Starting phenix.real_space_refine on Fri Jan 19 05:51:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/01_2024/7uzs_26917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/01_2024/7uzs_26917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/01_2024/7uzs_26917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/01_2024/7uzs_26917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/01_2024/7uzs_26917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/01_2024/7uzs_26917.pdb" } resolution = 2.2 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= 0.327 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 S 23 5.16 5 C 3282 2.51 5 N 916 2.21 5 O 1146 1.98 5 H 5183 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X GLU 20": "OE1" <-> "OE2" Residue "X PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X GLU 177": "OE1" <-> "OE2" Residue "X GLU 311": "OE1" <-> "OE2" Residue "X GLU 373": "OE1" <-> "OE2" Residue "X GLU 400": "OE1" <-> "OE2" Residue "X GLU 449": "OE1" <-> "OE2" Residue "X ASP 490": "OD1" <-> "OD2" Residue "X GLU 504": "OE1" <-> "OE2" Residue "X GLU 540": "OE1" <-> "OE2" Residue "X GLU 596": "OE1" <-> "OE2" Residue "X GLU 599": "OE1" <-> "OE2" Residue "X GLU 645": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10550 Number of models: 1 Model: "" Number of chains: 1 Chain: "X" Number of atoms: 10550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 10550 Inner-chain residues flagged as termini: ['pdbres="ALA X 691 "'] Classifications: {'peptide': 658, 'water': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 627, None: 193} Not linked: pdbres="ALA X 691 " pdbres="HOH X 701 " Not linked: pdbres="HOH X 701 " pdbres="HOH X 702 " Not linked: pdbres="HOH X 702 " pdbres="HOH X 703 " Not linked: pdbres="HOH X 703 " pdbres="HOH X 704 " Not linked: pdbres="HOH X 704 " pdbres="HOH X 705 " ... (remaining 188 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 5.25, per 1000 atoms: 0.50 Number of scatterers: 10550 At special positions: 0 Unit cell: (97.11, 103.335, 73.04, 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) S 23 16.00 O 1146 8.00 N 916 7.00 C 3282 6.00 H 5183 1.00 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 - 3.50 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: 8.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1234 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 10 sheets defined 21.1% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 51 through 58 Processing helix chain 'X' and resid 151 through 159 Processing helix chain 'X' and resid 187 through 197 Processing helix chain 'X' and resid 201 through 206 removed outlier: 3.755A pdb=" N SER X 206 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 227 Processing helix chain 'X' and resid 247 through 258 removed outlier: 4.194A pdb=" N ILE X 251 " --> pdb=" O GLY X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 268 Processing helix chain 'X' and resid 269 through 282 removed outlier: 4.063A pdb=" N ALA X 273 " --> pdb=" O TRP X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 374 Processing helix chain 'X' and resid 381 through 389 removed outlier: 3.597A pdb=" N ILE X 389 " --> pdb=" O LEU X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 436 removed outlier: 3.899A pdb=" N TYR X 435 " --> pdb=" O ILE X 431 " (cutoff:3.500A) Processing helix chain 'X' and resid 441 through 459 Processing helix chain 'X' and resid 550 through 552 No H-bonds generated for 'chain 'X' and resid 550 through 552' Processing sheet with id=AA1, first strand: chain 'X' and resid 7 through 11 removed outlier: 6.539A pdb=" N SER X 101 " --> pdb=" O ARG X 97 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG X 97 " --> pdb=" O SER X 101 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR X 103 " --> pdb=" O GLU X 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 32 through 34 removed outlier: 6.828A pdb=" N LEU X 119 " --> pdb=" O LEU X 131 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN X 133 " --> pdb=" O TYR X 117 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR X 117 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR X 135 " --> pdb=" O GLY X 115 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY X 115 " --> pdb=" O THR X 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 163 through 170 Processing sheet with id=AA4, first strand: chain 'X' and resid 362 through 367 removed outlier: 4.060A pdb=" N SER X 362 " --> pdb=" O SER X 352 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR X 330 " --> pdb=" O LEU X 349 " (cutoff:3.500A) removed outlier: 11.835A pdb=" N THR X 328 " --> pdb=" O PRO X 351 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE X 323 " --> pdb=" O ALA X 295 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA X 295 " --> pdb=" O ILE X 323 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE X 325 " --> pdb=" O ALA X 293 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL X 288 " --> pdb=" O THR X 420 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR X 420 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR X 290 " --> pdb=" O ILE X 418 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE X 418 " --> pdb=" O THR X 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 303 through 309 removed outlier: 5.974A pdb=" N ILE X 304 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TRP X 396 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU X 306 " --> pdb=" O TRP X 396 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N CYS X 398 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR X 308 " --> pdb=" O CYS X 398 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 408 through 409 removed outlier: 6.352A pdb=" N ASP X 408 " --> pdb=" O PHE X 578 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLN X 580 " --> pdb=" O ASP X 408 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 408 through 409 removed outlier: 6.352A pdb=" N ASP X 408 " --> pdb=" O PHE X 578 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLN X 580 " --> pdb=" O ASP X 408 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE X 585 " --> pdb=" O THR X 560 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR X 560 " --> pdb=" O ILE X 585 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS X 505 " --> pdb=" O LEU X 533 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU X 533 " --> pdb=" O LYS X 505 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL X 507 " --> pdb=" O LEU X 531 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU X 531 " --> pdb=" O VAL X 507 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU X 509 " --> pdb=" O LYS X 529 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS X 529 " --> pdb=" O LEU X 509 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE X 511 " --> pdb=" O TRP X 527 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP X 527 " --> pdb=" O ILE X 511 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL X 513 " --> pdb=" O LYS X 525 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LYS X 525 " --> pdb=" O VAL X 513 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA X 515 " --> pdb=" O ALA X 523 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 475 through 480 Processing sheet with id=AA9, first strand: chain 'X' and resid 590 through 593 Processing sheet with id=AB1, first strand: chain 'X' and resid 597 through 599 removed outlier: 6.437A pdb=" N ALA X 598 " --> pdb=" O VAL X 685 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 585 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: 4.18 Time building geometry restraints manager: 8.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5168 1.03 - 1.23: 73 1.23 - 1.42: 2129 1.42 - 1.62: 3063 1.62 - 1.81: 31 Bond restraints: 10464 Sorted by residual: bond pdb=" N ILE X 284 " pdb=" CA ILE X 284 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.30e-03 1.88e+04 1.75e+01 bond pdb=" N ILE X 431 " pdb=" CA ILE X 431 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.04e-02 9.25e+03 1.35e+01 bond pdb=" C VAL X 288 " pdb=" O VAL X 288 " ideal model delta sigma weight residual 1.238 1.200 0.037 1.17e-02 7.31e+03 1.02e+01 bond pdb=" C PRO X 285 " pdb=" O PRO X 285 " ideal model delta sigma weight residual 1.233 1.196 0.038 1.23e-02 6.61e+03 9.34e+00 bond pdb=" C PRO X 367 " pdb=" O PRO X 367 " ideal model delta sigma weight residual 1.233 1.196 0.037 1.23e-02 6.61e+03 8.96e+00 ... (remaining 10459 not shown) Histogram of bond angle deviations from ideal: 97.46 - 104.86: 82 104.86 - 112.26: 12029 112.26 - 119.66: 2837 119.66 - 127.06: 3897 127.06 - 134.46: 75 Bond angle restraints: 18920 Sorted by residual: angle pdb=" N LEU X 131 " pdb=" CA LEU X 131 " pdb=" C LEU X 131 " ideal model delta sigma weight residual 112.90 107.59 5.31 1.31e+00 5.83e-01 1.64e+01 angle pdb=" CA THR X 432 " pdb=" C THR X 432 " pdb=" O THR X 432 " ideal model delta sigma weight residual 120.63 116.26 4.37 1.08e+00 8.57e-01 1.64e+01 angle pdb=" C THR X 135 " pdb=" CA THR X 135 " pdb=" CB THR X 135 " ideal model delta sigma weight residual 109.72 116.10 -6.38 1.73e+00 3.34e-01 1.36e+01 angle pdb=" CA PHE X 134 " pdb=" CB PHE X 134 " pdb=" CG PHE X 134 " ideal model delta sigma weight residual 