Starting phenix.real_space_refine on Thu Jul 2 15:22:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gry_34217/07_2026/8gry_34217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gry_34217/07_2026/8gry_34217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gry_34217/07_2026/8gry_34217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gry_34217/07_2026/8gry_34217.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gry_34217/07_2026/8gry_34217.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gry_34217/07_2026/8gry_34217.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gry_34217/07_2026/8gry_34217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gry_34217/07_2026/8gry_34217.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3164 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4121 2.51 5 N 1076 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6444 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4872 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 28, 'TRANS': 568} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" 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 chiralities: 1 Time building chain proxies: 1.15, per 1000 atoms: 0.18 Number of scatterers: 6444 At special positions: 0 Unit cell: (97.68, 76.56, 122.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1210 8.00 N 1076 7.00 C 4121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 B 601 " - " ASN B 343 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 278.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 53.4% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 19 through 53 removed outlier: 3.808A pdb=" N GLU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.582A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.523A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.973A pdb=" N SER A 106 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 193 removed outlier: 3.749A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.503A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 231 removed outlier: 4.196A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.992A pdb=" N GLN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.513A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.518A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.626A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 513 through 532 removed outlier: 4.022A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.751A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.506A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.645A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.657A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.990A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.112A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 294 hydrogen bonds defined for protein. 843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1147 1.33 - 1.45: 1861 1.45 - 1.57: 3561 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 6625 Sorted by residual: bond pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 1.469 1.430 0.039 1.28e-02 6.10e+03 9.20e+00 bond pdb=" C PRO B 499 " pdb=" O PRO B 499 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.30e-02 5.92e+03 5.97e+00 bond pdb=" N THR B 500 " pdb=" CA THR B 500 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.42e-02 4.96e+03 2.02e+00 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C2 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.54e+00 ... (remaining 6620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8771 1.56 - 3.12: 183 3.12 - 4.68: 42 4.68 - 6.24: 6 6.24 - 7.80: 1 Bond angle restraints: 9003 Sorted by residual: angle pdb=" N THR B 500 " pdb=" CA THR B 500 " pdb=" C THR B 500 " ideal model delta sigma weight residual 114.64 106.84 7.80 1.52e+00 4.33e-01 2.63e+01 angle pdb=" N PRO B 499 " pdb=" CD PRO B 499 " pdb=" CG PRO B 499 " ideal model delta sigma weight residual 103.20 98.77 4.43 1.50e+00 4.44e-01 8.71e+00 angle pdb=" CA GLU A 182 " pdb=" CB GLU A 182 " pdb=" CG GLU A 182 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.81e+00 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 121.54 126.11 -4.57 1.91e+00 2.74e-01 5.73e+00 angle pdb=" C ALA A 384 " pdb=" N TYR A 385 " pdb=" CA TYR A 385 " ideal model delta sigma weight residual 122.65 118.74 3.91 1.66e+00 3.63e-01 5.55e+00 ... (remaining 8998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 