Starting phenix.real_space_refine on Sun Apr 27 03:49:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wtu_37842/04_2025/8wtu_37842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wtu_37842/04_2025/8wtu_37842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wtu_37842/04_2025/8wtu_37842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wtu_37842/04_2025/8wtu_37842.map" model { file = "/net/cci-nas-00/data/ceres_data/8wtu_37842/04_2025/8wtu_37842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wtu_37842/04_2025/8wtu_37842.cif" } resolution = 2.7 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= 0.069 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 20 5.16 5 C 2918 2.51 5 N 673 2.21 5 O 737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4348 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4334 Classifications: {'peptide': 542} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 522} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.61, per 1000 atoms: 0.83 Number of scatterers: 4348 At special positions: 0 Unit cell: (75.65, 67.15, 91.8, 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 20 16.00 O 737 8.00 N 673 7.00 C 2918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 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 NAG-ASN " NAG A 701 " - " ASN A 184 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 528.9 milliseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 998 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 76.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.827A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 121 Proline residue: A 108 - end of helix removed outlier: 3.582A pdb=" N GLY A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 165 removed outlier: 3.889A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.512A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.544A pdb=" N CYS A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.607A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.896A pdb=" N ALA A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 319 removed outlier: 4.161A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.805A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 4.633A pdb=" N ALA A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.624A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 441 through 458 removed outlier: 3.659A pdb=" N PHE A 445 " --> pdb=" O HIS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.916A pdb=" N THR A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 464 through 476 removed outlier: 4.045A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 removed outlier: 3.634A pdb=" N LEU A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 removed outlier: 3.599A pdb=" N ILE A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 removed outlier: 3.527A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.630A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.572A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.623A pdb=" N GLY A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 removed outlier: 3.810A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 removed outlier: 3.575A pdb=" N PHE A 609 " --> pdb=" O ILE A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.923A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 250 hydrogen bonds defined for protein. 723 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: 1.15 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1264 1.34 - 1.46: 1123 1.46 - 1.58: 2071 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4489 Sorted by residual: bond pdb=" C PHE A 82 " pdb=" N PRO A 83 " ideal model delta sigma weight residual 1.334 1.360 -0.026 1.51e-02 4.39e+03 2.93e+00 bond pdb=" CB PRO A 285 " pdb=" CG PRO A 285 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.72e+00 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C3 NAG A 701 " pdb=" O3 NAG A 701 " ideal model delta sigma weight residual 1.403 1.424 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CA MET A 107 " pdb=" C MET A 107 " ideal model delta sigma weight residual 1.521 1.532 -0.011 1.14e-02 7.69e+03 8.98e-01 ... (remaining 4484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 6011 2.00 - 3.99: 99 3.99 - 5.99: 15 5.99 - 7.99: 0 7.99 - 9.98: 1 Bond angle restraints: 6126 Sorted by residual: angle pdb=" N VAL A 262 " pdb=" CA VAL A 262 " pdb=" C VAL A 262 " ideal model delta sigma weight residual 106.21 111.73 -5.52 1.07e+00 8.73e-01 2.66e+01 angle pdb=" N VAL A 69 " pdb=" CA VAL A 69 " pdb=" C VAL A 69 " ideal model delta sigma weight residual 113.47 108.74 4.73 1.01e+00 9.80e-01 2.20e+01 angle pdb=" N ILE A 537 " pdb=" CA ILE A 537 " pdb=" C ILE A 537 " ideal model delta sigma weight residual 111.81 108.41 3.40 8.60e-01 1.35e+00 1.56e+01 angle pdb=" C GLY A 106 " pdb=" N MET A 107 " pdb=" CA MET A 107 " ideal model delta sigma weight residual 119.78 115.17 4.61 1.24e+00 6.50e-01 1.38e+01 angle pdb=" N ILE A 592 " pdb=" CA ILE A 592 " pdb=" C ILE A 592 " ideal model delta sigma weight residual 113.10 109.51 3.59 9.70e-01 1.06e+00 1.37e+01 ... (remaining 6121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 2365 21.46 - 42.92: 127 42.92 - 64.38: 11 64.38 - 85.84: 11 85.84 - 107.30: 8 Dihedral angle restraints: 2522 sinusoidal: 954 harmonic: 1568 Sorted by residual: dihedral pdb=" CB CYS A 176 " pdb=" SG CYS A 176 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual 93.00 134.08 -41.08 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA LEU A 252 " pdb=" C LEU A 252 " pdb=" N TRP A 253 " pdb=" CA TRP A 253 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" C5 NAG A 701 " ideal model delta sinusoidal sigma weight residual 53.78 -53.52 107.30 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 2519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 414 0.032 - 0.065: 206 0.065 - 0.097: 47 0.097 - 0.129: 18 0.129 - 0.162: 3 Chirality restraints: 688 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CA TYR A 152 " pdb=" N TYR A 152 " pdb=" C TYR A 152 " pdb=" CB TYR A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA PRO A 513 " pdb=" N PRO A 513 " pdb=" C PRO A 513 " pdb=" CB PRO A 513 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 685 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C ILE A 103 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 103 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE A 104 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 253 " -0.013 2.00e-02 2.50e+03 1.31e-02 4.30e+00 pdb=" CG TRP A 253 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 253 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 253 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 253 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 253 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 253 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 253 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 253 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 253 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 512 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO A 513 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 513 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 513 " -0.028 5.00e-02 4.00e+02 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1259 2.82 - 3.34: 3972 3.34 - 3.86: 6955 3.86 - 4.38: 8045 4.38 - 4.90: 14339 Nonbonded interactions: 34570 Sorted by model distance: nonbonded pdb=" OG SER A 182 " pdb=" OE2 GLU A 212 " model vdw 2.301 3.040 nonbonded pdb=" NE2 HIS A 280 " pdb=" OG1 THR A 397 " model vdw 2.305 3.120 nonbonded pdb=" NZ LYS A 522 " pdb=" O ALA A 616 " model vdw 2.321 3.120 nonbonded pdb=" O ILE A 561 " pdb=" OG SER A 564 " model vdw 2.388 3.040 nonbonded pdb=" O PHE A 72 " pdb=" OH TYR A 271 " model vdw 2.443 3.040 ... (remaining 34565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.450 Find NCS groups from input model: 0.050 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:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.003 0.066 4491 Z= 0.145 Angle : 0.679 9.984 6131 Z= 0.441 Chirality : 0.041 0.162 688 Planarity : 0.005 0.052 743 Dihedral : 15.115 107.297 1521 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 0.10 (0.38), residues: 538 helix: 0.95 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -1.67 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 253 HIS 0.002 0.001 HIS A 222 PHE 0.014 0.001 PHE A 335 TYR 0.030 0.001 TYR A 152 ARG 0.002 0.000 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00122 ( 1) link_NAG-ASN : angle 0.69331 ( 3) hydrogen bonds : bond 0.14948 ( 250) hydrogen bonds : angle 5.46410 ( 723) SS BOND : bond 0.00358 ( 1) SS BOND : angle 1.26614 ( 2) covalent geometry : bond 0.00270 ( 4489) covalent geometry : angle 0.67837 ( 6126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.528 Fit side-chains REVERT: A 75 ASP cc_start: 0.7204 (t70) cc_final: 0.6959 (t70) REVERT: A 206 LYS cc_start: 0.7607 (ptpt) cc_final: 0.7118 (ptmt) REVERT: A 329 PHE cc_start: 0.7352 (m-80) cc_final: 