Starting phenix.real_space_refine on Sun Dec 29 09:01:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzs_26917/12_2024/7uzs_26917.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzs_26917/12_2024/7uzs_26917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uzs_26917/12_2024/7uzs_26917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzs_26917/12_2024/7uzs_26917.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzs_26917/12_2024/7uzs_26917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzs_26917/12_2024/7uzs_26917.cif" } 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. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10550 Number of models: 1 Model: "" Number of chains: 2 Chain: "X" Number of atoms: 10357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 10357 Classifications: {'peptide': 658} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 627} 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 Chain: "X" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Time building chain proxies: 2.65, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 724.3 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: 1.02 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: 4.34 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5168 1.03 - 1.23: 73 1.23 - 1.42: 2129 1.42 - 1.62: 3063 1.62 - 1.81: 31 Bond restraints: 10464 Sorted by residual: bond pdb=" N ILE X 284 " pdb=" CA ILE X 284 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.30e-03 1.88e+04 1.75e+01 bond pdb=" N ILE X 431 " pdb=" CA ILE X 431 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.04e-02 9.25e+03 1.35e+01 bond pdb=" C VAL X 288 " pdb=" O VAL X 288 " ideal model delta sigma weight residual 1.238 1.200 0.037 1.17e-02 7.31e+03 1.02e+01 bond pdb=" C PRO X 285 " pdb=" O PRO X 285 " ideal model delta sigma weight residual 1.233 1.196 0.038 1.23e-02 6.61e+03 9.34e+00 bond pdb=" C PRO X 367 " pdb=" O PRO X 367 " ideal model delta sigma weight residual 1.233 1.196 0.037 1.23e-02 6.61e+03 8.96e+00 ... (remaining 10459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 18707 2.31 - 4.62: 201 4.62 - 6.92: 11 6.92 - 9.23: 0 9.23 - 11.54: 1 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: 4359 17.89 - 35.77: 349 35.77 - 53.66: 138 53.66 - 71.54: 34 71.54 - 89.43: 21 Dihedral angle restraints: 4901 sinusoidal: 2690 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 4898 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 2.450 nonbonded pdb=" HE1 TRP X 179 " pdb=" OG SER X 248 " model vdw 1.679 2.450 nonbonded pdb=" O PRO X 557 " pdb=" HG1 THR X 560 " model vdw 1.700 2.450 nonbonded pdb=" HH TYR X 518 " pdb=" O HOH X 714 " model vdw 1.701 2.450 nonbonded pdb=" HG SER X 91 " pdb=" OG1 THR X 107 " model vdw 1.702 2.450 ... (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: 5.520 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: 0.000 Extract box with map and model: 5.540 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.350 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 599 GLU cc_start: 0.8204 (tt0) cc_final: 0.7913 (tt0) outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 3.1965 time to fit residues: 357.5592 Evaluate side-chains 98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 505 LYS Chi-restraints excluded: chain X residue 572 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 68 GLN X 175 GLN X 225 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5281 Z= 0.273 Angle : 0.570 5.496 7166 Z= 0.303 Chirality : 0.042 0.158 811 Planarity : 0.004 0.037 923 Dihedral : 6.472 77.601 721 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.58 % Allowed : 14.49 % 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: 1.19 (0.32), residues: 650 helix: 1.89 (0.47), residues: 118 sheet: 0.64 (0.31), residues: 245 loop : 0.63 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 333 HIS 0.005 0.001 HIS X 350 PHE 0.016 0.002 PHE X 639 TYR 0.019 0.002 TYR X 167 ARG 0.005 0.001 ARG X 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 442 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8140 (mp) REVERT: X 611 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7194 (tm-30) outliers start: 20 outliers final: 5 residues processed: 108 average time/residue: 3.2706 time to fit residues: 365.7886 Evaluate side-chains 101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 620 ASP Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5281 Z= 0.230 Angle : 0.537 5.239 7166 Z= 0.284 Chirality : 0.042 0.155 811 Planarity : 0.004 0.037 923 Dihedral : 4.924 30.167 713 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.22 % Allowed : 14.13 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.32), residues: 650 helix: 2.11 (0.47), residues: 118 sheet: 0.66 (0.31), residues: 246 loop : 0.56 (0.37), residues: 286 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 0.015 0.002 PHE X 639 TYR 0.018 0.002 TYR X 167 ARG 0.003 0.000 ARG X 155 *********************** 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 119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 442 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8141 (mp) REVERT: X 