3498 18.05 - 36.11: 330 36.11 - 54.16: 65 54.16 - 72.21: 11 72.21 - 90.27: 13 Dihedral angle restraints: 3917 sinusoidal: 1588 harmonic: 2329 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 166.76 -73.76 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 158.94 -65.94 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 130.04 -37.04 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 3914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 719 0.042 - 0.084: 162 0.084 - 0.126: 53 0.126 - 0.169: 4 0.169 - 0.211: 3 Chirality restraints: 941 Sorted by residual: chirality pdb=" C2 NAG B 601 " pdb=" C1 NAG B 601 " pdb=" C3 NAG B 601 " pdb=" N2 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.28 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C4 NAG B 601 " pdb=" C3 NAG B 601 " pdb=" C5 NAG B 601 " pdb=" O4 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 938 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " 0.045 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO A 258 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 89 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C GLN A 89 " 0.026 2.00e-02 2.50e+03 pdb=" O GLN A 89 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN A 90 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 182 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" CD GLU A 182 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU A 182 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 182 " -0.009 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 48 2.58 - 3.16: 5250 3.16 - 3.74: 9530 3.74 - 4.32: 12523 4.32 - 4.90: 21645 Nonbonded interactions: 48996 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP A 494 " pdb=" N GLU A 495 " model vdw 2.178 3.120 nonbonded pdb=" OG SER A 607 " pdb=" OD2 ASP A 609 " model vdw 2.234 3.040 nonbonded pdb=" O SER B 438 " pdb=" OG SER B 438 " model vdw 2.278 3.040 nonbonded pdb=" NE1 TRP A 478 " pdb=" OD2 ASP A 499 " model vdw 2.286 3.120 ... (remaining 48991 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: 12.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.680 Find NCS groups from input model: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 6635 Z= 0.179 Angle : 0.579 7.798 9020 Z= 0.315 Chirality : 0.041 0.211 941 Planarity : 0.004 0.069 1169 Dihedral : 15.106 90.265 2400 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.31), residues: 788 helix: 1.69 (0.29), residues: 367 sheet: 1.81 (0.92), residues: 39 loop : -1.35 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.015 0.001 TYR A 385 PHE 0.009 0.001 PHE A 592 TRP 0.022 0.002 TRP A 165 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 ( 6625) covalent geometry : angle 0.57822 / 0.31 ( 9003) SS BOND : bond 0.00096 / 0.05 ( 7) SS BOND : angle 0.63690 / 0.31 ( 14) hydrogen bonds : bond 0.13587 / 9.17 ( 294) hydrogen bonds : angle 5.51249 / 3.87 ( 843) metal coordination : bond 0.20094 / 10.09 ( 2) link_NAG-ASN : bond 0.00652 / 0.34 ( 1) link_NAG-ASN : angle 1.62800 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7319 (tp30) cc_final: 0.6860 (tp30) REVERT: A 77 SER cc_start: 0.8125 (t) cc_final: 0.7731 (p) REVERT: A 126 ILE cc_start: 0.8802 (tp) cc_final: 0.8517 (tt) REVERT: A 150 GLU cc_start: 0.6570 (pp20) cc_final: 0.6300 (tm-30) REVERT: A 313 LYS cc_start: 0.7795 (tttt) cc_final: 0.7534 (tmmt) REVERT: A 341 LYS cc_start: 0.7636 (mttp) cc_final: 0.7329 (mttp) REVERT: A 360 MET cc_start: 0.8291 (ttm) cc_final: 0.8077 (ttm) REVERT: A 376 MET cc_start: 0.7489 (tpp) cc_final: 0.7275 (ttp) REVERT: A 475 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7690 (ttpt) REVERT: A 517 THR cc_start: 0.6970 (p) cc_final: 0.6639 (p) REVERT: A 541 LYS cc_start: 0.6731 (mttt) cc_final: 0.6435 (mttt) REVERT: A 562 ASN cc_start: 0.7314 (t0) cc_final: 0.7037 (t0) REVERT: A 574 VAL cc_start: 0.8340 (m) cc_final: 0.8096 (p) REVERT: B 336 CYS cc_start: 0.4205 (m) cc_final: 0.3324 (m) REVERT: B 357 ARG cc_start: 0.6541 (ptm-80) cc_final: 0.6161 (ptm-80) REVERT: B 469 SER cc_start: 0.8276 (t) cc_final: 0.8067 (t) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.0713 time to fit residues: 19.2693 Evaluate side-chains 181 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN A 81 GLN ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.129291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116920 restraints weight = 10159.464| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.35 