113.80 117.38 -3.58 1.00e+00 1.00e+00 1.28e+01 angle pdb=" N ILE X 431 " pdb=" CA ILE X 431 " pdb=" C ILE X 431 " ideal model delta sigma weight residual 112.43 109.15 3.28 9.20e-01 1.18e+00 1.27e+01 ... (remaining 18915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4336 17.89 - 35.77: 325 35.77 - 53.66: 113 53.66 - 71.54: 25 71.54 - 89.43: 21 Dihedral angle restraints: 4820 sinusoidal: 2609 harmonic: 2211 Sorted by residual: dihedral pdb=" CB GLU X 540 " pdb=" CG GLU X 540 " pdb=" CD GLU X 540 " pdb=" OE1 GLU X 540 " ideal model delta sinusoidal sigma weight residual 0.00 89.43 -89.43 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU X 502 " pdb=" CG GLU X 502 " pdb=" CD GLU X 502 " pdb=" OE1 GLU X 502 " ideal model delta sinusoidal sigma weight residual 0.00 -86.66 86.66 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU X 572 " pdb=" CG GLU X 572 " pdb=" CD GLU X 572 " pdb=" OE1 GLU X 572 " ideal model delta sinusoidal sigma weight residual 0.00 -86.51 86.51 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 4817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 507 0.033 - 0.067: 197 0.067 - 0.100: 47 0.100 - 0.133: 50 0.133 - 0.167: 10 Chirality restraints: 811 Sorted by residual: chirality pdb=" CA LEU X 61 " pdb=" N LEU X 61 " pdb=" C LEU X 61 " pdb=" CB LEU X 61 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA ARG X 369 " pdb=" N ARG X 369 " pdb=" C ARG X 369 " pdb=" CB ARG X 369 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA VAL X 289 " pdb=" N VAL X 289 " pdb=" C VAL X 289 " pdb=" CB VAL X 289 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 808 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN X 64 " 0.246 2.00e-02 2.50e+03 2.92e-01 1.28e+03 pdb=" CD GLN X 64 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLN X 64 " -0.226 2.00e-02 2.50e+03 pdb=" NE2 GLN X 64 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN X 64 " -0.439 2.00e-02 2.50e+03 pdb="HE22 GLN X 64 " 0.455 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN X 133 " -0.221 2.00e-02 2.50e+03 2.56e-01 9.81e+02 pdb=" CD GLN X 133 " 0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN X 133 " 0.212 2.00e-02 2.50e+03 pdb=" NE2 GLN X 133 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN X 133 " 0.383 2.00e-02 2.50e+03 pdb="HE22 GLN X 133 " -0.390 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN X 434 " 0.130 2.00e-02 2.50e+03 1.40e-01 2.92e+02 pdb=" CG ASN X 434 " -0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN X 434 " -0.126 2.00e-02 2.50e+03 pdb=" ND2 ASN X 434 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN X 434 " 0.208 2.00e-02 2.50e+03 pdb="HD22 ASN X 434 " -0.202 2.00e-02 2.50e+03 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 995 2.22 - 2.82: 22673 2.82 - 3.41: 29308 3.41 - 4.01: 41980 4.01 - 4.60: 60517 Nonbonded interactions: 155473 Sorted by model distance: nonbonded pdb=" OD1 ASP X 669 " pdb=" H ASN X 675 " model vdw 1.628 1.850 nonbonded pdb=" HE1 TRP X 179 " pdb=" OG SER X 248 " model vdw 1.679 1.850 nonbonded pdb=" O PRO X 557 " pdb=" HG1 THR X 560 " model vdw 1.700 1.850 nonbonded pdb=" HH TYR X 518 " pdb=" O HOH X 714 " model vdw 1.701 1.850 nonbonded pdb=" HG SER X 91 " pdb=" OG1 THR X 107 " model vdw 1.702 1.850 ... (remaining 155468 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: 0.850 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: 0.170 Extract box with map and model: 5.090 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 37.140 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 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 : 0.004 0.044 5281 Z= 0.285 Angle : 0.721 6.385 7166 Z= 0.441 Chirality : 0.047 0.167 811 Planarity : 0.005 0.106 923 Dihedral : 17.955 89.429 1947 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.79 % Allowed : 16.99 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.32), residues: 650 helix: 1.50 (0.49), residues: 117 sheet: 0.52 (0.31), residues: 248 loop : 0.79 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 333 HIS 0.008 0.001 HIS X 350 PHE 0.020 0.002 PHE X 134 TYR 0.014 0.002 TYR X 167 ARG 0.014 0.000 ARG X 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 599 GLU cc_start: 0.8204 (tt0) cc_final: 0.7913 (tt0) outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 3.1472 time to fit residues: 352.2810 Evaluate side-chains 98 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 505 LYS Chi-restraints excluded: chain X residue 572 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 50.0000 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 66 optimal weight: 50.0000 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 50.