Starting phenix.real_space_refine on Wed Jun 4 17:52:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zxm_60544/06_2025/8zxm_60544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zxm_60544/06_2025/8zxm_60544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zxm_60544/06_2025/8zxm_60544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zxm_60544/06_2025/8zxm_60544.map" model { file = "/net/cci-nas-00/data/ceres_data/8zxm_60544/06_2025/8zxm_60544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zxm_60544/06_2025/8zxm_60544.cif" } resolution = 3.39 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= 0.099 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 2419 2.51 5 N 591 2.21 5 O 640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 3665 Number of models: 1 Model: "" Number of chains: 3 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 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.78, per 1000 atoms: 0.76 Number of scatterers: 3665 At special positions: 0 Unit cell: (90.304, 59.76, 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 640 8.00 N 591 7.00 C 2419 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: 1.02 Conformation dependent library (CDL) restraints added in 505.2 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: 31 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.603A pdb=" N ASN A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 removed outlier: 3.932A pdb=" N ALA A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 132 removed outlier: 4.973A pdb=" N PHE A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.640A pdb=" N THR A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.750A pdb=" N LEU A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 164 through 193 removed outlier: 3.810A pdb=" N LEU A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Proline residue: A 186 - end of helix Processing helix chain 'A' and resid 200 through 219 removed outlier: 3.772A pdb=" N VAL A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 removed outlier: 4.147A pdb=" N PHE A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.952A 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 308 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.545A pdb=" N VAL A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS A 326 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 328 " --> pdb=" O MET A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.640A pdb=" N GLY A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 370 removed outlier: 3.560A pdb=" N LEU A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.732A pdb=" N GLU A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N HIS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 404 removed outlier: 3.895A pdb=" N PHE A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 428 removed outlier: 3.526A pdb=" N SER A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 416 " --> pdb=" O PRO A 412 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 removed outlier: 4.150A pdb=" N GLY A 432 " --> pdb=" O GLY A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 433 through 441 removed outlier: 4.051A pdb=" N GLY A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 467 removed outlier: 4.107A pdb=" N ILE A 452 " --> pdb=" O PRO A 448 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 477 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: 3.512A pdb=" N GLN A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 516 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 708 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: 1.04 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 673 1.33 - 1.46: 1140 1.46 - 1.58: 1924 1.58 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 3759 Sorted by residual: bond pdb=" C LEU A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.329 1.366 -0.037 1.25e-02 6.40e+03 8.68e+00 bond pdb=" C ARG A 381 " pdb=" N PRO A 382 " ideal model delta sigma weight residual 1.335 1.361 -0.026 9.40e-03 1.13e+04 7.54e+00 bond pdb=" C ILE A 348 " pdb=" N PRO A 349 " ideal model delta sigma weight residual 1.329 1.359 -0.030 1.18e-02 7.18e+03 6.28e+00 bond pdb=" C TRP A 231 " pdb=" N PRO A 232 " ideal model delta sigma weight residual 1.335 1.366 -0.032 1.28e-02 6.10e+03 6.12e+00 bond pdb=" C TYR A 71 " pdb=" O TYR A 71 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.19e-02 7.06e+03 5.60e+00 ... (remaining 3754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 3998 1.48 - 2.96: 