r_work: 0.3376 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6635 Z= 0.176 Angle : 0.606 9.500 9020 Z= 0.309 Chirality : 0.044 0.299 941 Planarity : 0.005 0.055 1169 Dihedral : 3.948 14.159 864 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.58 % Allowed : 9.06 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.31), residues: 788 helix: 1.95 (0.28), residues: 373 sheet: 0.71 (0.86), residues: 49 loop : -1.32 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 493 TYR 0.020 0.001 TYR A 385 PHE 0.016 0.002 PHE A 592 TRP 0.011 0.001 TRP A 610 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 6625) covalent geometry : angle 0.60409 / 0.31 ( 9003) SS BOND : bond 0.00237 / 0.13 ( 7) SS BOND : angle 1.30008 / 0.58 ( 14) hydrogen bonds : bond 0.06103 / 3.95 ( 294) hydrogen bonds : angle 4.11522 / 2.90 ( 843) metal coordination : bond 0.01370 / 0.70 ( 2) link_NAG-ASN : bond 0.00369 / 0.19 ( 1) link_NAG-ASN : angle 1.17201 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8095 (tp30) cc_final: 0.7574 (tp30) REVERT: A 113 ASN cc_start: 0.8626 (t0) cc_final: 0.8411 (t0) REVERT: A 123 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7902 (ttm) REVERT: A 126 ILE cc_start: 0.9026 (tp) cc_final: 0.8656 (tt) REVERT: A 150 GLU cc_start: 0.7221 (pp20) cc_final: 0.6491 (tp30) REVERT: A 175 GLN cc_start: 0.8096 (mt0) cc_final: 0.7885 (mt0) REVERT: A 182 GLU cc_start: 0.8640 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 186 LEU cc_start: 0.7937 (mm) cc_final: 0.7528 (mm) REVERT: A 213 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 347 THR cc_start: 0.8425 (m) cc_final: 0.8087 (p) REVERT: A 475 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8267 (ttpt) REVERT: A 482 ARG cc_start: 0.8122 (ttm170) cc_final: 0.7850 (ttm-80) REVERT: A 527 GLU cc_start: 0.8335 (tt0) cc_final: 0.7960 (tt0) REVERT: A 557 MET cc_start: 0.8486 (tmm) cc_final: 0.8199 (ttp) REVERT: A 562 ASN cc_start: 0.7978 (t0) cc_final: 0.7730 (t0) REVERT: B 336 CYS cc_start: 0.6455 (m) cc_final: 0.5984 (m) REVERT: B 357 ARG cc_start: 0.7220 (ptm-80) cc_final: 0.6885 (ptm-80) REVERT: B 393 THR cc_start: 0.7190 (m) cc_final: 0.6823 (p) REVERT: B 433 VAL cc_start: 0.8409 (t) cc_final: 0.8071 (m) REVERT: B 469 SER cc_start: 0.8616 (t) cc_final: 0.8380 (t) outliers start: 11 outliers final: 7 residues processed: 199 average time/residue: 0.0703 time to fit residues: 17.9797 Evaluate side-chains 193 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 382 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 0.0040 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 42 optimal weight: 0.3980 chunk 54 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 64 optimal weight: 0.0370 chunk 37 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116958 restraints weight = 10071.443| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.30 r_work: 0.3391 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6635 Z= 0.130 Angle : 0.569 9.415 9020 Z= 0.287 Chirality : 0.043 0.295 941 Planarity : 0.004 0.049 1169 Dihedral : 3.845 13.429 864 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.01 % Allowed : 15.11 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.31), residues: 788 helix: 1.94 (0.28), residues: 369 sheet: 0.52 (0.84), residues: 51 loop : -1.30 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.025 0.001 TYR A 158 PHE 0.016 0.001 PHE A 369 TRP 0.012 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6625) covalent geometry : angle 0.56724 / 0.29 ( 9003) SS BOND : bond 0.00147 / 0.08 ( 7) SS BOND : angle 1.32219 / 0.65 ( 14) hydrogen bonds : bond 0.05120 / 3.29 ( 294) hydrogen bonds : angle 3.94474 / 2.76 ( 843) metal coordination : bond 0.00386 / 0.20 ( 2) link_NAG-ASN : bond 0.00319 / 0.17 ( 1) link_NAG-ASN : angle 1.12844 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 186 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8079 (tp30) cc_final: 0.7632 (tp30) REVERT: A 77 SER cc_start: 0.8351 (t) cc_final: 0.8049 (m) REVERT: A 113 ASN cc_start: 0.8634 (t0) cc_final: 0.8422 (t0) REVERT: A 123 MET cc_start: 0.8114 (ttp) cc_final: 0.7831 (ttm) REVERT: A 126 ILE cc_start: 0.9058 (tp) cc_final: 0.8689 (tt) REVERT: A 150 GLU cc_start: 0.7197 (pp20) cc_final: 0.6420 (tp30) REVERT: A 171 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6978 (mm-30) REVERT: A 213 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7450 (mm-30) REVERT: A 225 ASP cc_start: 0.7378 (m-30) cc_final: 0.7017 (m-30) REVERT: A 250 GLU cc_start: 0.8433 (tp30) cc_final: 0.8143 (tp30) REVERT: A 475 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8224 (ttpt) REVERT: A 482 ARG cc_start: 0.8122 (ttm170) cc_final: 0.7830 (ttm-80) REVERT: A 557 MET cc_start: 0.8455 (tmm) cc_final: 0.8116 (ttp) REVERT: A 562 ASN cc_start: 0.7918 (t0) cc_final: 0.7715 (t0) REVERT: B 357 ARG cc_start: 0.7245 (ptm-80) cc_final: 0.6881 (ptm-80) REVERT: B 469 SER cc_start: 0.8662 (t) cc_final: 0.8453 (t) outliers start: 7 outliers final: 6 residues processed: 188 average time/residue: 0.0752 time to fit residues: 17.8960 Evaluate side-chains 185 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 chunk 50 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110496 restraints weight = 10048.004| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.24 r_work: 0.3287 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 6635 Z= 0.303 Angle : 0.683 9.431 9020 Z= 0.359 Chirality : 0.049 0.298 941 Planarity : 0.005 0.048 1169 Dihedral : 4.609 18.446 864 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.45 % Allowed : 15.97 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.30), residues: 788 helix: 1.65 (0.27), residues: 369 sheet: 2.18 (0.92), residues: 39 loop : -1.64 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 160 TYR 0.022 0.002 TYR A 158 PHE 0.027 0.002 PHE A 592 TRP 0.012 0.002 TRP A 349 HIS 0.007 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.30 ( 6625) covalent geometry : angle 0.67989 / 0.36 ( 9003) SS BOND : bond 0.00376 / 0.19 ( 7) SS BOND : angle 1.70380 / 0.72 ( 14) hydrogen bonds : bond 0.08204 / 5.39 ( 294) hydrogen bonds : angle 4.45294 / 3.18 ( 843) metal coordination : bond 0.01098 / 0.58 ( 2) link_NAG-ASN : bond 0.00248 / 0.13 ( 1) link_NAG-ASN : angle 1.51567 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7222 (tm-30) REVERT: A 61 LYS cc_start: 0.8288 (mttt) cc_final: 0.7960 (mtmt) REVERT: A 75 GLU cc_start: 0.8077 (tp30) cc_final: 0.7652 (tp30) REVERT: A 87 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7934 (mp0) REVERT: A 113 ASN cc_start: 0.8813 (t0) cc_final: 0.8522 (t0) REVERT: A 123 MET cc_start: 0.8205 (ttp) cc_final: 0.7934 (ttm) REVERT: A 126 ILE cc_start: 0.9156 (tp) cc_final: 0.8770 (tt) REVERT: A 155 SER cc_start: 0.8988 (t) cc_final: 0.8300 (m) REVERT: A 181 GLU cc_start: 0.8175 (tt0) cc_final: 0.7819 (tt0) REVERT: A 213 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7546 (mm-30) REVERT: A 228 ASN cc_start: 0.7445 (m-40) cc_final: 0.7194 (m-40) REVERT: A 269 ASP cc_start: 0.7910 (t0) cc_final: 0.7697 (t0) REVERT: A 341 LYS cc_start: 0.8163 (mttm) cc_final: 0.7858 (mttp) REVERT: A 475 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8378 (ttpt) REVERT: A 509 ASP cc_start: 0.8754 (t70) cc_final: 0.8320 (t70) REVERT: A 557 MET cc_start: 0.8557 (tmm) cc_final: 0.8181 (ttp) REVERT: B 357 ARG cc_start: 0.7275 (ptm-80) cc_final: 0.6978 (ptm-80) REVERT: B 501 TYR cc_start: 0.8344 (m-10) cc_final: 0.7942 (m-80) outliers start: 17 outliers final: 11 residues processed: 195 average time/residue: 0.0740 time to fit residues: 18.6490 Evaluate side-chains 192 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.3980 chunk 65 optimal weight: 0.4980 chunk 32 optimal weight: 0.0970 chunk 35 optimal weight: 0.3980 chunk 3 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 chunk 37 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 1 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114147 restraints weight = 10108.482| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.33 r_work: 0.3341 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6635 Z= 0.144 Angle : 0.589 9.440 9020 Z= 0.302 Chirality : 0.043 0.281 941 Planarity : 0.004 0.045 1169 Dihedral : 4.178 16.468 864 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.44 % Allowed : 16.55 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.30), residues: 788 helix: 1.87 (0.28), residues: 363 sheet: 0.48 (0.81), residues: 51 loop : -1.56 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.023 0.001 TYR A 158 PHE 0.012 0.001 PHE A 142 TRP 0.013 0.001 TRP A 566 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 6625) covalent geometry : angle 0.58687 / 0.30 ( 9003) SS BOND : bond 0.00232 / 0.13 ( 7) SS BOND : angle 1.20167 / 0.50 ( 14) hydrogen bonds : bond 0.05618 / 3.61 ( 294) hydrogen bonds : angle 