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 175 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5281 Z= 0.193 Angle : 0.512 5.265 7166 Z= 0.268 Chirality : 0.041 0.139 811 Planarity : 0.004 0.035 923 Dihedral : 6.285 76.418 721 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.22 % Allowed : 14.67 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.32), residues: 650 helix: 1.97 (0.47), residues: 118 sheet: 0.67 (0.31), residues: 248 loop : 0.81 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 333 HIS 0.003 0.001 HIS X 350 PHE 0.013 0.002 PHE X 134 TYR 0.016 0.002 TYR X 167 ARG 0.003 0.000 ARG X 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 200 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7660 (mptt) REVERT: X 442 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8120 (mp) REVERT: X 611 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7190 (tm-30) outliers start: 18 outliers final: 7 residues processed: 110 average time/residue: 3.2003 time to fit residues: 364.6491 Evaluate side-chains 105 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 200 LYS Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 501 SER Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 620 ASP Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 77 optimal weight: 50.0000 chunk 83 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 175 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5281 Z= 0.250 Angle : 0.540 5.107 7166 Z= 0.285 Chirality : 0.041 0.145 811 Planarity : 0.004 0.038 923 Dihedral : 5.045 32.844 714 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.04 % Allowed : 14.49 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.32), residues: 650 helix: 1.99 (0.47), residues: 118 sheet: 0.75 (0.31), residues: 246 loop : 0.66 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 333 HIS 0.005 0.001 HIS X 350 PHE 0.017 0.002 PHE X 639 TYR 0.019 0.002 TYR X 167 ARG 0.003 0.000 ARG X 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 200 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7782 (mptt) REVERT: X 400 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5416 (mp0) REVERT: X 442 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8161 (mp) REVERT: X 611 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7211 (tm-30) outliers start: 17 outliers final: 4 residues processed: 109 average time/residue: 3.2260 time to fit residues: 363.9735 Evaluate side-chains 105 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 200 LYS Chi-restraints excluded: chain X residue 400 GLU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 620 ASP Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 50.0000 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 50.0000 chunk 82 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 22 optimal weight: 6.9990 chunk 68 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 175 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5281 Z= 0.416 Angle : 0.645 5.208 7166 Z= 0.345 Chirality : 0.044 0.154 811 Planarity : 0.006 0.044 923 Dihedral : 5.425 31.587 713 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.40 % Allowed : 14.13 % Favored : 82.47 % 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: 0.94 (0.31), residues: 650 helix: 1.61 (0.47), residues: 118 sheet: 0.72 (0.30), residues: 243 loop : 0.24 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 333 HIS 0.007 0.002 HIS X 350 PHE 0.025 0.003 PHE X 639 TYR 0.025 0.003 TYR X 167 ARG 0.006 0.001 ARG X 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: X 400 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5360 (mp0) REVERT: X 442 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8224 (mp) REVERT: X 611 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7685 (tm-30) outliers start: 19 outliers final: 5 residues processed: 108 average time/residue: 3.3508 time to fit residues: 374.4036 Evaluate side-chains 103 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 200 LYS Chi-restraints excluded: chain X residue 400 GLU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 50.0000 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 73 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 175 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5281 Z= 0.247 Angle : 0.550 5.303 7166 Z= 0.290 Chirality : 0.042 0.145 811 Planarity : 0.004 0.044 923 Dihedral : 5.125 29.045 713 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.33 % Allowed : 15.21 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.31), residues: 650 helix: 