Starting phenix.real_space_refine on Sun Mar 10 17:07:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3o_25666/03_2024/7t3o_25666.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3o_25666/03_2024/7t3o_25666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3o_25666/03_2024/7t3o_25666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3o_25666/03_2024/7t3o_25666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3o_25666/03_2024/7t3o_25666.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3o_25666/03_2024/7t3o_25666.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2241 2.51 5 N 560 2.21 5 O 583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 70": "NH1" <-> "NH2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3410 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3410 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 19, 'TRANS': 432} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 2.39, per 1000 atoms: 0.70 Number of scatterers: 3410 At special positions: 0 Unit cell: (75.68, 75.68, 81.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 583 8.00 N 560 7.00 C 2241 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 1.29 Conformation dependent library (CDL) restraints added in 648.1 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 74.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.826A pdb=" N ILE A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.873A pdb=" N ASN A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 4.716A pdb=" N PHE A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N PHE A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 137 " --> pdb=" O TRP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.707A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 177 through 191 Processing helix chain 'A' and resid 194 through 206 removed outlier: 4.458A pdb=" N LYS A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.504A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR A 216 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.548A pdb=" N GLN A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.594A pdb=" N TYR A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.918A pdb=" N MET A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.644A pdb=" N HIS A 271 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.922A pdb=" N PHE A 307 " --> pdb=" O TRP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 332 removed outlier: 3.724A pdb=" N ILE A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 325 " --> pdb=" O CYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 353 through 376 removed outlier: 3.582A pdb=" N LEU A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 364 - end of helix removed outlier: 3.678A pdb=" N ALA A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 405 removed outlier: 3.633A pdb=" N MET A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY A 392 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.648A pdb=" N ILE A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.653A pdb=" N PHE A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 431' Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.875A pdb=" N ASP A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 459 removed outlier: 3.790A pdb=" N VAL A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 removed outlier: 3.830A pdb=" N ILE A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 removed outlier: 3.824A pdb=" N ILE A 482 " --> pdb=" O TYR A 478 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 497 " --> pdb=" O PHE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.620A pdb=" N ASP A 507 " --> pdb=" O PRO A 504 " (cutoff:3.500A) 174 hydrogen bonds defined for protein. 516 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: 0.76 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1046 1.34 - 1.46: 759 1.46 - 1.57: 1661 1.57 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 3507 Sorted by residual: bond pdb=" CB ILE A 72 " pdb=" CG2 ILE A 72 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.03e+00 bond pdb=" CB THR A 194 " pdb=" CG2 THR A 194 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.70e-01 bond pdb=" CG1 ILE A 282 " pdb=" CD1 ILE A 282 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.44e-01 bond pdb=" CA LEU A 165 " pdb=" C LEU A 165 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.66e-02 3.63e+03 6.60e-01 bond pdb=" CB ASN A 450 " pdb=" CG ASN A 450 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.09e-01 ... (remaining 3502 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.76: 110 106.76 - 113.58: 1924 113.58 - 120.40: 1447 120.40 - 127.22: 1250 127.22 - 134.04: 49 Bond angle restraints: 4780 Sorted by residual: angle pdb=" N GLY A 234 " pdb=" CA GLY A 234 " pdb=" C GLY A 234 " ideal model delta sigma weight residual 114.67 111.01 3.66 1.10e+00 8.26e-01 1.10e+01 angle pdb=" N MET A 98 " pdb=" CA MET A 