4.05228 / 2.85 ( 843) metal coordination : bond 0.00441 / 0.23 ( 2) link_NAG-ASN : bond 0.00276 / 0.15 ( 1) link_NAG-ASN : angle 1.18830 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8101 (tp30) cc_final: 0.7560 (tp30) REVERT: A 87 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7880 (mp0) REVERT: A 113 ASN cc_start: 0.8767 (t0) cc_final: 0.8534 (t0) REVERT: A 123 MET cc_start: 0.8178 (ttp) cc_final: 0.7883 (ttm) REVERT: A 126 ILE cc_start: 0.9075 (tp) cc_final: 0.8698 (tt) REVERT: A 181 GLU cc_start: 0.8058 (tt0) cc_final: 0.7720 (tt0) REVERT: A 213 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7575 (mm-30) REVERT: A 225 ASP cc_start: 0.7471 (m-30) cc_final: 0.7110 (m-30) REVERT: A 228 ASN cc_start: 0.7435 (m-40) cc_final: 0.7153 (m-40) REVERT: A 250 GLU cc_start: 0.8333 (tp30) cc_final: 0.8019 (tm-30) REVERT: A 269 ASP cc_start: 0.7997 (t0) cc_final: 0.7759 (t0) REVERT: A 341 LYS cc_start: 0.8116 (mttm) cc_final: 0.7855 (mttp) REVERT: A 347 THR cc_start: 0.8523 (m) cc_final: 0.8138 (p) REVERT: A 475 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8296 (ttpt) REVERT: A 509 ASP cc_start: 0.8695 (t70) cc_final: 0.8421 (t70) REVERT: A 517 THR cc_start: 0.7564 (p) cc_final: 0.7276 (p) REVERT: A 557 MET cc_start: 0.8502 (tmm) cc_final: 0.8097 (ttp) REVERT: A 598 GLN cc_start: 0.8249 (tp40) cc_final: 0.7959 (tp40) REVERT: B 357 ARG cc_start: 0.7253 (ptm-80) cc_final: 0.6868 (ptm-80) REVERT: B 501 TYR cc_start: 0.8343 (m-10) cc_final: 0.7905 (m-80) outliers start: 10 outliers final: 6 residues processed: 189 average time/residue: 0.0675 time to fit residues: 16.6064 Evaluate side-chains 187 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 181 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 0.0020 chunk 12 optimal weight: 0.0770 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.2946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113314 restraints weight = 10136.707| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.32 r_work: 0.3319 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6635 Z= 0.158 Angle : 0.609 9.421 9020 Z= 0.309 Chirality : 0.044 0.279 941 Planarity : 0.004 0.043 1169 Dihedral : 4.215 24.349 864 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.16 % Allowed : 16.55 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.30), residues: 788 helix: 1.89 (0.28), residues: 364 sheet: 0.32 (0.80), residues: 51 loop : -1.57 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.019 0.001 TYR A 158 PHE 0.013 0.001 PHE A 592 TRP 0.012 0.001 TRP A 566 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 6625) covalent geometry : angle 0.60531 / 0.31 ( 9003) SS BOND : bond 0.00250 / 0.13 ( 7) SS BOND : angle 1.64758 / 0.79 ( 14) hydrogen bonds : bond 0.05870 / 3.82 ( 294) hydrogen bonds : angle 4.01453 / 2.83 ( 843) metal coordination : bond 0.00440 / 0.23 ( 2) link_NAG-ASN : bond 0.00304 / 0.16 ( 1) link_NAG-ASN : angle 1.22470 / 0.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8105 (tp30) cc_final: 0.7649 (tp30) REVERT: A 77 SER cc_start: 0.8429 (t) cc_final: 0.8132 (m) REVERT: A 87 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7899 (mp0) REVERT: A 113 ASN cc_start: 0.8734 (t0) cc_final: 0.8520 (t0) REVERT: A 123 MET cc_start: 0.8179 (ttp) cc_final: 0.7932 (ttm) REVERT: A 126 ILE cc_start: 0.9081 (tp) cc_final: 0.8706 (tt) REVERT: A 151 ILE cc_start: 0.6687 (tp) cc_final: 0.6123 (tp) REVERT: A 155 SER cc_start: 0.8930 (t) cc_final: 0.8111 (m) REVERT: A 165 TRP cc_start: 0.7877 (t60) cc_final: 0.7648 (t60) REVERT: A 181 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: A 206 ASP cc_start: 0.8265 (t0) cc_final: 0.7978 (t0) REVERT: A 213 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7615 (mm-30) REVERT: A 225 ASP cc_start: 0.7542 (m-30) cc_final: 0.7169 (m-30) REVERT: A 228 ASN cc_start: 0.7404 (m-40) cc_final: 0.7129 (m-40) REVERT: A 250 GLU cc_start: 0.8337 (tp30) cc_final: 0.7968 (tm-30) REVERT: A 269 ASP cc_start: 0.8069 (t0) cc_final: 0.7806 (t0) REVERT: A 347 THR cc_start: 0.8526 (m) cc_final: 0.8073 (p) REVERT: A 517 THR cc_start: 0.7628 (p) cc_final: 0.7325 (p) REVERT: A 557 MET cc_start: 0.8495 (tmm) cc_final: 0.8103 (ttp) REVERT: A 598 GLN cc_start: 0.8271 (tp40) cc_final: 0.7980 (tp40) REVERT: B 357 ARG cc_start: 0.7283 (ptm-80) cc_final: 0.6907 (ptm-80) REVERT: B 501 TYR cc_start: 0.8336 (m-10) cc_final: 0.7888 (m-80) outliers start: 15 outliers final: 14 residues