611 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7183 (tm-30) outliers start: 18 outliers final: 6 residues processed: 112 average time/residue: 3.3871 time to fit residues: 392.6390 Evaluate side-chains 104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 118 SER Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 620 ASP Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 0.0070 chunk 30 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 68 GLN 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: 4 ------------------------------------------------------------------------------- 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 : 0.003 0.026 5281 Z= 0.194 Angle : 0.514 5.412 7166 Z= 0.271 Chirality : 0.041 0.151 811 Planarity : 0.004 0.038 923 Dihedral : 4.795 26.971 713 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: 1.22 (0.33), residues: 650 helix: 2.24 (0.48), residues: 118 sheet: 0.53 (0.31), residues: 251 loop : 0.63 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 333 HIS 0.003 0.001 HIS X 350 PHE 0.013 0.002 PHE X 639 TYR 0.016 0.002 TYR X 167 ARG 0.002 0.000 ARG X 155 *********************** 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 116 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 442 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8130 (mp) REVERT: X 611 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7529 (tm-30) outliers start: 15 outliers final: 8 residues processed: 110 average time/residue: 3.3186 time to fit residues: 377.7627 Evaluate side-chains 109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 118 SER Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 530 LYS Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 620 ASP Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 32 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 64 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: 0.8642 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5281 Z= 0.211 Angle : 0.521 5.124 7166 Z= 0.275 Chirality : 0.041 0.152 811 Planarity : 0.004 0.039 923 Dihedral : 4.833 24.134 713 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: 1.20 (0.32), residues: 650 helix: 2.28 (0.48), residues: 118 sheet: 0.50 (0.31), residues: 254 loop : 0.61 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 333 HIS 0.004 0.001 HIS X 350 PHE 0.012 0.002 PHE X 639 TYR 0.017 0.002 TYR X 167 ARG 0.003 0.000 ARG X 155 *********************** 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 119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 442 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8142 (mp) REVERT: X 611 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7543 (tm-30) outliers start: 15 outliers final: 7 residues processed: 112 average time/residue: 3.3990 time to fit residues: 393.8574 Evaluate side-chains 108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 118 SER Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 530 LYS Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 620 ASP Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 68 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: 0.8628 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5281 Z= 0.173 Angle : 0.500 5.049 7166 Z= 0.262 Chirality : 0.041 0.148 811 Planarity : 0.004 0.039 923 Dihedral : 4.602 16.107 712 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: 1.33 (0.33), residues: 650 helix: 2.36 (0.48), residues: 118 sheet: 0.57 (0.31), residues: 252 loop : 0.71 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 333 HIS 0.002 0.001 HIS X 350 PHE 0.010 0.001 PHE X 292 TYR 0.015 0.002 TYR X 167 ARG 0.002 0.000 ARG X 155 *********************** 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 112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 442 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8116 (mp) REVERT: X 611 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: X 649 CYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7187 (m) outliers start: 14 outliers final: 7 residues processed: 106 average time/residue: 3.3496 time to fit residues: 367.6694 Evaluate side-chains 105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 64 GLN Chi-restraints excluded: chain X residue 118 SER Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 530 LYS Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 620 ASP Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 68 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: 0.8646 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5281 Z= 0.231 Angle : 0.537 5.513 7166 Z= 0.283 Chirality : 0.042 0.153 811 Planarity : 0.004 0.039 923 Dihedral : 4.773 16.678 712 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.15 % Allowed : 16.46 % Favored : 81.40 % 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: 1.19 (0.32), residues: 650 helix: 2.21 (0.47), residues: 118 sheet: 0.52 (0.31), residues: 254 loop : 0.59 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 333 HIS 0.004 0.001 HIS X 350 PHE 0.013 0.002 PHE X 639 TYR 0.018 0.002 TYR X 167 ARG 0.003 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 114 