1.82 (0.47), residues: 118 sheet: 0.69 (0.30), residues: 245 loop : 0.34 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 333 HIS 0.004 0.001 HIS X 350 PHE 0.018 0.002 PHE X 639 TYR 0.020 0.002 TYR X 167 ARG 0.003 0.000 ARG X 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: X 200 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7745 (mptt) REVERT: X 400 GLU cc_start: 0.5665 (OUTLIER) cc_final: 0.5352 (mp0) REVERT: X 442 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8168 (mp) REVERT: X 611 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7628 (tm-30) outliers start: 13 outliers final: 5 residues processed: 112 average time/residue: 3.3843 time to fit residues: 392.0919 Evaluate side-chains 108 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 200 LYS Chi-restraints excluded: chain X residue 400 GLU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 530 LYS Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 50.0000 chunk 16 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 79 optimal weight: 50.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 175 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5281 Z= 0.302 Angle : 0.586 5.761 7166 Z= 0.309 Chirality : 0.042 0.149 811 Planarity : 0.005 0.047 923 Dihedral : 5.226 27.468 713 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.22 % Allowed : 14.67 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.31), residues: 650 helix: 1.72 (0.47), residues: 118 sheet: 0.52 (0.30), residues: 254 loop : 0.28 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 333 HIS 0.005 0.002 HIS X 350 PHE 0.019 0.002 PHE X 639 TYR 0.022 0.002 TYR X 167 ARG 0.004 0.000 ARG X 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.864 Fit side-chains REVERT: X 200 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7864 (mptt) REVERT: X 400 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.5359 (mp0) REVERT: X 442 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8196 (mp) REVERT: X 611 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7640 (tm-30) outliers start: 18 outliers final: 6 residues processed: 108 average time/residue: 3.2984 time to fit residues: 368.5098 Evaluate side-chains 109 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 200 LYS Chi-restraints excluded: chain X residue 400 GLU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 531 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 620 ASP Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 69 optimal weight: 50.0000 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 50.0000 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 175 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5281 Z= 0.304 Angle : 0.590 5.969 7166 Z= 0.310 Chirality : 0.042 0.149 811 Planarity : 0.005 0.049 923 Dihedral : 5.219 25.749 713 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.33 % Allowed : 15.56 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.31), residues: 650 helix: 1.70 (0.47), residues: 118 sheet: 0.56 (0.30), residues: 251 loop : 0.26 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 333 HIS 0.005 0.002 HIS X 350 PHE 0.018 0.002 PHE X 639 TYR 0.022 0.002 TYR X 167 ARG 0.004 0.000 ARG X 450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 200 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7859 (mptt) REVERT: X 225 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: X 400 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5361 (mp0) REVERT: X 442 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8200 (mp) REVERT: X 611 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7637 (tm-30) outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 3.3257 time to fit residues: 357.2700 Evaluate side-chains 109 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 198 LYS Chi-restraints excluded: chain X residue 200 LYS Chi-restraints excluded: chain X residue 225 GLN Chi-restraints excluded: chain X residue 400 GLU Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 531 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 620 ASP Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 74 optimal weight: 50.0000 chunk 78 optimal weight: 50.