Starting phenix.real_space_refine on Wed Jun 4 17:44:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zxn_60545/06_2025/8zxn_60545.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zxn_60545/06_2025/8zxn_60545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zxn_60545/06_2025/8zxn_60545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zxn_60545/06_2025/8zxn_60545.map" model { file = "/net/cci-nas-00/data/ceres_data/8zxn_60545/06_2025/8zxn_60545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zxn_60545/06_2025/8zxn_60545.cif" } resolution = 3.06 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= 0.149 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 15 5.16 5 C 2414 2.51 5 N 587 2.21 5 O 637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3653 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3625 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 25, 'TRANS': 445} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.89, per 1000 atoms: 0.79 Number of scatterers: 3653 At special positions: 0 Unit cell: (88.976, 61.088, 70.384, 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 15 16.00 O 637 8.00 N 587 7.00 C 2414 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 - 3.00 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 90 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 430.3 milliseconds 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 856 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.636A pdb=" N LEU A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.760A pdb=" N SER A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 removed outlier: 3.696A pdb=" N ARG A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 132 removed outlier: 4.756A pdb=" N PHE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.530A pdb=" N ALA A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 164 through 193 Proline residue: A 186 - end of helix removed outlier: 3.567A pdb=" N SER A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.819A pdb=" N ARG A 198 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 220 removed outlier: 3.873A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 removed outlier: 4.206A pdb=" N PHE A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.739A pdb=" N ALA A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.540A pdb=" N PHE A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.695A pdb=" N GLN A 328 " --> pdb=" O MET A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 removed outlier: 3.505A pdb=" N ILE A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N SER A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 376 removed outlier: 3.593A pdb=" N LEU A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 removed outlier: 3.603A pdb=" N LEU A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 428 removed outlier: 3.711A pdb=" N LEU A 414 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 416 " --> pdb=" O PRO A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.825A pdb=" N ILE A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.600A pdb=" N ILE A 452 " --> pdb=" O PRO A 448 " (cutoff:3.500A) Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 481 through 499 Processing helix chain 'A' and resid 506 through 519 removed outlier: 3.846A pdb=" N GLN A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A 516 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ARG A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 756 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: 0.95 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 916 1.34 - 1.47: 1165 1.47 - 1.59: 1643 1.59 - 1.72: 0 1.72 - 1.85: 22 Bond restraints: 3746 Sorted by residual: bond pdb=" C ALA A 80 " pdb=" N PRO A 81 " ideal model delta sigma weight residual 1.334 1.367 -0.033 8.40e-03 1.42e+04 1.54e+01 bond pdb=" C ILE A 348 " pdb=" N PRO A 349 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.70e+00 bond pdb=" C LEU A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.25e-02 6.40e+03 6.82e+00 bond pdb=" CA SER A 193 " pdb=" CB SER A 193 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.73e-02 3.34e+03 5.95e+00 bond pdb=" C TRP A 231 " pdb=" N PRO A 232 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.28e-02 6.10e+03 5.48e+00 ... (remaining 3741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 3622 1.20 - 2.41: 1137 2.41 - 3.61: 287 3.61 - 4.81: 50 4.81 - 6.01: 9 Bond angle restraints: 5105 Sorted by residual: angle pdb=" CA ASP A 102 " pdb=" CB ASP A 102 " pdb=" CG