940 2.96 - 4.44: 162 4.44 - 5.92: 22 5.92 - 7.40: 2 Bond angle restraints: 5124 Sorted by residual: angle pdb=" CA PHE A 88 " pdb=" CB PHE A 88 " pdb=" CG PHE A 88 " ideal model delta sigma weight residual 113.80 118.53 -4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" CA PHE A 337 " pdb=" CB PHE A 337 " pdb=" CG PHE A 337 " ideal model delta sigma weight residual 113.80 118.24 -4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" N GLU A 306 " pdb=" CA GLU A 306 " pdb=" CB GLU A 306 " ideal model delta sigma weight residual 110.26 104.30 5.96 1.49e+00 4.50e-01 1.60e+01 angle pdb=" CA PHE A 117 " pdb=" CB PHE A 117 " pdb=" CG PHE A 117 " ideal model delta sigma weight residual 113.80 117.72 -3.92 1.00e+00 1.00e+00 1.54e+01 angle pdb=" C GLN A 446 " pdb=" N ARG A 447 " pdb=" CA ARG A 447 " ideal model delta sigma weight residual 120.09 124.62 -4.53 1.25e+00 6.40e-01 1.32e+01 ... (remaining 5119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2034 17.85 - 35.69: 131 35.69 - 53.53: 27 53.53 - 71.37: 8 71.37 - 89.21: 4 Dihedral angle restraints: 2204 sinusoidal: 861 harmonic: 1343 Sorted by residual: dihedral pdb=" CA ASN A 145 " pdb=" C ASN A 145 " pdb=" N GLY A 146 " pdb=" CA GLY A 146 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA LEU A 373 " pdb=" C LEU A 373 " pdb=" N VAL A 374 " pdb=" CA VAL A 374 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL A 313 " pdb=" C VAL A 313 " pdb=" N ARG A 314 " pdb=" CA ARG A 314 " ideal model delta harmonic sigma weight residual -180.00 -161.47 -18.53 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 282 0.049 - 0.098: 175 0.098 - 0.147: 110 0.147 - 0.196: 31 0.196 - 0.245: 8 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 -2.33 -0.07 2.00e-02 2.50e+03 1.31e+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 1.50e+00 chirality pdb=" CA PHE A 394 " pdb=" N PHE A 394 " pdb=" C PHE A 394 " pdb=" CB PHE A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 603 not shown) Planarity restraints: 631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.077 2.00e-02 2.50e+03 6.44e-02 5.18e+01 pdb=" C7 NAG B 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.056 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.106 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 494 " -0.044 2.00e-02 2.50e+03 2.34e-02 1.09e+01 pdb=" CG TYR A 494 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 494 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 494 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 494 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 494 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 494 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 494 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 507 " 0.038 2.00e-02 2.50e+03 2.12e-02 8.97e+00 pdb=" CG TYR A 507 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 507 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 507 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 507 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 507 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 507 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 507 " 0.019 2.00e-02 2.50e+03 ... (remaining 628 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1914 3.01 - 3.48: 3719 3.48 - 3.96: 5919 3.96 - 4.43: 6733 4.43 - 4.90: 10892 Nonbonded interactions: 29177 Sorted by model distance: nonbonded pdb=" OD2 ASP A 102 " pdb=" OG1 THR A 105 " model vdw 2.540 3.040 nonbonded pdb=" OG1 THR A 506 " pdb=" OE1 GLU A 509 " model vdw 2.575 3.040 nonbonded pdb=" N PRO A 194 " pdb=" O PRO A 194 " model vdw 2.610 2.496 nonbonded pdb=" C SER A 255 " pdb=" OG SER A 255 " model vdw 2.620 2.616 nonbonded pdb=" O ILE A 335 " pdb=" OG1 THR A 339 " model vdw 2.623 3.040 ... (remaining 29172 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 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 0.048 3761 Z= 0.585 Angle : 1.316 8.806 5130 Z= 0.876 Chirality : 0.083 0.245 606 Planarity : 0.009 0.071 630 Dihedral : 13.578 89.214 1348 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: -3.84 (0.32), residues: 469 helix: -2.68 (0.21), residues: 355 sheet: None (None), residues: 0 loop : -1.14 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.008 TRP A 110 HIS 0.012 0.004 HIS A 139 PHE 0.039 0.008 PHE A 463 TYR 0.044 0.009 TYR A 494 ARG 0.017 0.003 ARG A 96 Details of bonding type rmsd link_NAG-ASN : bond 0.01894 ( 1) link_NAG-ASN : angle 3.59071 ( 3) link_BETA1-4 : bond 0.04780 ( 1) link_BETA1-4 : angle 