98 " pdb=" C MET A 98 " ideal model delta sigma weight residual 113.18 110.17 3.01 1.33e+00 5.65e-01 5.12e+00 angle pdb=" C ILE A 159 " pdb=" N LEU A 160 " pdb=" CA LEU A 160 " ideal model delta sigma weight residual 120.44 117.74 2.70 1.36e+00 5.41e-01 3.94e+00 angle pdb=" N VAL A 354 " pdb=" CA VAL A 354 " pdb=" C VAL A 354 " ideal model delta sigma weight residual 108.88 112.99 -4.11 2.16e+00 2.14e-01 3.62e+00 angle pdb=" CA VAL A 354 " pdb=" C VAL A 354 " pdb=" N PRO A 355 " ideal model delta sigma weight residual 118.88 121.67 -2.79 1.54e+00 4.22e-01 3.29e+00 ... (remaining 4775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 1806 17.31 - 34.61: 157 34.61 - 51.92: 25 51.92 - 69.22: 3 69.22 - 86.53: 2 Dihedral angle restraints: 1993 sinusoidal: 708 harmonic: 1285 Sorted by residual: dihedral pdb=" CA LEU A 232 " pdb=" C LEU A 232 " pdb=" N ALA A 233 " pdb=" CA ALA A 233 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CB GLU A 278 " pdb=" CG GLU A 278 " pdb=" CD GLU A 278 " pdb=" OE1 GLU A 278 " ideal model delta sinusoidal sigma weight residual 0.00 -86.53 86.53 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU A 283 " pdb=" CG GLU A 283 " pdb=" CD GLU A 283 " pdb=" OE1 GLU A 283 " ideal model delta sinusoidal sigma weight residual 0.00 -85.28 85.28 1 3.00e+01 1.11e-03 9.79e+00 ... (remaining 1990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 242 0.030 - 0.060: 190 0.060 - 0.089: 80 0.089 - 0.119: 26 0.119 - 0.149: 1 Chirality restraints: 539 Sorted by residual: chirality pdb=" CB THR A 273 " pdb=" CA THR A 273 " pdb=" OG1 THR A 273 " pdb=" CG2 THR A 273 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA PRO A 208 " pdb=" N PRO A 208 " pdb=" C PRO A 208 " pdb=" CB PRO A 208 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA THR A 325 " pdb=" N THR A 325 " pdb=" C THR A 325 " pdb=" CB THR A 325 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 536 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 503 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 504 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 120 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO A 121 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 133 " -0.010 2.00e-02 2.50e+03 6.51e-03 1.06e+00 pdb=" CG TRP A 133 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 133 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 133 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 133 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 133 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 133 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 133 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 133 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 133 " -0.001 2.00e-02 2.50e+03 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1038 2.81 - 3.33: 3216 3.33 - 3.85: 5150 3.85 - 4.38: 5860 4.38 - 4.90: 10411 Nonbonded interactions: 25675 Sorted by model distance: nonbonded pdb=" NH1 ARG A 70 " pdb=" OE1 GLU A 278 " model vdw 2.284 2.520 nonbonded pdb=" OH TYR A 223 " pdb=" NH2 ARG A 322 " model vdw 2.288 2.520 nonbonded pdb=" NE ARG A 213 " pdb=" OD2 ASP A 371 " model vdw 2.320 2.520 nonbonded pdb=" OD1 ASN A 100 " pdb=" N ASN A 101 " model vdw 2.352 2.520 nonbonded pdb=" O THR A 468 " pdb=" OG1 THR A 468 " model vdw 2.389 2.440 ... (remaining 25670 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=0.00 max=1.00 mean=0.99 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.380 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.630 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.006 0.038 3507 Z= 0.381 Angle : 0.685 7.348 4780 Z= 0.368 Chirality : 0.046 0.149 539 Planarity : 0.003 0.029 595 Dihedral : 13.487 86.531 1179 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.29 % Allowed : 10.85 % Favored : 88.86 % 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: -3.36 (0.35), residues: 450 helix: -1.66 (0.27), residues: 297 sheet: None (None), residues: 0 loop : -3.19 (0.44), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 133 HIS 0.004 0.001 HIS A 407 PHE 0.016 0.001 PHE A 343 TYR 0.017 0.001 TYR A 135 ARG 0.001 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 238 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7939 (mm-40) REVERT: A 277 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7791 (tm-30) REVERT: A 377 GLN cc_start: 0.8561 (mt0) cc_final: 0.8307 (tm-30) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.1900 time to fit residues: 21.9400 Evaluate side-chains 78 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 HIS A 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3507 Z= 0.192 Angle : 0.583 7.299 4780 Z= 0.291 Chirality : 0.042 0.151 539 Planarity : 0.003 0.036 595 Dihedral : 4.737 45.805 491 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.64 % Allowed : 21.11 % Favored : 76.25 % 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: -1.79 (0.40), residues: 450 helix: -0.42 (0.31), residues: 306 sheet: None (None), residues: 0 loop : -2.77 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 324 HIS 0.004 0.001 HIS A 487 PHE 0.012 0.001 PHE A 343 TYR 0.011 0.001 TYR A 135 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 128 HIS cc_start: 0.8735 (m170) cc_final: 0.8526 (m-70) REVERT: A 238 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7815 (mm-40) REVERT: A 277 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 379 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8286 (pp) outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.1705 time to fit residues: 20.0612 Evaluate side-chains 86 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 414 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3507 Z= 0.203 Angle : 0.578 7.253 4780 Z= 0.289 Chirality : 0.041 0.153 539 Planarity : 0.003 0.041 595 Dihedral : 4.632 47.482 491 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.81 % Allowed : 21.11 % Favored : 75.07 % 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 (0.41), residues: 450 helix: 0.05 (0.32), residues: 309 sheet: None (None), residues: 0 loop : -2.38 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 324 HIS 0.004 0.001 HIS A 487 PHE 0.012 0.001 PHE A 343 TYR 0.012 0.001 TYR A 135 ARG 0.001 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 128 HIS cc_start: 0.8731 (m170) cc_final: 0.8500 (m-70) REVERT: A 238 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7835 (mm-40) REVERT: A 379 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8313 (pp) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 0.1669 time to fit residues: 18.3430 Evaluate side-chains 91 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.0060 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3507 Z= 0.222 Angle : 0.576 7.281 4780 Z= 0.290 Chirality : 0.042 0.161 539 Planarity : 0.003 0.044 595 Dihedral : 4.677 49.912 491 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.40 % Allowed : 23.17 % Favored : 72.43 % 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: -0.69 (0.42), residues: 450 helix: 0.34 (0.32), residues: 309 sheet: None (None), residues: 0 loop : -2.18 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 260 HIS 0.004 0.001 HIS A 487 PHE 0.014 0.001 PHE A 343 TYR 0.013 0.001 TYR A 135 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 238 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7811 (mm-40) REVERT: A 379 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8294 (pp) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.1695 time to fit residues: 17.9703 Evaluate side-chains 88 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 492 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 37 optimal weight: 0.0970 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3507 Z= 0.153 Angle : 0.553 7.350 4780 Z= 0.277 Chirality : 0.041 0.203 539 Planarity : 0.003 0.046 595 Dihedral : 4.440 50.943 491 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.81 % Allowed : 24.34 % Favored : 71.85 % 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: -0.37 (0.43), residues: 450 helix: 0.59 (0.33), residues: 306 sheet: None (None), residues: 0 loop : -2.02 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 260 HIS 0.004 0.001 HIS A 487 PHE 0.009 0.001 PHE A 343 TYR 0.010 0.001 TYR A 135 ARG 0.001 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8275 (pp) outliers start: 13 outliers final: 8 residues processed: 100 average time/residue: 0.1593 time to fit residues: 19.4440 Evaluate side-chains 90 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.0570 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3507 Z= 0.184 Angle : 0.564 7.257 4780 Z= 0.282 Chirality : 0.042 0.189 539 Planarity : 0.003 0.046 595 Dihedral : 4.488 52.978 491 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.81 % Allowed : 24.63 % Favored : 71.55 % 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: -0.31 (0.43), residues: 450 helix: 0.58 (0.32), residues: 314 sheet: None (None), residues: 0 loop : -2.01 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 260 HIS 0.004 0.001 HIS A 487 PHE 0.021 0.001 PHE A 372 TYR 0.012 0.001 TYR A 135 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 379 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8256 (pp) outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 0.1628 time to fit residues: 19.8382 Evaluate side-chains 95 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 377 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3507 Z= 0.234 Angle : 0.588 7.266 4780 Z= 0.298 Chirality : 0.043 0.172 539 Planarity : 0.003 0.047 595 Dihedral : 4.711 56.618 491 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.52 % Allowed : 25.81 % Favored : 70.67 % 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: -0.24 (0.43), residues: 450 helix: 0.63 (0.33), residues: 314 sheet: None (None), residues: 0 loop : -2.00 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.005 0.001 HIS A 487 PHE 0.017 0.001 PHE A 372 TYR 0.014 0.001 TYR A 135 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.386 Fit side-chains REVERT: A 174 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8274 (mtm180) REVERT: A 277 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 379 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8280 (pp) outliers start: 12 outliers final: 11 residues processed: 94 average time/residue: 0.1637 time to fit residues: 18.8419 Evaluate side-chains 92 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 414 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.0970 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3507 Z= 0.219 Angle : 0.589 7.360 4780 Z= 0.297 Chirality : 0.042 0.152 539 Planarity : 0.003 0.047 595 Dihedral : 4.755 59.452 491 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.52 % Allowed : 26.10 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.43), residues: 450 helix: 0.68 (0.32), residues: 314 sheet: None (None), residues: 0 loop : -1.92 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.004 0.001 HIS A 487 PHE 0.017 0.001 PHE A 372 TYR 0.013 0.001 TYR A 135 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.419 Fit side-chains REVERT: A 174 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8259 (mtm180) REVERT: A 379 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8269 (pp) outliers start: 12 outliers final: 11 residues processed: 93 average time/residue: 0.1622 time to fit residues: 18.3187 Evaluate side-chains 93 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 414 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.0170 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3507 Z= 0.181 Angle : 0.570 7.350 4780 Z= 0.287 Chirality : 0.041 0.139 539 Planarity : 0.003 0.047 595 Dihedral : 4.601 57.961 491 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.81 % Allowed : 25.51 % Favored : 70.67 % 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: -0.02 (0.43), residues: 450 helix: 0.76 (0.32), residues: 314 sheet: None (None), residues: 0 loop : -1.80 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.005 0.001 HIS A 487 PHE 0.016 0.001 PHE A 372 TYR 0.012 0.001 TYR A 135 ARG 0.001 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.387 Fit side-chains REVERT: A 174 ARG cc_start: 0.8568 (ttp80) cc_final: 0.8275 (mtm180) REVERT: A 379 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8254 (pp) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 0.1587 time to fit residues: 17.6061 Evaluate side-chains 93 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 414 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 0.0970 chunk 10 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3507 Z= 0.160 Angle : 0.558 7.443 4780 Z= 0.279 Chirality : 0.040 0.126 539 Planarity : 0.003 0.047 595 Dihedral : 4.365 54.592 491 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.81 % Allowed : 24.93 % Favored : 71.26 % 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: 0.11 (0.43), residues: 450 helix: 0.88 (0.32), residues: 310 sheet: None (None), residues: 0 loop : -1.74 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.004 0.001 HIS A 487 PHE 0.016 0.001 PHE A 372 TYR 0.011 0.001 TYR A 135 ARG 0.001 0.000 ARG A 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.394 Fit side-chains REVERT: A 153 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7426 (ttp-170) REVERT: A 174 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8258 (mtm180) REVERT: A 279 ARG cc_start: 0.8333 (ttp-170) cc_final: 0.8130 (ttp-170) REVERT: A 344 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6378 (mt-10) REVERT: A 379 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8226 (pp) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.1598 time to fit residues: 19.5410 Evaluate side-chains 103 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 414 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 1 optimal weight: 0.0270 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110092 restraints weight = 5064.342| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.73 r_work: 0.3185 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3507 Z= 0.208 Angle : 0.586 7.592 4780 Z= 0.296 Chirality : 0.042 0.150 539 Planarity : 0.003 0.047 595 Dihedral : 4.369 50.578 491 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.52 % Allowed : 26.10 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.43), residues: 450 helix: 0.82 (0.32), residues: 315 sheet: None (None), residues: 0 loop : -1.65 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.004 0.001 HIS A 487 PHE 0.016 0.001 PHE A 372 TYR 0.013 0.001 TYR A 135 ARG 0.001 0.000 ARG A 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1312.72 seconds wall clock time: 24 minutes 15.76 seconds (1455.76 seconds total)