ASP A 102 " ideal model delta sigma weight residual 112.60 117.85 -5.25 1.00e+00 1.00e+00 2.76e+01 angle pdb=" CA ASP A 177 " pdb=" CB ASP A 177 " pdb=" CG ASP A 177 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" N VAL A 213 " pdb=" CA VAL A 213 " pdb=" CB VAL A 213 " ideal model delta sigma weight residual 110.54 116.55 -6.01 1.36e+00 5.41e-01 1.95e+01 angle pdb=" CA PHE A 337 " pdb=" CB PHE A 337 " pdb=" CG PHE A 337 " ideal model delta sigma weight residual 113.80 118.15 -4.35 1.00e+00 1.00e+00 1.89e+01 angle pdb=" CA PHE A 441 " pdb=" CB PHE A 441 " pdb=" CG PHE A 441 " ideal model delta sigma weight residual 113.80 117.66 -3.86 1.00e+00 1.00e+00 1.49e+01 ... (remaining 5100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2077 17.88 - 35.75: 95 35.75 - 53.63: 21 53.63 - 71.50: 6 71.50 - 89.38: 5 Dihedral angle restraints: 2204 sinusoidal: 861 harmonic: 1343 Sorted by residual: dihedral pdb=" CA GLY A 379 " pdb=" C GLY A 379 " pdb=" N ARG A 380 " pdb=" CA ARG A 380 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLY A 432 " pdb=" C GLY A 432 " pdb=" N ILE A 433 " pdb=" CA ILE A 433 " ideal model delta harmonic sigma weight residual 180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLY A 136 " pdb=" C GLY A 136 " pdb=" N ARG A 137 " pdb=" CA ARG A 137 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 2201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 292 0.048 - 0.097: 196 0.097 - 0.145: 76 0.145 - 0.193: 38 0.193 - 0.242: 4 Chirality restraints: 606 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.19e+01 chirality pdb=" CA TRP A 231 " pdb=" N TRP A 231 " pdb=" C TRP A 231 " pdb=" CB TRP A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA PRO A 382 " pdb=" N PRO A 382 " pdb=" C PRO A 382 " pdb=" CB PRO A 382 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 603 not shown) Planarity restraints: 630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 137 " -0.338 9.50e-02 1.11e+02 1.52e-01 1.57e+01 pdb=" NE ARG A 137 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 137 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG A 137 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 137 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 336 " 0.046 2.00e-02 2.50e+03 2.36e-02 1.40e+01 pdb=" CG TRP A 336 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP A 336 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 336 " -0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP A 336 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 336 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 336 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 336 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 336 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 336 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 110 " -0.045 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP A 110 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 110 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 110 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP A 110 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 110 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 110 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 110 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 110 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 110 " -0.028 2.00e-02 2.50e+03 ... (remaining 627 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 1723 2.99 - 3.47: 3724 3.47 - 3.95: 5977 3.95 - 4.42: 6829 4.42 - 4.90: 11273 Nonbonded interactions: 29526 Sorted by model distance: nonbonded pdb=" OE1 GLU A 191 " pdb=" OG SER A 255 " model vdw 2.516 3.040 nonbonded pdb=" OE1 GLU A 440 " pdb=" OG1 THR A 502 " model vdw 2.591 3.040 nonbonded pdb=" OD1 ASP A 102 " pdb=" OG1 THR A 105 " model vdw 2.598 3.040 nonbonded pdb=" O ILE A 335 " pdb=" OG1 THR A 339 " model vdw 2.608 3.040 nonbonded pdb=" OE2 GLU A 223 " pdb=" OH TYR A 355 " model vdw 2.613 3.040 ... (remaining 29521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.470 Find NCS groups from input model: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 : 0.009 0.045 3748 Z= 0.562 Angle : 1.272 12.166 5111 Z= 0.856 Chirality : 0.076 0.242 606 Planarity : 0.010 0.152 629 Dihedral : 12.395 89.379 1348 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.77 % Allowed : 2.32 % Favored : 96.91 % 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: -3.05 (0.32), residues: 469 helix: -2.20 (0.21), residues: 365 sheet: None (None), residues: 0 loop : -0.34 (0.62), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.010 TRP A 336 HIS 0.007 0.003 HIS A 377 PHE 0.033 0.007 PHE A 337 TYR 0.039 0.008 TYR A 84 ARG 0.022 0.003 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00840 ( 1) link_NAG-ASN : angle 4.52920 ( 3) link_BETA1-4 : bond 0.03979 ( 1) link_BETA1-4 : angle 7.23965 ( 3) hydrogen bonds : bond 0.22368 ( 254) hydrogen bonds : angle 8.93944 ( 756) covalent geometry : bond 0.00849 ( 3746) covalent geometry : angle 1.25544 ( 5105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.434 Fit side-chains REVERT: A 91 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6502 (tt0) REVERT: A 155 MET cc_start: 0.8451 (mtm) cc_final: 0.8169 (mtm) REVERT: A 271 LYS cc_start: 0.5800 (tttt) cc_final: 0.5413 (tttm) REVERT: A 285 GLU cc_start: 0.6637 (mm-30) cc_final: 0.6141 (mm-30) REVERT: A 324 MET cc_start: 0.8583 (mmt) cc_final: 0.8333 (mmm) REVERT: A 327 TYR cc_start: 0.8366 (t80) cc_final: 0.8021 (t80) REVERT: A 444 GLN cc_start: 0.7872 (tt0) cc_final: 0.7441 (tp40) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.2098 time to fit residues: 13.6845 Evaluate side-chains 37 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 339 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 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 333 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.124188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.092882 restraints weight = 3820.632| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.04 r_work: 0.2783 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3748 Z= 0.141 Angle : 0.614 6.107 5111 Z= 0.316 Chirality : 0.043 0.148 606 Planarity : 0.005 0.035 629 Dihedral : 5.187 57.967 549 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.80 % Allowed : 4.12 % Favored : 94.07 % 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: 0.18 (0.38), residues: 469 helix: 0.35 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.29 (0.65), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 231 HIS 0.002 0.001 HIS A 139 PHE 0.010 0.001 PHE A 117 TYR 0.010 0.001 TYR A 312 ARG 0.003 0.000 ARG A 137 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 1) link_NAG-ASN : angle 3.70471 ( 3) link_BETA1-4 : bond 0.00267 ( 1) link_BETA1-4 : angle 1.73073 ( 3) hydrogen bonds : bond 0.04984 ( 254) hydrogen bonds : angle 4.63076 ( 756) covalent geometry : bond 0.00299 ( 3746) covalent geometry : angle 0.60596 ( 5105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.375 Fit side-chains REVERT: A 91 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6734 (tt0) REVERT: A 94 GLU cc_start: 0.6827 (tt0) cc_final: 0.6100 (tm-30) REVERT: A 155 MET cc_start: 0.8883 (mtm) cc_final: 0.8626 (mtm) REVERT: A 271 LYS cc_start: 0.6652 (tttt) cc_final: 0.5776 (tttm) REVERT: A 285 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6281 (mm-30) REVERT: A 444 GLN cc_start: 0.7660 (tt0) cc_final: 0.7300 (tp40) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.2010 time to fit residues: 11.2430 Evaluate side-chains 44 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 5 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.125725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.094753 restraints weight = 3796.521| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.99 r_work: 0.2824 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3748 Z= 0.118 Angle : 0.541 5.151 5111 Z= 0.275 Chirality : 0.041 0.141 606 Planarity : 0.004 0.034 629 Dihedral : 4.733 59.278 548 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.55 % Allowed : 5.41 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.40), residues: 469 helix: 1.41 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.57 (0.61), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 231 HIS 0.002 0.000 HIS A 139 PHE 0.010 0.001 PHE A 469 TYR 0.012 0.001 TYR A 327 ARG 0.001 0.000 ARG A 300 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 1) link_NAG-ASN : angle 3.19824 ( 3) link_BETA1-4 : bond 0.00445 ( 1) link_BETA1-4 : angle 1.34049 ( 3) hydrogen bonds : bond 0.03939 ( 254) hydrogen bonds : angle 4.10242 ( 756) covalent geometry : bond 0.00260 ( 3746) covalent geometry : angle 0.53469 ( 5105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.373 Fit side-chains REVERT: A 91 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6881 (tt0) REVERT: A 271 LYS cc_start: 0.6675 (tttt) cc_final: 0.5807 (tttm) REVERT: A 285 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6202 (mm-30) REVERT: A 444 GLN cc_start: 0.7432 (tt0) cc_final: 0.7170 (tp-100) outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 0.2389 time to fit residues: 13.7365 Evaluate side-chains 42 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.124505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.093917 restraints weight = 3835.330| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.99 r_work: 0.2793 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3748 Z= 0.122 Angle : 0.535 5.219 5111 Z= 0.271 Chirality : 0.041 0.142 606 Planarity : 0.005 0.033 629 Dihedral : 4.650 59.375 548 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 5.93 % Favored : 91.75 % 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: 1.89 (0.40), residues: 469 helix: 1.71 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.44 (0.63), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 231 HIS 0.004 0.001 HIS A 97 PHE 0.010 0.001 PHE A 469 TYR 0.009 0.001 TYR A 312 ARG 0.002 0.000 ARG A 381 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 1) link_NAG-ASN : angle 3.18120 ( 3) link_BETA1-4 : bond 0.00362 ( 1) link_BETA1-4 : angle 1.22326 ( 3) hydrogen bonds : bond 0.03858 ( 254) hydrogen bonds : angle 4.00989 ( 756) covalent geometry : bond 0.00284 ( 3746) covalent geometry : angle 0.52936 ( 5105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.407 Fit side-chains REVERT: A 91 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6814 (tt0) REVERT: A 174 MET cc_start: 0.8634 (tpt) cc_final: 0.8263 (tpt) REVERT: A 195 LYS cc_start: 0.7853 (tttt) cc_final: 0.7283 (pttt) REVERT: A 271 LYS cc_start: 0.6656 (tttt) cc_final: 0.5776 (tttm) REVERT: A 285 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6089 (mm-30) REVERT: A 444 GLN cc_start: 0.7397 (tt0) cc_final: 0.7178 (tp40) outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 0.1925 time to fit residues: 11.0835 Evaluate side-chains 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 515 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 333 ASN A 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.124253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.093909 restraints weight = 3850.515| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.97 r_work: 0.2814 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3748 Z= 0.128 Angle : 0.535 5.234 5111 Z= 0.269 Chirality : 0.041 0.145 606 Planarity : 0.004 0.032 629 Dihedral : 4.617 59.444 548 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.84 % Allowed : 5.67 % Favored : 91.49 % 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: 2.01 (0.40), residues: 469 helix: 1.80 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.41 (0.63), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 231 HIS 0.003 0.001 HIS A 97 PHE 0.010 0.001 PHE A 469 TYR 0.007 0.001 TYR A 84 ARG 0.002 0.000 ARG A 381 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 1) link_NAG-ASN : angle 3.10663 ( 3) link_BETA1-4 : bond 0.00349 ( 1) link_BETA1-4 : angle 1.14777 ( 3) hydrogen bonds : bond 0.03888 ( 254) hydrogen bonds : angle 3.98904 ( 756) covalent geometry : bond 0.00304 ( 3746) covalent geometry : angle 0.52892 ( 5105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.372 Fit side-chains REVERT: A 195 LYS cc_start: 0.7847 (tttt) cc_final: 0.7331 (pttt) REVERT: A 262 GLU cc_start: 0.7035 (mp0) cc_final: 0.6663 (mp0) REVERT: A 271 LYS cc_start: 0.6708 (tttt) cc_final: 0.5847 (tttm) REVERT: A 285 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6564 (mm-30) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.1866 time to fit residues: 10.9945 Evaluate side-chains 45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 515 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 42 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.117566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.091076 restraints weight = 4105.440| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.62 r_work: 0.2777 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3748 Z= 0.153 Angle : 0.561 5.406 5111 Z= 0.281 Chirality : 0.042 0.157 606 Planarity : 0.005 0.032 629 Dihedral : 4.659 59.104 548 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.58 % Allowed : 6.19 % Favored : 91.24 % 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: 1.94 (0.40), residues: 469 helix: 1.75 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.45 (0.64), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 231 HIS 0.003 0.001 HIS A 97 PHE 0.012 0.001 PHE A 117 TYR 0.008 0.001 TYR A 312 ARG 0.002 0.000 ARG A 381 