0.6679 (t80) REVERT: A 375 ASN cc_start: 0.7708 (m-40) cc_final: 0.7238 (m110) REVERT: A 528 PHE cc_start: 0.6736 (m-10) cc_final: 0.6427 (m-80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 1.2321 time to fit residues: 115.0527 Evaluate side-chains 51 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 289 ASN A 292 ASN A 350 ASN A 507 GLN A 555 ASN A 596 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.137194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.124621 restraints weight = 4437.199| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 0.80 r_work: 0.3093 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4491 Z= 0.139 Angle : 0.576 6.755 6131 Z= 0.297 Chirality : 0.042 0.174 688 Planarity : 0.005 0.050 743 Dihedral : 6.211 45.102 605 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.53 % Allowed : 9.19 % Favored : 89.28 % 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: 0.55 (0.38), residues: 538 helix: 1.27 (0.29), residues: 353 sheet: None (None), residues: 0 loop : -1.43 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 253 HIS 0.004 0.001 HIS A 280 PHE 0.016 0.002 PHE A 94 TYR 0.025 0.002 TYR A 111 ARG 0.003 0.000 ARG A 301 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 1) link_NAG-ASN : angle 0.61358 ( 3) hydrogen bonds : bond 0.06729 ( 250) hydrogen bonds : angle 4.49217 ( 723) SS BOND : bond 0.00782 ( 1) SS BOND : angle 2.77099 ( 2) covalent geometry : bond 0.00273 ( 4489) covalent geometry : angle 0.57417 ( 6126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.449 Fit side-chains REVERT: A 206 LYS cc_start: 0.7991 (ptpt) cc_final: 0.7468 (ptmt) REVERT: A 329 PHE cc_start: 0.8095 (m-80) cc_final: 0.7459 (t80) REVERT: A 375 ASN cc_start: 0.8074 (m-40) cc_final: 0.7721 (m110) REVERT: A 381 THR cc_start: 0.8085 (p) cc_final: 0.7725 (t) REVERT: A 436 GLN cc_start: 0.7968 (mm110) cc_final: 0.7668 (mp-120) REVERT: A 586 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7852 (mt-10) outliers start: 7 outliers final: 2 residues processed: 55 average time/residue: 1.0649 time to fit residues: 61.1761 Evaluate side-chains 52 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.137205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.125093 restraints weight = 4489.999| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 0.76 r_work: 0.3117 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4491 Z= 0.127 Angle : 0.525 6.330 6131 Z= 0.276 Chirality : 0.040 0.128 688 Planarity : 0.005 0.049 743 Dihedral : 4.467 26.849 605 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.97 % Allowed : 9.41 % Favored : 88.62 % 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 (0.38), residues: 538 helix: 1.55 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -1.43 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 553 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE A 409 TYR 0.016 0.002 TYR A 84 ARG 0.002 0.000 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 1) link_NAG-ASN : angle 1.38358 ( 3) hydrogen bonds : bond 0.06343 ( 250) hydrogen bonds : angle 4.40399 ( 723) SS BOND : bond 0.00530 ( 1) SS BOND : angle 2.41401 ( 2) covalent geometry : bond 0.00246 ( 4489) covalent geometry : angle 0.52201 ( 6126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.498 Fit side-chains REVERT: A 206 LYS cc_start: 0.7910 (ptpt) cc_final: 0.7322 (pttt) REVERT: A 329 PHE cc_start: 0.8010 (m-80) cc_final: 0.7483 (t80) REVERT: A 375 ASN cc_start: 0.8059 (m-40) cc_final: 0.7708 (m110) REVERT: A 381 THR cc_start: 0.7992 (p) cc_final: 0.7757 (t) REVERT: A 436 GLN cc_start: 0.7907 (mm110) cc_final: 0.7547 (mp-120) REVERT: A 586 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7647 (mt-10) outliers start: 9 outliers final: 3 residues processed: 54 average time/residue: 1.2139 time to fit residues: 68.3193 Evaluate side-chains 51 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.137523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.125238 restraints weight = 4506.327| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 0.79 r_work: 0.3147 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4491 Z= 0.119 Angle : 0.498 5.905 6131 Z= 0.263 Chirality : 0.039 0.126 688 Planarity : 0.005 0.050 743 Dihedral : 4.068 21.449 605 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.41 % Allowed : 10.50 % Favored : 87.09 % 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: 1.06 (0.38), residues: 538 helix: 1.77 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.011 0.001 PHE A 409 TYR 0.016 0.001 TYR A 84 