5.38277 ( 3) hydrogen bonds : bond 0.23139 ( 237) hydrogen bonds : angle 9.75867 ( 708) covalent geometry : bond 0.00894 ( 3759) covalent geometry : angle 1.30724 ( 5124) *********************** 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 55 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.402 Fit side-chains REVERT: A 99 ARG cc_start: 0.4769 (pmt170) cc_final: 0.4153 (ptt180) REVERT: A 174 MET cc_start: 0.8207 (tpp) cc_final: 0.7687 (tpp) REVERT: A 444 GLN cc_start: 0.6815 (mm110) cc_final: 0.6575 (tp-100) outliers start: 7 outliers final: 3 residues processed: 53 average time/residue: 0.2333 time to fit residues: 14.7391 Evaluate side-chains 36 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 213 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 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 = 0.3863 r_free = 0.3863 target = 0.159122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118364 restraints weight = 3857.116| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.28 r_work: 0.3248 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3761 Z= 0.151 Angle : 0.648 6.429 5130 Z= 0.338 Chirality : 0.045 0.155 606 Planarity : 0.005 0.031 630 Dihedral : 5.705 59.998 554 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 5.67 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.38), residues: 469 helix: -0.76 (0.26), residues: 368 sheet: None (None), residues: 0 loop : -0.46 (0.68), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 231 HIS 0.001 0.000 HIS A 97 PHE 0.014 0.002 PHE A 337 TYR 0.013 0.002 TYR A 355 ARG 0.008 0.001 ARG A 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 1) link_NAG-ASN : angle 2.76954 ( 3) link_BETA1-4 : bond 0.00419 ( 1) link_BETA1-4 : angle 1.77459 ( 3) hydrogen bonds : bond 0.05472 ( 237) hydrogen bonds : angle 5.05475 ( 708) covalent geometry : bond 0.00328 ( 3759) covalent geometry : angle 0.64371 ( 5124) *********************** 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 44 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.384 Fit side-chains REVERT: A 195 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6381 (tttp) REVERT: A 263 LYS cc_start: 0.5595 (mmtt) cc_final: 0.5287 (mmtt) REVERT: A 391 MET cc_start: 0.6990 (mtt) cc_final: 0.6722 (mtt) outliers start: 9 outliers final: 5 residues processed: 42 average time/residue: 0.1915 time to fit residues: 9.9263 Evaluate side-chains 36 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 501 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 377 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103180 restraints weight = 3748.791| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.21 r_work: 0.3015 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3761 Z= 0.129 Angle : 0.575 5.565 5130 Z= 0.293 Chirality : 0.043 0.146 606 Planarity : 0.005 0.030 630 Dihedral : 5.063 57.588 553 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.80 % Allowed : 8.51 % Favored : 89.69 % 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: -0.21 (0.40), residues: 469 helix: 0.06 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.35 (0.70), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 231 HIS 0.001 0.000 HIS A 97 PHE 0.011 0.001 PHE A 441 TYR 0.008 0.001 TYR A 355 ARG 0.004 0.000 ARG A 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 1) link_NAG-ASN : angle 2.15761 ( 3) link_BETA1-4 : bond 0.00406 ( 1) link_BETA1-4 : angle 1.43324 ( 3) hydrogen bonds : bond 0.04196 ( 237) hydrogen bonds : angle 4.28482 ( 708) covalent geometry : bond 0.00298 ( 3759) covalent geometry : angle 0.57188 ( 5124) *********************** 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 38 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.386 Fit side-chains REVERT: A 306 GLU cc_start: 0.7954 (tp30) cc_final: 0.6532 (mt-10) REVERT: A 440 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6420 (tt0) outliers start: 7 outliers final: 6 residues processed: 37 average time/residue: 0.1137 time to fit residues: 5.8767 Evaluate side-chains 33 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 501 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.103073 restraints weight = 3830.982| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.27 r_work: 0.3016 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3761 Z= 0.122 Angle : 0.536 5.382 5130 Z= 0.271 Chirality : 0.042 0.144 606 Planarity : 0.005 0.033 630 Dihedral : 3.957 15.327 547 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.84 % Allowed : 