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 1) link_NAG-ASN : angle 3.10616 ( 3) link_BETA1-4 : bond 0.00340 ( 1) link_BETA1-4 : angle 1.14368 ( 3) hydrogen bonds : bond 0.04224 ( 254) hydrogen bonds : angle 4.07658 ( 756) covalent geometry : bond 0.00385 ( 3746) covalent geometry : angle 0.55525 ( 5105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.413 Fit side-chains REVERT: A 94 GLU cc_start: 0.6525 (tt0) cc_final: 0.5876 (pt0) REVERT: A 174 MET cc_start: 0.8536 (tpt) cc_final: 0.7800 (tpt) REVERT: A 195 LYS cc_start: 0.7733 (tttt) cc_final: 0.7213 (pttt) REVERT: A 262 GLU cc_start: 0.6639 (mp0) cc_final: 0.6337 (mp0) REVERT: A 271 LYS cc_start: 0.6592 (tttt) cc_final: 0.5720 (tttm) REVERT: A 285 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6328 (mm-30) outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 0.2002 time to fit residues: 11.6113 Evaluate side-chains 47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 515 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.092293 restraints weight = 4044.809| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.62 r_work: 0.2803 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3748 Z= 0.132 Angle : 0.542 5.867 5111 Z= 0.270 Chirality : 0.041 0.150 606 Planarity : 0.004 0.031 629 Dihedral : 4.636 59.497 548 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.58 % Allowed : 6.70 % Favored : 90.72 % 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: 2.08 (0.41), residues: 469 helix: 1.86 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.42 (0.66), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 231 HIS 0.003 0.001 HIS A 97 PHE 0.010 0.001 PHE A 469 TYR 0.007 0.001 TYR A 84 ARG 0.002 0.000 ARG A 381 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 1) link_NAG-ASN : angle 3.08250 ( 3) link_BETA1-4 : bond 0.00339 ( 1) link_BETA1-4 : angle 1.11075 ( 3) hydrogen bonds : bond 0.03931 ( 254) hydrogen bonds : angle 4.00087 ( 756) covalent geometry : bond 0.00318 ( 3746) covalent geometry : angle 0.53649 ( 5105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.367 Fit side-chains REVERT: A 94 GLU cc_start: 0.6449 (tt0) cc_final: 0.5793 (pt0) REVERT: A 174 MET cc_start: 0.8527 (tpt) cc_final: 0.8067 (tpt) REVERT: A 195 LYS cc_start: 0.7834 (tttt) cc_final: 0.7279 (pttt) REVERT: A 271 LYS cc_start: 0.6555 (tttt) cc_final: 0.5681 (tttm) REVERT: A 285 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6391 (mm-30) outliers start: 10 outliers final: 9 residues processed: 46 average time/residue: 0.1798 time to fit residues: 10.1802 Evaluate side-chains 46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 515 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.0060 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.119496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.092749 restraints weight = 4048.269| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.65 r_work: 0.2798 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3748 Z= 0.123 Angle : 0.537 6.509 5111 Z= 0.267 Chirality : 0.041 0.145 606 Planarity : 0.004 0.031 629 Dihedral : 4.583 58.991 548 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.32 % Allowed : 7.22 % Favored : 90.46 % 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: 2.19 (0.41), residues: 469 helix: 1.92 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.35 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 231 HIS 0.003 0.001 HIS A 97 PHE 0.010 0.001 PHE A 469 TYR 0.009 0.001 TYR A 312 ARG 0.002 0.000 ARG A 381 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 1) link_NAG-ASN : angle 3.03059 ( 3) link_BETA1-4 : bond 0.00350 ( 1) link_BETA1-4 : angle 1.08955 ( 3) hydrogen bonds : bond 0.03759 ( 254) hydrogen bonds : angle 3.94954 ( 756) covalent geometry : bond 0.00291 ( 3746) covalent geometry : angle 0.53164 ( 5105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.397 Fit side-chains REVERT: A 174 MET cc_start: 0.8438 (tpt) cc_final: 0.7993 (tpt) REVERT: A 195 LYS cc_start: 0.7707 (tttt) cc_final: 0.7180 (pttt) REVERT: A 271 LYS cc_start: 0.6390 (tttt) cc_final: 0.5519 (tttm) outliers start: 9 outliers final: 8 residues processed: 46 average time/residue: 0.1929 time to fit residues: 10.8988 Evaluate side-chains 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 515 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.093135 restraints weight = 4002.185| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.63 r_work: 0.2829 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3748 Z= 0.124 Angle : 0.538 7.000 5111 