Starting phenix.real_space_refine on Sat Dec 9 08:26:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/12_2023/7uzs_26917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/12_2023/7uzs_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_26917/12_2023/7uzs_26917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/12_2023/7uzs_26917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/12_2023/7uzs_26917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/12_2023/7uzs_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-1.21rc1-5172/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: 5.45, per 1000 atoms: 0.52 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: 9.07 Conformation dependent library (CDL) restraints added in 1.5 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: 0.91 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: 4.01 Time building geometry restraints manager: 9.18 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: 4293 17.89 - 35.77: 325 35.77 - 53.66: 113 53.66 - 71.54: 25 71.54 - 89.43: 21 Dihedral angle restraints: 4777 sinusoidal: 2566 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 4774 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: 0.970 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: 0.200 Extract box with map and model: 4.860 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 38.670 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.380 ------------------------------------------------------------------------------- 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 : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 3.1313 time to fit residues: 350.1364 Evaluate side-chains 96 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.0892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 50.0000 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 50.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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: 0.8650 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5281 Z= 0.222 Angle : 0.534 5.324 7166 Z= 0.280 Chirality : 0.041 0.142 811 Planarity : 0.004 0.037 923 Dihedral : 4.704 16.482 712 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.40 % Allowed : 14.67 % 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: 1.27 (0.32), residues: 650 helix: 1.91 (0.47), residues: 118 sheet: 0.65 (0.31), residues: 248 loop : 0.74 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 333 HIS 0.004 0.001 HIS X 350 PHE 0.014 0.002 PHE X 134 TYR 0.017 0.002 TYR X 167 ARG 0.003 0.000 ARG X 450 *********************** 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 115 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 110 average time/residue: 3.2016 time to fit residues: 364.5091 Evaluate side-chains 108 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1236 time to fit residues: 1.5717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 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: 2.9990 chunk 62 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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: 0.8666 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5281 Z= 0.287 Angle : 0.571 5.114 7166 Z= 0.303 Chirality : 0.042 0.148 811 Planarity : 0.005 0.040 923 Dihedral : 4.995 16.907 712 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.40 % Allowed : 13.60 % Favored : 83.01 % 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: 1.14 (0.31), residues: 650 helix: 1.83 (0.47), residues: 118 sheet: 0.69 (0.30), residues: 246 loop : 0.51 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 333 HIS 0.006 0.001 HIS X 350 PHE 0.019 0.002 PHE X 639 TYR 0.021 0.002 TYR X 167 ARG 0.004 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 120 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 113 average time/residue: 3.1923 time to fit residues: 373.2015 Evaluate side-chains 108 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.1734 time to fit residues: 1.9538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 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: 5.9990 ------------------------------------------------------------------------------- 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 611 GLN X 646 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5281 Z= 0.389 Angle : 0.635 5.615 7166 Z= 0.339 Chirality : 0.044 0.153 811 Planarity : 0.006 0.053 923 Dihedral : 5.308 17.559 712 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.76 % Allowed : 13.77 % 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: 0.89 (0.31), residues: 650 helix: 1.57 (0.47), residues: 118 sheet: 0.71 (0.30), residues: 243 loop : 0.20 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 333 HIS 0.006 0.002 HIS X 350 PHE 0.025 0.003 PHE X 639 TYR 0.025 0.003 TYR X 167 ARG 0.005 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 117 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.889 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 108 average time/residue: 3.3682 time to fit residues: 376.1160 Evaluate side-chains 105 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1230 time to fit residues: 1.6537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 70 optimal weight: 50.0000 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 175 GLN X 225 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0981 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= 0.251 Angle : 0.555 5.053 7166 Z= 0.293 Chirality : 0.042 0.145 811 Planarity : 0.004 0.042 923 Dihedral : 5.018 16.641 712 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.50 % Allowed : 15.03 % 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: 1.84 (0.47), residues: 118 sheet: 0.68 (0.31), residues: 245 loop : 0.33 (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 114 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.849 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 109 average time/residue: 3.2929 time to fit residues: 370.9761 Evaluate side-chains 107 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.1640 time to fit residues: 1.7656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 20 optimal weight: 0.2980 chunk 82 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 79 optimal weight: 50.