Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 21:06:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/04_2023/7uzs_26917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/04_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_26917/04_2023/7uzs_26917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/04_2023/7uzs_26917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/04_2023/7uzs_26917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzs_26917/04_2023/7uzs_26917.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 4.93, per 1000 atoms: 0.47 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: 9.12 Conformation dependent library (CDL) restraints added in 854.8 milliseconds 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: 0.43 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: 4.02 Time building geometry restraints manager: 9.44 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: 3745 17.89 - 35.77: 306 35.77 - 53.66: 91 53.66 - 71.54: 25 71.54 - 89.43: 21 Dihedral angle restraints: 4188 sinusoidal: 1977 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 4185 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 6.690 Check model and map are aligned: 0.360 Set scattering table: 0.000 Process input model: 37.190 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.560 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 3.1076 time to fit residues: 347.7994 Evaluate side-chains 96 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.9898 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 66 optimal weight: 50.0000 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 50.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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: 0.8634 moved from start: 0.0474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 5281 Z= 0.169 Angle : 0.502 5.050 7166 Z= 0.260 Chirality : 0.041 0.136 811 Planarity : 0.003 0.037 923 Dihedral : 4.492 16.148 712 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 3.40 % 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: 1.39 (0.32), residues: 650 helix: 2.01 (0.47), residues: 118 sheet: 0.69 (0.31), residues: 248 loop : 0.87 (0.37), residues: 284 *********************** 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 : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 110 average time/residue: 3.1489 time to fit residues: 358.5556 Evaluate side-chains 107 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.7204 time to fit residues: 3.5782 ------------------------------------------------------------------------------- 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: 0.3980 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: 1.9990 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: 0.8657 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5281 Z= 0.250 Angle : 0.547 5.104 7166 Z= 0.288 Chirality : 0.041 0.145 811 Planarity : 0.004 0.039 923 Dihedral : 4.838 16.594 712 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 3.04 % 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: 1.30 (0.32), residues: 650 helix: 2.00 (0.47), residues: 118 sheet: 0.73 (0.30), residues: 246 loop : 0.67 (0.36), residues: 286 *********************** 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: 17 poor density : 103 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 112 average time/residue: 3.1636 time to fit residues: 366.6555 Evaluate side-chains 105 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1692 time to fit residues: 1.9235 ------------------------------------------------------------------------------- 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: 5.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 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: 5.1990 ------------------------------------------------------------------------------- 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: 0.8675 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 5281 Z= 0.342 Angle : 0.605 6.111 7166 Z= 0.321 Chirality : 0.043 0.151 811 Planarity : 0.005 0.041 923 Dihedral : 5.154 17.385 712 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 3.40 % 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: 1.05 (0.31), residues: 650 helix: 1.75 (0.47), residues: 118 sheet: 0.72 (0.30), residues: 243 loop : 0.37 (0.35), residues: 289 *********************** 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 114 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.903 Fit side-chains outliers start: 19 outliers final: 6 residues processed: 108 average time/residue: 3.3618 time to fit residues: 375.9709 Evaluate side-chains 105 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1289 time to fit residues: 1.6288 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 70 optimal weight: 50.0000 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 50.0000 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 128 GLN X 175 GLN ** X 508 GLN ** 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: 0.8677 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 5281 Z= 0.354 Angle : 0.619 5.949 7166 Z= 0.328 Chirality : 0.043 0.151 811 Planarity : 0.005 0.041 923 Dihedral : 5.250 17.256 712 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.68 % 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: 0.91 (0.31), residues: 650 helix: 1.62 (0.47), residues: 118 sheet: 0.72 (0.30), residues: 243 loop : 0.20 (0.34), residues: 289 *********************** 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 115 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.847 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 109 average time/residue: 3.3804 time to fit residues: 380.9729 Evaluate side-chains 103 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1754 time to fit residues: 1.9301 ------------------------------------------------------------------------------- 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: 6.9990 chunk 48 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 38 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 79 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 128 GLN X 175 GLN ** X 508 GLN ** 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: 0.8680 moved from start: 0.1101 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= 0.368 