7.99 % Favored : 89.18 % 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: 0.25 (0.41), residues: 469 helix: 0.45 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.46 (0.71), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.011 0.001 PHE A 469 TYR 0.008 0.001 TYR A 327 ARG 0.003 0.000 ARG A 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 1) link_NAG-ASN : angle 1.98632 ( 3) link_BETA1-4 : bond 0.00332 ( 1) link_BETA1-4 : angle 1.20048 ( 3) hydrogen bonds : bond 0.03793 ( 237) hydrogen bonds : angle 4.01379 ( 708) covalent geometry : bond 0.00285 ( 3759) covalent geometry : angle 0.53321 ( 5124) *********************** 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 45 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.5734 (pmt170) cc_final: 0.4996 (ptt180) outliers start: 11 outliers final: 5 residues processed: 44 average time/residue: 0.1847 time to fit residues: 10.1208 Evaluate side-chains 37 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 384 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 14 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 45 optimal weight: 0.0020 chunk 39 optimal weight: 0.0040 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.168854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130100 restraints weight = 3939.017| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.15 r_work: 0.3432 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3761 Z= 0.105 Angle : 0.511 5.136 5130 Z= 0.257 Chirality : 0.041 0.142 606 Planarity : 0.004 0.033 630 Dihedral : 3.775 14.217 547 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.06 % Allowed : 10.31 % Favored : 87.63 % 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: 0.62 (0.41), residues: 469 helix: 0.74 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -0.44 (0.70), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.009 0.001 PHE A 441 TYR 0.007 0.001 TYR A 73 ARG 0.003 0.000 ARG A 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00044 ( 1) link_NAG-ASN : angle 1.93946 ( 3) link_BETA1-4 : bond 0.00364 ( 1) link_BETA1-4 : angle 1.14387 ( 3) hydrogen bonds : bond 0.03346 ( 237) hydrogen bonds : angle 3.83838 ( 708) covalent geometry : bond 0.00232 ( 3759) covalent geometry : angle 0.50805 ( 5124) *********************** 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 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.357 Fit side-chains REVERT: A 99 ARG cc_start: 0.6327 (pmt170) cc_final: 0.5523 (ptt180) REVERT: A 128 VAL cc_start: 0.6617 (OUTLIER) cc_final: 0.6190 (p) REVERT: A 440 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6534 (tt0) outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 0.1833 time to fit residues: 9.7528 Evaluate side-chains 39 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 384 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 20 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.167919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129506 restraints weight = 3946.494| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.12 r_work: 0.3414 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3761 Z= 0.115 Angle : 0.518 5.180 5130 Z= 0.262 Chirality : 0.041 0.143 606 Planarity : 0.004 0.034 630 Dihedral : 3.689 13.853 547 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.80 % Allowed : 11.34 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.41), residues: 469 helix: 0.89 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -0.52 (0.69), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 139 PHE 0.009 0.001 PHE A 469 TYR 0.009 0.001 TYR A 507 ARG 0.002 0.000 ARG A 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 1) link_NAG-ASN : angle 1.88383 ( 3) link_BETA1-4 : bond 0.00361 ( 1) link_BETA1-4 : angle 1.11458 ( 3) hydrogen bonds : bond 0.03462 ( 237) hydrogen bonds : angle 3.79682 ( 708) covalent geometry : bond 0.00267 ( 3759) covalent geometry : angle 0.51591 ( 5124) *********************** 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 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.384 Fit side-chains REVERT: A 99 ARG cc_start: 0.6377 (pmt170) cc_final: 0.5516 (ptt180) REVERT: A 128 VAL cc_start: 0.6538 (OUTLIER) cc_final: 0.6154 (p) REVERT: A 306 GLU cc_start: 0.7877 (tp30) cc_final: 0.6654 (mt-10) REVERT: A 509 GLU cc_start: 0.7329 (mp0) cc_final: 0.7032 (mp0) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.2142 time to fit residues: 11.1637 Evaluate side-chains 42 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128552 