ARG 0.002 0.000 ARG A 301 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 1) link_NAG-ASN : angle 1.01882 ( 3) hydrogen bonds : bond 0.05931 ( 250) hydrogen bonds : angle 4.31857 ( 723) SS BOND : bond 0.00508 ( 1) SS BOND : angle 2.22311 ( 2) covalent geometry : bond 0.00227 ( 4489) covalent geometry : angle 0.49557 ( 6126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.440 Fit side-chains REVERT: A 206 LYS cc_start: 0.7869 (ptpt) cc_final: 0.7281 (pttt) REVERT: A 329 PHE cc_start: 0.7965 (m-80) cc_final: 0.7528 (t80) REVERT: A 375 ASN cc_start: 0.8053 (m-40) cc_final: 0.7701 (m110) REVERT: A 381 THR cc_start: 0.7904 (p) cc_final: 0.7692 (t) REVERT: A 436 GLN cc_start: 0.7889 (mm110) cc_final: 0.7553 (mp-120) REVERT: A 541 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7243 (mptt) REVERT: A 586 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8007 (mp0) outliers start: 11 outliers final: 5 residues processed: 59 average time/residue: 1.1065 time to fit residues: 68.0745 Evaluate side-chains 57 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.132638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.120047 restraints weight = 4558.390| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 0.79 r_work: 0.3062 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4491 Z= 0.150 Angle : 0.560 6.555 6131 Z= 0.297 Chirality : 0.042 0.137 688 Planarity : 0.005 0.053 743 Dihedral : 4.331 21.773 605 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.63 % Allowed : 11.16 % Favored : 86.21 % 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: 0.98 (0.37), residues: 538 helix: 1.63 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.21 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 553 HIS 0.004 0.001 HIS A 280 PHE 0.018 0.002 PHE A 409 TYR 0.018 0.002 TYR A 84 ARG 0.003 0.001 ARG A 301 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 1) link_NAG-ASN : angle 1.06311 ( 3) hydrogen bonds : bond 0.07372 ( 250) hydrogen bonds : angle 4.49179 ( 723) SS BOND : bond 0.00645 ( 1) SS BOND : angle 2.84851 ( 2) covalent geometry : bond 0.00304 ( 4489) covalent geometry : angle 0.55775 ( 6126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.502 Fit side-chains REVERT: A 206 LYS cc_start: 0.7957 (ptpt) cc_final: 0.7335 (pttt) REVERT: A 329 PHE cc_start: 0.8006 (m-80) cc_final: 0.7503 (t80) REVERT: A 375 ASN cc_start: 0.8128 (m-40) cc_final: 0.7697 (m110) REVERT: A 377 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 381 THR cc_start: 0.8043 (p) cc_final: 0.7786 (t) REVERT: A 436 GLN cc_start: 0.7918 (mm110) cc_final: 0.7599 (mp-120) REVERT: A 541 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7317 (mptt) REVERT: A 586 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7688 (mt-10) outliers start: 12 outliers final: 5 residues processed: 50 average time/residue: 1.1881 time to fit residues: 62.0687 Evaluate side-chains 53 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.137576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.124941 restraints weight = 4488.245| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 0.79 r_work: 0.3134 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4491 Z= 0.113 Angle : 0.482 5.793 6131 Z= 0.256 Chirality : 0.039 0.130 688 Planarity : 0.005 0.053 743 Dihedral : 3.944 21.464 605 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.63 % Allowed : 11.82 % Favored : 85.56 % 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: 538 helix: 1.94 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.28 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.010 0.001 PHE A 409 TYR 0.015 0.001 TYR A 84 ARG 0.001 0.000 ARG A 301 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 1) link_NAG-ASN : angle 0.82185 ( 3) hydrogen bonds : bond 0.05629 ( 250) hydrogen bonds : angle 4.28784 ( 723) SS BOND : bond 0.00376 ( 1) SS BOND : angle 2.15163 ( 2) covalent geometry : bond 0.00211 ( 4489) covalent geometry : angle 0.48033 ( 6126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.605 Fit side-chains REVERT: A 206 LYS cc_start: 0.7861 (ptpt) cc_final: 0.7265 (pttt) REVERT: A 329 PHE cc_start: 0.8030 (m-80) cc_final: 0.7518 (t80) REVERT: A 375 ASN cc_start: 0.8060 (m-40) cc_final: 0.7650 (m110) REVERT: A 377 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: A 381 THR cc_start: 0.7910 (p) cc_final: 0.7677 (t) REVERT: A 436 GLN cc_start: 0.7924 (mm110) cc_final: 0.7513 (mp-120) REVERT: A 541 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7260 (mptt) REVERT: A 586 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8006 (mp0) outliers start: 12 outliers final: 6 residues processed: 59 average time/residue: 1.5201 time to fit residues: 93.0688 Evaluate side-chains 57 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.133907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.121343 restraints weight = 4514.632| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.79 r_work: 0.3100 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4491 Z= 0.135 Angle : 0.525 6.450 6131 Z= 0.279 Chirality : 0.041 0.127 688 Planarity : 0.005 0.055 743 Dihedral : 4.147 21.934 605 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.84 % Allowed : 11.60 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.38), residues: 538 helix: 1.92 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -1.24 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 553 HIS 0.004 0.001 HIS A 280 PHE 0.016 0.001 PHE A 409 TYR 0.017 0.002 TYR A 84 ARG 0.002 0.000 ARG A 301 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 1) link_NAG-ASN : angle 0.84617 ( 3) hydrogen bonds : bond 0.06743 ( 250) hydrogen bonds : angle 4.39022 ( 723) SS BOND : bond 0.00489 ( 1) SS BOND : angle 2.43177 ( 2) covalent geometry : bond 0.00266 ( 4489) covalent geometry : angle 0.52280 ( 6126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.619 Fit side-chains REVERT: A 206 LYS cc_start: 0.7935 (ptpt) cc_final: 0.7396 (pttp) REVERT: A 329 PHE cc_start: 0.8014 (m-80) cc_final: 0.7541 (t80) REVERT: A 375 ASN cc_start: 0.8104 (m-40) cc_final: 0.7690 (m110) REVERT: A 377 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: A 381 THR cc_start: 0.7965 (p) cc_final: 0.7736 (t) REVERT: A 436 GLN cc_start: 0.7903 (mm110) cc_final: 0.7515 (mp-120) REVERT: A 541 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7289 (mptt) REVERT: A 586 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7629 (mt-10) outliers start: 13 outliers final: 7 residues processed: 53 average time/residue: 1.7182 time to fit residues: 95.0338 Evaluate side-chains 55 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.0470 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.135541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.122757 restraints weight = 4424.172| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 0.83 r_work: 0.3127 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4491 Z= 0.122 Angle : 0.499 6.193 6131 Z= 0.265 Chirality : 0.040 0.126 688 Planarity : 0.005 0.054 743 Dihedral : 4.014 21.541 605 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.41 % Allowed : 12.04 % Favored : 85.56 % 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: 1.61 (0.38), residues: 538 helix: 2.21 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -1.04 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.012 0.001 PHE A 409 TYR 0.016 0.001 TYR A 84 ARG 0.002 0.000 ARG A 301 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 1) link_NAG-ASN : angle 0.76817 ( 3) hydrogen bonds : bond 0.06118 ( 250) hydrogen bonds : angle 4.32572 ( 723) SS BOND : bond 0.00392 ( 1) SS BOND : angle 2.24074 ( 2) covalent geometry : bond 0.00234 ( 4489) covalent geometry : angle 0.49697 ( 6126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.446 Fit side-chains REVERT: A 206 LYS cc_start: 0.7833 (ptpt) cc_final: 0.7261 (pttp) REVERT: A 329 PHE cc_start: 0.8017 (m-80) cc_final: 0.7557 (t80) REVERT: A 375 ASN cc_start: 0.8085 (m-40) cc_final: 0.7676 (m110) REVERT: A 377 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: A 381 THR cc_start: 0.7907 (p) cc_final: 0.7701 (t) REVERT: A 425 GLU cc_start: 0.8626 (tp30) cc_final: 0.8410 (tp30) REVERT: A 436 GLN cc_start: 0.7907 (mm110) cc_final: 0.7516 (mp-120) REVERT: A 541 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7272 (mptt) REVERT: A 586 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8025 (mp0) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 1.6263 time to fit residues: 87.9865 Evaluate side-chains 55 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 0.0170 chunk 25 optimal weight: 0.