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 442 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8152 (mp) REVERT: X 611 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7557 (tm-30) outliers start: 12 outliers final: 7 residues processed: 107 average time/residue: 3.3901 time to fit residues: 376.5454 Evaluate side-chains 108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 118 SER Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 620 ASP Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5281 Z= 0.179 Angle : 0.508 5.348 7166 Z= 0.265 Chirality : 0.041 0.148 811 Planarity : 0.004 0.039 923 Dihedral : 4.603 16.181 712 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.33 % Allowed : 16.28 % Favored : 81.40 % 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: 1.32 (0.33), residues: 650 helix: 2.34 (0.48), residues: 118 sheet: 0.58 (0.31), residues: 252 loop : 0.69 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 90 HIS 0.002 0.001 HIS X 350 PHE 0.010 0.001 PHE X 292 TYR 0.015 0.002 TYR X 167 ARG 0.002 0.000 ARG X 155 *********************** 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 112 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 442 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8119 (mp) REVERT: X 611 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: X 649 CYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7185 (m) outliers start: 13 outliers final: 5 residues processed: 106 average time/residue: 3.4001 time to fit residues: 372.7515 Evaluate side-chains 104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 118 SER Chi-restraints excluded: chain X residue 407 THR Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 611 GLN Chi-restraints excluded: chain X residue 649 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 0.0470 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 68 GLN X 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5281 Z= 0.148 Angle : 0.486 5.630 7166 Z= 0.250 Chirality : 0.041 0.143 811 Planarity : 0.003 0.038 923 Dihedral : 4.316 15.342 712 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.25 % Allowed : 17.89 % Favored : 80.86 % 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: 1.45 (0.33), residues: 650 helix: 2.43 (0.48), residues: 118 sheet: 0.64 (0.31), residues: 252 loop : 0.80 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 90 HIS 0.002 0.001 HIS X 210 PHE 0.007 0.001 PHE X 292 TYR 0.012 0.001 TYR X 167 ARG 0.002 0.000 ARG X 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 230 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 442 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8051 (mp) REVERT: X 649 CYS cc_start: 0.7574 (t) cc_final: 0.7165 (m) outliers start: 7 outliers final: 3 residues processed: 104 average time/residue: 3.4636 time to fit residues: 374.1058 Evaluate side-chains 101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 118 SER Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 534 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 68 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: 0.8638 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5281 Z= 0.225 Angle : 0.532 5.758 7166 Z= 0.279 Chirality : 0.042 0.151 811 Planarity : 0.004 0.038 923 Dihedral : 4.661 16.205 712 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.61 % Allowed : 18.07 % Favored : 80.32 % 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: 1.26 (0.33), residues: 650 helix: 2.26 (0.48), residues: 118 sheet: 0.56 (0.31), residues: 254 loop : 0.64 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 179 HIS 0.004 0.001 HIS X 350 PHE 0.011 0.002 PHE X 292 TYR 0.018 0.002 TYR X 167 ARG 0.003 0.000 ARG X 155 ********************** 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 105 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 442 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8138 (mp) outliers start: 9 outliers final: 5 residues processed: 100 average time/residue: 3.4173 time to fit residues: 354.3686 Evaluate side-chains 104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 118 SER Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 442 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 620 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 646 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.109916 restraints weight = 13318.591| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.05 r_work: 0.3040 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5281 Z= 0.174 Angle : 0.510 6.078 7166 Z= 0.265 Chirality : 0.041 0.146 811 Planarity : 0.004 0.039 923 Dihedral : 4.530 15.655 712 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.07 % Allowed : 18.43 % Favored : 80.50 % 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 (0.33), residues: 650 helix: 2.30 (0.48), residues: 118 sheet: 0.62 (0.31), residues: 252 loop : 0.72 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 90 HIS 0.002 0.001 HIS X 350 PHE 0.012 0.002 PHE X 548 TYR 0.014 0.002 TYR X 167 ARG 0.002 0.000 ARG X 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6603.28 seconds wall clock time: 117 minutes 36.13 seconds (7056.13 seconds total)