restraints weight = 3934.725| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.21 r_work: 0.3389 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3761 Z= 0.126 Angle : 0.532 5.240 5130 Z= 0.267 Chirality : 0.042 0.143 606 Planarity : 0.004 0.034 630 Dihedral : 3.692 13.864 547 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.58 % Allowed : 10.82 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.41), residues: 469 helix: 0.97 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -0.55 (0.69), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 97 PHE 0.011 0.001 PHE A 469 TYR 0.008 0.001 TYR A 327 ARG 0.002 0.000 ARG A 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 1) link_NAG-ASN : angle 1.87357 ( 3) link_BETA1-4 : bond 0.00304 ( 1) link_BETA1-4 : angle 1.05534 ( 3) hydrogen bonds : bond 0.03597 ( 237) hydrogen bonds : angle 3.79830 ( 708) covalent geometry : bond 0.00305 ( 3759) covalent geometry : angle 0.52961 ( 5124) *********************** 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 46 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.401 Fit side-chains REVERT: A 99 ARG cc_start: 0.6211 (pmt170) cc_final: 0.5409 (ptt180) REVERT: A 128 VAL cc_start: 0.6749 (OUTLIER) cc_final: 0.6491 (p) REVERT: A 284 GLN cc_start: 0.6252 (mp-120) cc_final: 0.5937 (mp10) REVERT: A 509 GLU cc_start: 0.7402 (mp0) cc_final: 0.7128 (mp0) outliers start: 10 outliers final: 8 residues processed: 45 average time/residue: 0.2033 time to fit residues: 11.1606 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 : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 chunk 28 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.169435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129917 restraints weight = 3893.032| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.17 r_work: 0.3409 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3761 Z= 0.112 Angle : 0.510 5.215 5130 Z= 0.256 Chirality : 0.041 0.142 606 Planarity : 0.004 0.034 630 Dihedral : 3.614 13.850 547 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.32 % Allowed : 11.60 % Favored : 86.08 % 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: 1.04 (0.41), residues: 469 helix: 1.07 (0.29), residues: 367 sheet: None (None), residues: 0 loop : -0.45 (0.69), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.001 0.000 HIS A 97 PHE 0.009 0.001 PHE A 469 TYR 0.007 0.001 TYR A 73 ARG 0.002 0.000 ARG A 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 1) link_NAG-ASN : angle 1.82255 ( 3) link_BETA1-4 : bond 0.00326 ( 1) link_BETA1-4 : angle 1.00994 ( 3) hydrogen bonds : bond 0.03375 ( 237) hydrogen bonds : angle 3.71603 ( 708) covalent geometry : bond 0.00266 ( 3759) covalent geometry : angle 0.50770 ( 5124) *********************** 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 42 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.371 Fit side-chains REVERT: A 99 ARG cc_start: 0.6254 (pmt170) cc_final: 0.5415 (ptt180) REVERT: A 128 VAL cc_start: 0.6586 (OUTLIER) cc_final: 0.6362 (p) REVERT: A 257 ARG cc_start: 0.6362 (tmt170) cc_final: 0.6145 (tmt170) REVERT: A 284 GLN cc_start: 0.6217 (mp-120) cc_final: 0.5913 (mp10) REVERT: A 509 GLU cc_start: 0.7371 (mp0) cc_final: 0.7102 (mp0) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 0.2116 time to fit residues: 10.7500 Evaluate side-chains 40 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 384 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 38 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 0.0070 chunk 39 optimal weight: 0.0270 chunk 12 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.2856 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.172343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.134582 restraints weight = 3888.004| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.31 r_work: 0.3460 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3761 Z= 0.101 Angle : 0.499 5.156 5130 Z= 0.250 Chirality : 0.040 0.141 606 Planarity : 0.004 0.033 630 Dihedral : 3.474 13.497 547 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.80 % Allowed : 12.37 % Favored : 85.82 % 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: 1.28 (0.42), residues: 469 helix: 1.22 (0.29), residues: 369 sheet: None (None), residues: 0 loop : -0.33 (0.70), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.001 0.000 HIS A 97 PHE 0.008 0.001 PHE A 208 TYR 0.006 0.001 TYR A 73 ARG 0.002 0.000 ARG A 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 1) link_NAG-ASN : angle 1.87068 ( 3) link_BETA1-4 : bond 0.00337 ( 1) link_BETA1-4 : angle 1.02238 ( 3) hydrogen bonds : bond 0.03030 ( 237) hydrogen bonds : angle 3.61714 ( 708) covalent geometry : bond 0.00220 ( 3759) covalent geometry : angle 0.49642 ( 5124) *********************** 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 42 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.392 Fit side-chains REVERT: A 99 ARG cc_start: 0.6221 (pmt170) cc_final: 0.5368 (ptt180) REVERT: A 128 VAL cc_start: 0.6405 (OUTLIER) cc_final: 0.6198 (p) REVERT: A 160 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7644 (mt0) REVERT: A 284 GLN cc_start: 0.6393 (mp-120) cc_final: 0.6112 (mp10) REVERT: A 300 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.6259 (ttt-90) REVERT: A 384 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6567 (tp) REVERT: A 440 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6479 (tt0) REVERT: A 509 GLU cc_start: 0.7357 (mp0) cc_final: 0.7028 (mp0) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.1853 time to fit residues: 9.4573 Evaluate side-chains 41 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 384 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.0050 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.0670 overall best weight: 0.3732 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.146147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107155 restraints weight = 3789.143| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.20 r_work: 0.3086 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3761 Z= 0.102 Angle : 0.494 5.168 5130 Z= 0.248 Chirality : 0.040 0.139 606 Planarity : 0.004 0.033 630 Dihedral : 3.433 13.106 547 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.32 % Allowed : 12.37 % Favored : 85.31 % 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: 1.40 (0.42), residues: 469 helix: 1.34 (0.29), residues: 368 sheet: None (None), residues: 0 loop : -0.38 (0.69), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 231 HIS 0.001 0.000 HIS A 97 PHE 0.008 0.001 PHE A 469 TYR 0.006 0.001 TYR A 73 ARG 0.002 0.000 ARG A 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 1) link_NAG-ASN : angle 1.91879 ( 3) link_BETA1-4 : bond 0.00339 ( 1) link_BETA1-4 : angle 1.03399 ( 3) hydrogen bonds : bond 0.03009 ( 237) hydrogen bonds : angle 3.59388 ( 708) covalent geometry : bond 0.00230 ( 3759) covalent geometry : angle 0.49167 ( 5124) ********************** 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 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 99 ARG cc_start: 0.5824 (pmt170) cc_final: 0.4922 (ptt180) REVERT: A 160 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7403 (mt0) REVERT: A 284 GLN cc_start: 0.6121 (mp-120) cc_final: 0.5847 (mp10) REVERT: A 300 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.5849 (ttt-90) REVERT: A 370 PHE cc_start: 0.7136 (m-80) cc_final: 0.6834 (m-10) REVERT: A 384 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.6016 (tp) REVERT: A 509 GLU cc_start: 0.7031 (mp0) cc_final: 0.6602 (mp0) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.1966 time to fit residues: 10.2779 Evaluate side-chains 43 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 0.0470 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.145980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.105989 restraints weight = 3809.557| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.31 r_work: 0.3151 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3761 Z= 0.108 Angle : 0.504 5.204 5130 Z= 0.253 Chirality : 0.041 0.139 606 Planarity : 0.004 0.033 630 Dihedral : 3.435 13.230 547 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.32 % Allowed : 12.37 % Favored : 85.31 % 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: 1.38 (0.41), residues: 469 helix: 1.31 (0.29), residues: 368 sheet: None (None), residues: 0 loop : -0.35 (0.69), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 231 HIS 0.001 0.000 HIS A 97 PHE 0.009 0.001 PHE A 469 TYR 0.007 0.001 TYR A 73 ARG 0.002 0.000 ARG A 505 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 1) link_NAG-ASN : angle 1.92157 ( 3) link_BETA1-4 : bond 0.00328 ( 1) link_BETA1-4 : angle 1.00322 ( 3) hydrogen bonds : bond 0.03146 ( 237) hydrogen bonds : angle 3.61309 ( 708) covalent geometry : bond 0.00253 ( 3759) covalent geometry : angle 0.50189 ( 5124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1971.86 seconds wall clock time: 34 minutes 38.08 seconds (2078.08 seconds total)