processed: 179 average time/residue: 0.0591 time to fit residues: 14.2585 Evaluate side-chains 186 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 0.0170 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 25 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113277 restraints weight = 10149.548| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.33 r_work: 0.3324 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6635 Z= 0.165 Angle : 0.612 9.437 9020 Z= 0.310 Chirality : 0.044 0.278 941 Planarity : 0.004 0.042 1169 Dihedral : 4.241 24.316 864 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.30 % Allowed : 17.84 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.30), residues: 788 helix: 1.88 (0.28), residues: 364 sheet: 0.31 (0.80), residues: 51 loop : -1.57 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.018 0.001 TYR A 158 PHE 0.016 0.001 PHE A 142 TRP 0.011 0.001 TRP A 566 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 6625) covalent geometry : angle 0.60865 / 0.31 ( 9003) SS BOND : bond 0.00274 / 0.14 ( 7) SS BOND : angle 1.73901 / 0.82 ( 14) hydrogen bonds : bond 0.05942 / 3.86 ( 294) hydrogen bonds : angle 4.06344 / 2.86 ( 843) metal coordination : bond 0.00554 / 0.29 ( 2) link_NAG-ASN : bond 0.00297 / 0.16 ( 1) link_NAG-ASN : angle 1.23821 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8114 (tp30) cc_final: 0.7661 (tp30) REVERT: A 77 SER cc_start: 0.8439 (t) cc_final: 0.8150 (m) REVERT: A 87 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7900 (mp0) REVERT: A 113 ASN cc_start: 0.8776 (t0) cc_final: 0.8540 (t0) REVERT: A 123 MET cc_start: 0.8222 (ttp) cc_final: 0.7923 (ttm) REVERT: A 126 ILE cc_start: 0.9101 (tp) cc_final: 0.8712 (tt) REVERT: A 151 ILE cc_start: 0.6783 (tp) cc_final: 0.6251 (tp) REVERT: A 155 SER cc_start: 0.8929 (t) cc_final: 0.8149 (m) REVERT: A 165 TRP cc_start: 0.7857 (t60) cc_final: 0.7620 (t60) REVERT: A 181 GLU cc_start: 0.8113 (tt0) cc_final: 0.7746 (tt0) REVERT: A 213 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7608 (mm-30) REVERT: A 225 ASP cc_start: 0.7550 (m-30) cc_final: 0.7183 (m-30) REVERT: A 228 ASN cc_start: 0.7444 (m-40) cc_final: 0.7171 (m-40) REVERT: A 250 GLU cc_start: 0.8284 (tp30) cc_final: 0.7913 (tm-30) REVERT: A 347 THR cc_start: 0.8541 (m) cc_final: 0.8075 (p) REVERT: A 509 ASP cc_start: 0.8667 (t70) cc_final: 0.8411 (t70) REVERT: A 517 THR cc_start: 0.7646 (p) cc_final: 0.7339 (p) REVERT: A 557 MET cc_start: 0.8520 (tmm) cc_final: 0.8080 (ttp) REVERT: A 598 GLN cc_start: 0.8263 (tp40) cc_final: 0.7978 (tp40) REVERT: B 357 ARG cc_start: 0.7279 (ptm-80) cc_final: 0.6907 (ptm-80) REVERT: B 501 TYR cc_start: 0.8335 (m-10) cc_final: 0.7905 (m-80) outliers start: 16 outliers final: 14 residues processed: 180 average time/residue: 0.0657 time to fit residues: 15.7317 Evaluate side-chains 188 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 0.0060 chunk 50 optimal weight: 0.2980 chunk 41 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 76 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 74 optimal weight: 0.0170 chunk 60 optimal weight: 0.0870 chunk 33 optimal weight: 0.3980 overall best weight: 0.0812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.129912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.117750 restraints weight = 10099.013| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.31 r_work: 0.3399 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6635 Z= 0.109 Angle : 0.579 9.449 9020 Z= 0.289 Chirality : 0.042 0.276 941 Planarity : 0.004 0.041 1169 Dihedral : 3.842 24.541 864 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.45 % Allowed : 17.70 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.30), residues: 788 helix: 2.03 (0.28), residues: 365 sheet: 1.40 (0.90), residues: 41 loop : -1.55 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.019 0.001 TYR A 158 PHE 0.012 0.001 PHE B 456 TRP 0.013 0.001 TRP A 163 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 6625) covalent geometry : angle 0.57729 / 0.29 ( 9003) SS BOND : bond 0.00212 / 0.12 ( 7) SS BOND : angle 1.17176 / 0.53 ( 14) hydrogen bonds : bond 0.03999 / 2.54 ( 294) hydrogen bonds : angle 3.80239 / 2.66 ( 843) metal coordination : bond 0.00154 / 0.08 ( 2) link_NAG-ASN : bond 0.00391 / 0.21 ( 1) link_NAG-ASN : angle 1.17927 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8082 (tp30) cc_final: 0.7642 (tp30) REVERT: A 77 SER cc_start: 