Angle : 0.629 5.138 7166 Z= 0.334 Chirality : 0.044 0.152 811 Planarity : 0.005 0.042 923 Dihedral : 5.302 17.449 712 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 3.58 % 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: 0.83 (0.31), residues: 650 helix: 1.57 (0.47), residues: 118 sheet: 0.71 (0.30), residues: 243 loop : 0.09 (0.34), residues: 289 *********************** 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 118 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.905 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 110 average time/residue: 3.3636 time to fit residues: 382.6361 Evaluate side-chains 108 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.1486 time to fit residues: 1.8470 ------------------------------------------------------------------------------- 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: 7.9990 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: 4.9990 chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 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 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8664 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 5281 Z= 0.248 Angle : 0.566 5.595 7166 Z= 0.296 Chirality : 0.042 0.144 811 Planarity : 0.004 0.039 923 Dihedral : 5.044 16.690 712 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 2.86 % 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: 1.81 (0.47), residues: 118 sheet: 0.68 (0.30), residues: 245 loop : 0.22 (0.35), residues: 287 *********************** 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 117 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.811 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 110 average time/residue: 3.2028 time to fit residues: 364.7106 Evaluate side-chains 110 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1107 time to fit residues: 1.5968 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 74 optimal weight: 50.0000 chunk 78 optimal weight: 50.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 225 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 611 GLN X 646 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 5281 Z= 0.249 Angle : 0.566 5.625 7166 Z= 0.295 Chirality : 0.042 0.145 811 Planarity : 0.004 0.039 923 Dihedral : 5.005 16.752 712 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 : 2.86 % 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: 0.98 (0.31), residues: 650 helix: 1.83 (0.47), residues: 118 sheet: 0.69 (0.30), residues: 245 loop : 0.23 (0.35), residues: 287 *********************** 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 116 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.757 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 112 average time/residue: 3.2237 time to fit residues: 373.3188 Evaluate side-chains 111 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1960 time to fit residues: 1.7400 ------------------------------------------------------------------------------- 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: 2.9990 chunk 59 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 50.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 128 GLN X 175 GLN ** X 508 GLN ** 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: 0.8668 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 5281 Z= 0.283 Angle : 0.586 5.850 7166 Z= 0.307 Chirality : 0.042 0.149 811 Planarity : 0.004 0.039 923 Dihedral : 5.100 16.904 712 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 2.68 % 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: 1.74 (0.47), residues: 118 sheet: 0.64 (0.30), residues: 248 loop : 0.16 (0.35), residues: 284 *********************** 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 118 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.875 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 112 average time/residue: 3.2956 time to fit residues: 381.8938 Evaluate side-chains 111 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.1755 time to fit residues: 1.8845 ------------------------------------------------------------------------------- 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: 8.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 chunk 84 optimal weight: 50.0000 chunk 77 optimal weight: 50.0000 chunk 67 optimal weight: 50.0000 chunk 7 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 71 optimal weight: 50.0000 overall best weight: 2.1542 ------------------------------------------------------------------------------- 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: 0.8648 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5281 Z= 0.194 Angle : 0.534 6.453 7166 Z= 0.276 Chirality : 0.041 0.138 811 Planarity : 0.004 0.039 923 Dihedral : 4.800 16.240 712 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 2.15 % 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: 1.98 (0.47), residues: 118 sheet: 0.71 (0.30), residues: 248 loop : 0.39 (0.36), residues: 284 ********************** 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 112 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 111 average time/residue: 3.2031 time to fit residues: 367.9099 Evaluate side-chains 108 residues out of total 564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 2.4174 time to fit residues: 3.6380 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 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: 0.4980 chunk 12 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 overall best weight: 3.4386 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.127216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.107095 restraints weight = 13271.269| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.04 r_work: 0.2993 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 5281 Z= 0.252 Angle : 0.565 5.473 7166 Z= 0.296 Chirality : 0.042 0.147 811 Planarity : 0.004 0.040 923 Dihedral : 4.969 16.695 712 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.15 % 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 (0.32), residues: 650 helix: 1.85 (0.47), residues: 118 sheet: 0.70 (0.30), residues: 248 loop : 0.31 (0.36), residues: 284 =============================================================================== Job complete usr+sys time: 6036.82 seconds wall clock time: 105 minutes 51.70 seconds (6351.70 seconds total)