7149 (p0) cc_final: 0.6638 (p0) REVERT: B 294 ARG cc_start: 0.6186 (mtp180) cc_final: 0.5020 (mtp180) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1703 time to fit residues: 25.3326 Evaluate side-chains 96 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4698 moved from start: 0.7269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9046 Z= 0.164 Angle : 0.594 7.129 12172 Z= 0.326 Chirality : 0.043 0.168 1336 Planarity : 0.004 0.037 1488 Dihedral : 4.457 18.401 1156 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.25), residues: 1050 helix: 0.24 (0.20), residues: 594 sheet: -1.27 (0.51), residues: 112 loop : -1.30 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 174 HIS 0.011 0.001 HIS B 213 PHE 0.027 0.002 PHE A 12 TYR 0.036 0.002 TYR B 203 ARG 0.003 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4286 (ttt) cc_final: 0.2281 (mmt) REVERT: B 28 ARG cc_start: 0.6392 (tpm170) cc_final: 0.4239 (ttt-90) REVERT: B 119 PHE cc_start: 0.6886 (m-10) cc_final: 0.6632 (m-80) REVERT: B 152 ASN cc_start: 0.6925 (m-40) cc_final: 0.6603 (t0) REVERT: B 174 TRP cc_start: 0.2241 (t60) cc_final: 0.1907 (t60) REVERT: B 239 HIS cc_start: 0.6509 (m90) cc_final: 0.6186 (m-70) REVERT: B 240 ASP cc_start: 0.7005 (p0) cc_final: 0.6672 (p0) REVERT: B 266 MET cc_start: 0.6328 (ptm) cc_final: 0.6055 (ptm) REVERT: B 294 ARG cc_start: 0.6268 (mtp180) cc_final: 0.5069 (mtp180) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1592 time to fit residues: 23.1142 Evaluate side-chains 95 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 0.0050 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 0.0370 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 0.0040 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 0.0030 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4577 moved from start: 0.7660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9046 Z= 0.154 Angle : 0.628 9.200 12172 Z= 0.337 Chirality : 0.044 0.199 1336 Planarity : 0.003 0.037 1488 Dihedral : 4.345 17.131 1156 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1050 helix: 0.25 (0.20), residues: 600 sheet: -1.27 (0.50), residues: 114 loop : -1.45 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 174 HIS 0.007 0.001 HIS B 213 PHE 0.020 0.001 PHE B 22 TYR 0.030 0.002 TYR B 203 ARG 0.002 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4302 (ttt) cc_final: 0.2455 (mmt) REVERT: B 28 ARG cc_start: 0.6479 (tpm170) cc_final: 0.4481 (ttt-90) REVERT: B 119 PHE cc_start: 0.6944 (m-10) cc_final: 0.6510 (m-80) REVERT: B 152 ASN cc_start: 0.7096 (m-40) cc_final: 0.6746 (t0) REVERT: B 216 ILE cc_start: 0.8349 (mt) cc_final: 0.8063 (mt) REVERT: B 240 ASP cc_start: 0.6872 (p0) cc_final: 0.6459 (p0) REVERT: B 266 MET cc_start: 0.6164 (ptm) cc_final: 0.5961 (ptm) REVERT: B 290 LEU cc_start: 0.6175 (mm) cc_final: 0.5723 (mt) REVERT: B 294 ARG cc_start: 0.6087 (mtp180) cc_final: 0.4791 (mtp180) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1666 time to fit residues: 24.7213 Evaluate side-chains 96 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 84 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.0060 chunk 89 optimal weight: 0.7980 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4575 moved from start: 0.7957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9046 Z= 0.170 Angle : 0.641 9.276 12172 Z= 0.337 Chirality : 0.044 0.227 1336 Planarity : 0.004 0.036 1488 Dihedral : 4.309 17.982 1156 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1050 helix: 0.13 (0.20), residues: 592 sheet: -1.22 (0.51), residues: 114 loop : -1.34 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 39 HIS 0.004 0.001 HIS B 213 PHE 0.021 0.001 PHE B 22 TYR 0.028 0.002 TYR B 203 ARG 0.003 0.000 ARG A 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4298 (ttt) cc_final: 0.2307 (mmt) REVERT: B 28 ARG cc_start: 0.6431 (tpm170) cc_final: 0.4391 (ttt-90) REVERT: B 119 PHE cc_start: 0.6698 (m-10) cc_final: 0.6449 (m-80) REVERT: B 152 ASN cc_start: 0.7091 (m-40) cc_final: 0.6720 (t0) REVERT: B 216 ILE cc_start: 0.7470 (mt) cc_final: 0.6951 (mt) REVERT: B 240 ASP cc_start: 0.6928 (p0) cc_final: 0.6444 (p0) REVERT: B 291 LEU cc_start: 0.7534 (tp) cc_final: 0.7268 (tp) REVERT: B 294 ARG cc_start: 0.6011 (mtp180) cc_final: 0.4763 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1596 time to fit residues: 22.7955 Evaluate side-chains 96 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 12 optimal weight: 0.0370 chunk 23 optimal weight: 0.0670 chunk 84 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.151070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.106379 restraints weight = 13284.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.110750 restraints weight = 8953.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.113749 restraints weight = 6571.424| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.8244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9046 Z= 0.148 Angle : 0.614 8.874 12172 Z= 0.326 Chirality : 0.044 0.202 1336 Planarity : 0.004 0.036 1488 Dihedral : 4.225 17.527 1156 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.25), residues: 1050 helix: 0.11 (0.20), residues: 592 sheet: -1.08 (0.53), residues: 114 loop : -1.31 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.004 0.001 HIS A 282 PHE 0.019 0.001 PHE A 22 TYR 0.025 0.002 TYR B 261 ARG 0.003 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1742.89 seconds wall clock time: 42 minutes 7.13 seconds (2527.13 seconds total)