0.8411 (t) cc_final: 0.8108 (m) REVERT: A 87 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7846 (mp0) REVERT: A 113 ASN cc_start: 0.8710 (t0) cc_final: 0.8509 (t0) REVERT: A 123 MET cc_start: 0.8098 (ttp) cc_final: 0.7838 (ttm) REVERT: A 126 ILE cc_start: 0.9025 (tp) cc_final: 0.8638 (tt) REVERT: A 151 ILE cc_start: 0.6650 (tp) cc_final: 0.6120 (tp) REVERT: A 155 SER cc_start: 0.8916 (t) cc_final: 0.8131 (m) REVERT: A 179 LEU cc_start: 0.8491 (mt) cc_final: 0.8274 (mp) REVERT: A 181 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: A 213 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 225 ASP cc_start: 0.7546 (m-30) cc_final: 0.7199 (m-30) REVERT: A 250 GLU cc_start: 0.8161 (tp30) cc_final: 0.7732 (tm-30) REVERT: A 347 THR cc_start: 0.8455 (m) cc_final: 0.7984 (p) REVERT: A 358 ILE cc_start: 0.8764 (mt) cc_final: 0.8386 (tt) REVERT: A 369 PHE cc_start: 0.6212 (t80) cc_final: 0.5255 (t80) REVERT: A 419 LYS cc_start: 0.7239 (tptt) cc_final: 0.6985 (tptp) REVERT: A 557 MET cc_start: 0.8442 (tmm) cc_final: 0.8003 (ttp) REVERT: B 357 ARG cc_start: 0.7258 (ptm-80) cc_final: 0.6892 (ptm-80) REVERT: B 501 TYR cc_start: 0.8244 (m-10) cc_final: 0.7823 (m-80) outliers start: 17 outliers final: 12 residues processed: 175 average time/residue: 0.0686 time to fit residues: 15.5151 Evaluate side-chains 172 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.0570 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 74 optimal weight: 0.0670 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 68 optimal weight: 0.0030 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 overall best weight: 0.2646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.126792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114643 restraints weight = 10317.255| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.33 r_work: 0.3342 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6635 Z= 0.149 Angle : 0.616 9.449 9020 Z= 0.309 Chirality : 0.043 0.283 941 Planarity : 0.004 0.041 1169 Dihedral : 4.017 22.414 864 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.73 % Allowed : 19.42 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.30), residues: 788 helix: 1.96 (0.28), residues: 366 sheet: 0.27 (0.80), residues: 51 loop : -1.51 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.021 0.001 TYR A 385 PHE 0.019 0.001 PHE A 142 TRP 0.017 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 6625) covalent geometry : angle 0.61390 / 0.31 ( 9003) SS BOND : bond 0.00190 / 0.10 ( 7) SS BOND : angle 1.44178 / 0.67 ( 14) hydrogen bonds : bond 0.05386 / 3.49 ( 294) hydrogen bonds : angle 3.92949 / 2.76 ( 843) metal coordination : bond 0.00404 / 0.21 ( 2) link_NAG-ASN : bond 0.00315 / 0.17 ( 1) link_NAG-ASN : angle 1.28234 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8245 (m-40) cc_final: 0.8040 (m-40) REVERT: A 75 GLU cc_start: 0.8088 (tp30) cc_final: 0.7643 (tp30) REVERT: A 77 SER cc_start: 0.8424 (t) cc_final: 0.8126 (m) REVERT: A 87 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7886 (mp0) REVERT: A 113 ASN cc_start: 0.8722 (t0) cc_final: 0.8472 (t0) REVERT: A 123 MET cc_start: 0.8197 (ttp) cc_final: 0.7894 (ttm) REVERT: A 126 ILE cc_start: 0.9067 (tp) cc_final: 0.8696 (tt) REVERT: A 151 ILE cc_start: 0.6768 (tp) cc_final: 0.6304 (tp) REVERT: A 155 SER cc_start: 0.8919 (t) cc_final: 0.8185 (m) REVERT: A 181 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: A 213 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 225 ASP cc_start: 0.7588 (m-30) cc_final: 0.7236 (m-30) REVERT: A 250 GLU cc_start: 0.8233 (tp30) cc_final: 0.7755 (tm-30) REVERT: A 267 LEU cc_start: 0.8581 (mt) cc_final: 0.8376 (mm) REVERT: A 313 LYS cc_start: 0.8110 (tttt) cc_final: 0.7705 (tttt) REVERT: A 347 THR cc_start: 0.8471 (m) cc_final: 0.7991 (p) REVERT: A 358 ILE cc_start: 0.8762 (mt) cc_final: 0.8424 (tt) REVERT: A 517 THR cc_start: 0.7606 (p) cc_final: 0.7299 (p) REVERT: A 557 MET cc_start: 0.8497 (tmm) cc_final: 0.8048 (ttp) REVERT: B 357 ARG cc_start: 0.7272 (ptm-80) cc_final: 0.6884 (ptm-80) REVERT: B 501 TYR cc_start: 0.8322 (m-10) cc_final: 0.7964 (m-80) outliers start: 12 outliers final: 10 residues processed: 171 average time/residue: 0.0636 time to fit residues: 14.5377 Evaluate side-chains 176 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.0670 chunk 36 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 60 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 