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.134965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.121994 restraints weight = 4512.546| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 0.84 r_work: 0.3109 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4491 Z= 0.126 Angle : 0.508 6.489 6131 Z= 0.270 Chirality : 0.040 0.125 688 Planarity : 0.005 0.054 743 Dihedral : 4.044 21.836 605 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.84 % Allowed : 11.38 % Favored : 85.78 % 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: 1.60 (0.38), residues: 538 helix: 2.20 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -1.02 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 553 HIS 0.003 0.001 HIS A 280 PHE 0.013 0.001 PHE A 409 TYR 0.016 0.001 TYR A 84 ARG 0.002 0.000 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 1) link_NAG-ASN : angle 0.71875 ( 3) hydrogen bonds : bond 0.06317 ( 250) hydrogen bonds : angle 4.34021 ( 723) SS BOND : bond 0.00399 ( 1) SS BOND : angle 2.26973 ( 2) covalent geometry : bond 0.00243 ( 4489) covalent geometry : angle 0.50644 ( 6126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.593 Fit side-chains REVERT: A 206 LYS cc_start: 0.7843 (ptpt) cc_final: 0.7263 (pttp) REVERT: A 329 PHE cc_start: 0.8062 (m-80) cc_final: 0.7548 (t80) REVERT: A 375 ASN cc_start: 0.8098 (m-40) cc_final: 0.7682 (m110) REVERT: A 377 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: A 381 THR cc_start: 0.7945 (p) cc_final: 0.7685 (t) REVERT: A 436 GLN cc_start: 0.7908 (mm110) cc_final: 0.7509 (mp-120) REVERT: A 541 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7281 (mptt) REVERT: A 586 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7624 (mt-10) outliers start: 13 outliers final: 8 residues processed: 54 average time/residue: 1.5884 time to fit residues: 88.9019 Evaluate side-chains 57 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.0970 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.137570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.125292 restraints weight = 4411.802| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 0.77 r_work: 0.3139 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4491 Z= 0.113 Angle : 0.481 6.183 6131 Z= 0.255 Chirality : 0.039 0.131 688 Planarity : 0.005 0.053 743 Dihedral : 3.866 21.472 605 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.19 % Allowed : 12.25 % Favored : 85.56 % 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: 1.73 (0.39), residues: 538 helix: 2.28 (0.28), residues: 344 sheet: None (None), residues: 0 loop : -0.99 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 585 HIS 0.003 0.001 HIS A 280 PHE 0.009 0.001 PHE A 409 TYR 0.015 0.001 TYR A 84 ARG 0.002 0.000 ARG A 301 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 1) link_NAG-ASN : angle 0.65317 ( 3) hydrogen bonds : bond 0.05567 ( 250) hydrogen bonds : angle 4.26728 ( 723) SS BOND : bond 0.00326 ( 1) SS BOND : angle 1.98934 ( 2) covalent geometry : bond 0.00211 ( 4489) covalent geometry : angle 0.47958 ( 6126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.454 Fit side-chains REVERT: A 206 LYS cc_start: 0.7791 (ptpt) cc_final: 0.7231 (pttp) REVERT: A 329 PHE cc_start: 0.8017 (m-80) cc_final: 0.7563 (t80) REVERT: A 375 ASN cc_start: 0.8058 (m-40) cc_final: 0.7658 (m110) REVERT: A 377 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: A 436 GLN cc_start: 0.7890 (mm110) cc_final: 0.7500 (mp-120) REVERT: A 586 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8006 (mp0) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 1.0654 time to fit residues: 62.4097 Evaluate side-chains 54 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.0020 chunk 41 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.4066 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.138927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.126043 restraints weight = 4492.951| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 0.82 r_work: 0.3155 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4491 Z= 0.107 Angle : 0.467 6.414 6131 Z= 0.248 Chirality : 0.038 0.131 688 Planarity : 0.005 0.052 743 Dihedral : 3.780 21.528 605 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.41 % Allowed : 12.04 % Favored : 85.56 % 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: 1.83 (0.39), residues: 538 helix: 2.34 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -0.94 (0.49), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 585 HIS 0.002 0.001 HIS A 280 PHE 0.009 0.001 PHE A 335 TYR 0.014 0.001 TYR A 84 ARG 0.001 0.000 ARG A 301 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 1) link_NAG-ASN : angle 0.59891 ( 3) hydrogen bonds : bond 0.05199 ( 250) hydrogen bonds : angle 4.18355 ( 723) SS BOND : bond 0.00317 ( 1) SS BOND : angle 1.85100 ( 2) covalent geometry : bond 0.00198 ( 4489) covalent geometry : angle 0.46542 ( 6126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3735.86 seconds wall clock time: 66 minutes 24.95 seconds (3984.95 seconds total)