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 175 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 559 ASN X 646 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5281 Z= 0.169 Angle : 0.513 5.292 7166 Z= 0.265 Chirality : 0.041 0.138 811 Planarity : 0.004 0.042 923 Dihedral : 4.684 15.928 712 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.15 % Allowed : 15.74 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.32), residues: 650 helix: 2.04 (0.47), residues: 118 sheet: 0.63 (0.30), residues: 254 loop : 0.55 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 90 HIS 0.003 0.001 HIS X 210 PHE 0.010 0.001 PHE X 292 TYR 0.015 0.001 TYR X 167 ARG 0.003 0.000 ARG X 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 200 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7620 (mptt) REVERT: X 442 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8128 (mp) REVERT: X 611 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7579 (tm-30) outliers start: 12 outliers final: 5 residues processed: 105 average time/residue: 3.3040 time to fit residues: 358.9386 Evaluate side-chains 106 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 118 SER Chi-restraints excluded: chain X residue 200 LYS Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 531 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 chunk 78 optimal weight: 50.0000 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 50.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 175 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5281 Z= 0.374 Angle : 0.633 6.010 7166 Z= 0.334 Chirality : 0.043 0.155 811 Planarity : 0.005 0.045 923 Dihedral : 5.210 17.597 712 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.15 % Allowed : 15.92 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.31), residues: 650 helix: 1.66 (0.47), residues: 118 sheet: 0.76 (0.30), residues: 243 loop : 0.21 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP X 333 HIS 0.006 0.002 HIS X 350 PHE 0.016 0.003 PHE X 639 TYR 0.025 0.003 TYR X 679 ARG 0.005 0.001 ARG X 450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 442 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8224 (mp) REVERT: X 611 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7643 (tm-30) outliers start: 12 outliers final: 5 residues processed: 101 average time/residue: 3.3370 time to fit residues: 348.5186 Evaluate side-chains 103 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 200 LYS Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 620 ASP Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 84 optimal weight: 50.0000 chunk 77 optimal weight: 50.0000 chunk 67 optimal weight: 50.0000 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 71 optimal weight: 50.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 175 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5281 Z= 0.170 Angle : 0.518 6.164 7166 Z= 0.266 Chirality : 0.041 0.140 811 Planarity : 0.004 0.042 923 Dihedral : 4.691 16.129 712 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.61 % Allowed : 16.46 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.32), residues: 650 helix: 2.02 (0.47), residues: 118 sheet: 0.74 (0.31), residues: 248 loop : 0.52 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 90 HIS 0.003 0.001 HIS X 210 PHE 0.010 0.001 PHE X 292 TYR 0.014 0.001 TYR X 167 ARG 0.003 0.000 ARG X 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: X 200 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7616 (mptt) REVERT: X 442 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8123 (mp) REVERT: X 611 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7581 (tm-30) outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 3.1990 time to fit residues: 337.8020 Evaluate side-chains 104 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 200 LYS Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 445 LYS Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 67 optimal weight: 50.0000 chunk 28 optimal weight: 10.0000 chunk 69 optimal weight: 50.0000 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 175 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.126376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.106229 restraints weight = 13316.400| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.04 r_work: 0.2982 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5281 Z= 0.232 Angle : 0.549 6.167 7166 Z= 0.286 Chirality : 0.041 0.145 811 Planarity : 0.004 0.041 923 Dihedral : 4.852 16.411 712 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.79 % Allowed : 16.64 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.32), residues: 650 helix: 1.95 (0.47), residues: 118 sheet: 0.74 (0.31), residues: 248 loop : 0.46 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 333 HIS 0.004 0.001 HIS X 350 PHE 0.014 0.002 PHE X 548 TYR 0.019 0.002 TYR X 167 ARG 0.002 0.000 ARG X 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6014.77 seconds wall clock time: 105 minutes 35.74 seconds (6335.74 seconds total)