73 optimal weight: 0.5980 chunk 43 optimal weight: 0.0970 overall best weight: 0.0872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118156 restraints weight = 9993.943| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.29 r_work: 0.3407 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6635 Z= 0.111 Angle : 0.585 9.507 9020 Z= 0.291 Chirality : 0.042 0.285 941 Planarity : 0.004 0.041 1169 Dihedral : 3.783 23.568 864 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.73 % Allowed : 19.14 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.30), residues: 788 helix: 2.07 (0.28), residues: 366 sheet: 1.35 (0.89), residues: 41 loop : -1.54 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.019 0.001 TYR A 385 PHE 0.014 0.001 PHE B 456 TRP 0.019 0.001 TRP A 165 HIS 0.002 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6625) covalent geometry : angle 0.58357 / 0.29 ( 9003) SS BOND : bond 0.00127 / 0.08 ( 7) SS BOND : angle 1.06149 / 0.48 ( 14) hydrogen bonds : bond 0.03996 / 2.55 ( 294) hydrogen bonds : angle 3.77986 / 2.65 ( 843) metal coordination : bond 0.00189 / 0.10 ( 2) link_NAG-ASN : bond 0.00368 / 0.19 ( 1) link_NAG-ASN : angle 1.25793 / 0.66 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8217 (m-40) cc_final: 0.7998 (m-40) REVERT: A 75 GLU cc_start: 0.8063 (tp30) cc_final: 0.7628 (tp30) REVERT: A 77 SER cc_start: 0.8392 (t) cc_final: 0.8087 (m) REVERT: A 87 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7887 (mp0) REVERT: A 123 MET cc_start: 0.8101 (ttp) cc_final: 0.7844 (ttm) REVERT: A 126 ILE cc_start: 0.9033 (tp) cc_final: 0.8651 (tt) REVERT: A 155 SER cc_start: 0.8919 (t) cc_final: 0.8238 (m) REVERT: A 179 LEU cc_start: 0.8516 (mt) cc_final: 0.8284 (mp) REVERT: A 181 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: A 213 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 225 ASP cc_start: 0.7539 (m-30) cc_final: 0.7198 (m-30) REVERT: A 250 GLU cc_start: 0.8092 (tp30) cc_final: 0.7644 (tm-30) REVERT: A 269 ASP cc_start: 0.8094 (t0) cc_final: 0.7875 (t0) REVERT: A 297 MET cc_start: 0.8128 (mtt) cc_final: 0.7919 (mtm) REVERT: A 313 LYS cc_start: 0.8081 (tttt) cc_final: 0.7569 (ttmm) REVERT: A 347 THR cc_start: 0.8433 (m) cc_final: 0.7839 (p) REVERT: A 358 ILE cc_start: 0.8748 (mt) cc_final: 0.8389 (tt) REVERT: A 369 PHE cc_start: 0.6247 (t80) cc_final: 0.5376 (t80) REVERT: A 557 MET cc_start: 0.8447 (tmm) cc_final: 0.7971 (ttp) REVERT: A 562 ASN cc_start: 0.7954 (t0) cc_final: 0.7741 (t0) REVERT: A 598 GLN cc_start: 0.8245 (tp40) cc_final: 0.7959 (tp40) REVERT: B 357 ARG cc_start: 0.7235 (ptm-80) cc_final: 0.6781 (ptm-80) REVERT: B 394 ASN cc_start: 0.7742 (m-40) cc_final: 0.7350 (m-40) REVERT: B 501 TYR cc_start: 0.8247 (m-10) cc_final: 0.7867 (m-80) outliers start: 12 outliers final: 11 residues processed: 166 average time/residue: 0.0610 time to fit residues: 13.4665 Evaluate side-chains 180 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.6980 chunk 45 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 64 optimal weight: 0.0010 chunk 74 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 0.0470 overall best weight: 0.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.130066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117869 restraints weight = 10043.453| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.29 r_work: 0.3406 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6635 Z= 0.113 Angle : 0.592 9.562 9020 Z= 0.293 Chirality : 0.042 0.293 941 Planarity : 0.004 0.040 1169 Dihedral : 3.719 21.946 864 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.73 % Allowed : 19.57 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.31), residues: 788 helix: 2.08 (0.28), residues: 367 sheet: 1.30 (0.89), residues: 41 loop : -1.48 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 466 TYR 0.019 0.001 TYR A 385 PHE 0.014 0.001 PHE B 456 TRP 0.018 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6625) covalent geometry : angle 0.59099 / 0.29 ( 9003) SS BOND : bond 0.00128 / 0.07 ( 7) SS BOND : angle 0.98112 / 0.44 ( 14) hydrogen bonds : bond 0.04069 / 2.60 ( 294) hydrogen bonds : angle 3.74837 / 2.63 ( 843) metal coordination : bond 0.00186 / 0.10 ( 2) link_NAG-ASN : bond 0.00365 / 0.19 ( 1) link_NAG-ASN : angle 1.30596 / 0.69 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1686.29 seconds wall clock time: 29 minutes 28.82 seconds (1768.82 seconds total)