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- 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 611 GLN X 646 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5281 Z= 0.317 Angle : 0.596 5.755 7166 Z= 0.315 Chirality : 0.043 0.150 811 Planarity : 0.005 0.043 923 Dihedral : 5.168 17.227 712 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: 1.69 (0.47), residues: 118 sheet: 0.70 (0.30), residues: 246 loop : 0.22 (0.35), residues: 286 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 0.020 0.002 PHE X 639 TYR 0.022 0.003 TYR X 167 ARG 0.004 0.001 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 117 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.772 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 111 average time/residue: 3.3239 time to fit residues: 381.3751 Evaluate side-chains 110 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.1763 time to fit residues: 2.1605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 69 optimal weight: 50.0000 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 50.0000 chunk 51 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 175 GLN X 225 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 559 ASN X 646 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5281 Z= 0.209 Angle : 0.534 5.499 7166 Z= 0.278 Chirality : 0.041 0.141 811 Planarity : 0.004 0.041 923 Dihedral : 4.848 16.212 712 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.68 % Allowed : 15.38 % 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: 1.12 (0.32), residues: 650 helix: 1.95 (0.47), residues: 118 sheet: 0.70 (0.30), residues: 248 loop : 0.41 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 333 HIS 0.003 0.001 HIS X 350 PHE 0.014 0.002 PHE X 639 TYR 0.017 0.002 TYR X 167 ARG 0.002 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 116 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 110 average time/residue: 3.2616 time to fit residues: 370.9887 Evaluate side-chains 107 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.1972 time to fit residues: 1.7404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 74 optimal weight: 50.0000 chunk 78 optimal weight: 50.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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: 0.8636 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5281 Z= 0.165 Angle : 0.501 5.548 7166 Z= 0.258 Chirality : 0.041 0.142 811 Planarity : 0.003 0.041 923 Dihedral : 4.557 15.788 712 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.33 % Allowed : 15.74 % 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: 1.35 (0.32), residues: 650 helix: 2.22 (0.48), residues: 118 sheet: 0.76 (0.31), residues: 248 loop : 0.61 (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 210 PHE 0.010 0.001 PHE X 292 TYR 0.014 0.001 TYR X 167 ARG 0.002 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 111 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 3.3279 time to fit residues: 372.4601 Evaluate side-chains 109 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.1546 time to fit residues: 1.9230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 50.0000 overall best weight: 4.7944 ------------------------------------------------------------------------------- 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 611 GLN X 646 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5281 Z= 0.323 Angle : 0.598 6.039 7166 Z= 0.314 Chirality : 0.043 0.153 811 Planarity : 0.005 0.041 923 Dihedral : 5.071 17.260 712 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.33 % Allowed : 15.74 % 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: 1.06 (0.31), residues: 650 helix: 1.85 (0.47), residues: 118 sheet: 0.72 (0.30), residues: 246 loop : 0.33 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 333 HIS 0.006 0.002 HIS X 350 PHE 0.014 0.003 PHE X 639 TYR 0.022 0.003 TYR X 167 ARG 0.004 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 112 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.777 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 3.3571 time to fit residues: 378.7747 Evaluate side-chains 109 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1929 time to fit residues: 1.6926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 0.0470 chunk 84 optimal weight: 50.0000 chunk 77 optimal weight: 50.0000 chunk 67 optimal weight: 50.0000 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 71 optimal weight: 50.0000 overall best weight: 2.6086 ------------------------------------------------------------------------------- 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: 0.8653 moved from start: 0.0982 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= 0.216 Angle : 0.544 6.427 7166 Z= 0.282 Chirality : 0.041 0.141 811 Planarity : 0.004 0.041 923 Dihedral : 4.819 16.269 712 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.43 % Allowed : 16.64 % 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: 1.13 (0.32), residues: 650 helix: 1.96 (0.47), residues: 118 sheet: 0.70 (0.31), residues: 248 loop : 0.43 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 333 HIS 0.003 0.001 HIS X 350 PHE 0.012 0.002 PHE X 292 TYR 0.017 0.002 TYR X 167 ARG 0.002 0.000 ARG X 450 ********************** 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 110 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 110 average time/residue: 3.3404 time to fit residues: 379.9223 Evaluate side-chains 107 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.2569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 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: 2.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.127159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.107000 restraints weight = 13241.273| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.03 r_work: 0.2983 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1015 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= 0.242 Angle : 0.559 5.719 7166 Z= 0.291 Chirality : 0.042 0.145 811 Planarity : 0.004 0.041 923 Dihedral : 4.912 16.775 712 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.50 % Allowed : 15.92 % 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: 1.07 (0.32), residues: 650 helix: 1.88 (0.47), residues: 118 sheet: 0.68 (0.30), residues: 248 loop : 0.38 (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 0.020 0.002 TYR X 679 ARG 0.003 0.000 ARG X 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6139.21 seconds wall clock time: 108 minutes 17.18 seconds (6497.18 seconds total)