Z= 0.267 Chirality : 0.041 0.147 606 Planarity : 0.004 0.031 629 Dihedral : 4.560 59.046 548 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.06 % Allowed : 7.73 % Favored : 90.21 % 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: 2.25 (0.41), residues: 469 helix: 1.96 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.28 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 231 HIS 0.003 0.001 HIS A 97 PHE 0.010 0.001 PHE A 469 TYR 0.006 0.001 TYR A 84 ARG 0.002 0.000 ARG A 381 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 1) link_NAG-ASN : angle 2.98207 ( 3) link_BETA1-4 : bond 0.00344 ( 1) link_BETA1-4 : angle 1.05878 ( 3) hydrogen bonds : bond 0.03727 ( 254) hydrogen bonds : angle 3.92531 ( 756) covalent geometry : bond 0.00296 ( 3746) covalent geometry : angle 0.53269 ( 5105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.379 Fit side-chains REVERT: A 94 GLU cc_start: 0.6430 (tt0) cc_final: 0.5243 (mt-10) REVERT: A 174 MET cc_start: 0.8552 (tpt) cc_final: 0.8075 (tpt) REVERT: A 195 LYS cc_start: 0.7758 (tttt) cc_final: 0.7361 (ptpt) REVERT: A 271 LYS cc_start: 0.6614 (tttt) cc_final: 0.5734 (tttm) REVERT: A 273 PHE cc_start: 0.7331 (m-80) cc_final: 0.6827 (m-80) outliers start: 8 outliers final: 8 residues processed: 44 average time/residue: 0.2006 time to fit residues: 10.8174 Evaluate side-chains 44 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 515 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 8 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.093472 restraints weight = 4017.440| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.65 r_work: 0.2815 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3748 Z= 0.119 Angle : 0.531 6.966 5111 Z= 0.263 Chirality : 0.040 0.144 606 Planarity : 0.004 0.031 629 Dihedral : 4.513 58.615 548 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 7.47 % Favored : 90.21 % 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: 2.34 (0.41), residues: 469 helix: 2.03 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.28 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 231 HIS 0.003 0.001 HIS A 97 PHE 0.010 0.001 PHE A 469 TYR 0.010 0.001 TYR A 312 ARG 0.002 0.000 ARG A 381 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 1) link_NAG-ASN : angle 2.93333 ( 3) link_BETA1-4 : bond 0.00346 ( 1) link_BETA1-4 : angle 1.03649 ( 3) hydrogen bonds : bond 0.03619 ( 254) hydrogen bonds : angle 3.89132 ( 756) covalent geometry : bond 0.00280 ( 3746) covalent geometry : angle 0.52548 ( 5105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 938 Ramachandran restraints generated. 469 Oldfield, 0 Emsley, 469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.404 Fit side-chains REVERT: A 78 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8174 (m) REVERT: A 94 GLU cc_start: 0.6447 (tt0) cc_final: 0.5269 (mt-10) REVERT: A 174 MET cc_start: 0.8505 (tpt) cc_final: 0.8044 (tpt) REVERT: A 195 LYS cc_start: 0.7667 (tttt) cc_final: 0.7293 (ptpt) REVERT: A 271 LYS cc_start: 0.6518 (tttt) cc_final: 0.5638 (tttm) REVERT: A 273 PHE cc_start: 0.7198 (m-80) cc_final: 0.6663 (m-80) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 0.1770 time to fit residues: 9.5492 Evaluate side-chains 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 515 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.119410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.092837 restraints weight = 4026.143| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.63 r_work: 0.2807 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3748 Z= 0.130 Angle : 0.544 6.952 5111 Z= 0.269 Chirality : 0.041 0.149 606 Planarity : 0.004 0.031 629 Dihedral : 4.560 59.580 548 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.06 % Allowed : 7.73 % Favored : 90.21 % 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: 2.27 (0.41), residues: 469 helix: 1.97 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.27 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 231 HIS 0.003 0.001 HIS A 97 PHE 0.010 0.001 PHE A 469 TYR 0.007 0.001 TYR A 84 ARG 0.002 0.000 ARG A 381 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 1) link_NAG-ASN : angle 2.97059 ( 3) link_BETA1-4 : bond 0.00340 ( 1) link_BETA1-4 : angle 1.04375 ( 3) hydrogen bonds : bond 0.03800 ( 254) hydrogen bonds : angle 3.93168 ( 756) covalent geometry : bond 0.00315 ( 3746) covalent geometry : angle 0.53846 ( 5105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2316.33 seconds wall clock time: 40 minutes 13.00 seconds (2413.00 seconds total)