Starting phenix.real_space_refine on Sun Jul 27 05:36:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gry_34217/07_2025/8gry_34217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gry_34217/07_2025/8gry_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_2025/8gry_34217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gry_34217/07_2025/8gry_34217.map" model { file = "/net/cci-nas-00/data/ceres_data/8gry_34217/07_2025/8gry_34217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gry_34217/07_2025/8gry_34217.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.70, per 1000 atoms: 1.04 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: 1.49 Conformation dependent library (CDL) restraints added in 956.4 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: 0.70 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: 1.79 Time building geometry restraints manager: 1.83 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 - 19.39: 3544 19.39 - 38.78: 310 38.78 - 58.17: 55 58.17 - 77.56: 11 77.56 - 96.95: 18 Dihedral angle restraints: 3938 sinusoidal: 1609 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 3935 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: 416.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.360 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 442.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 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 : 16.151 96.951 2421 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.11 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 (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: 0.44 (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 TRP 0.022 0.002 TRP A 165 HIS 0.004 0.001 HIS A 401 PHE 0.009 0.001 PHE A 592 TYR 0.015 0.001 TYR A 385 ARG 0.004 0.000 ARG A 340 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 1) link_NAG-ASN : angle 1.62800 ( 3) hydrogen bonds : bond 0.13587 ( 294) hydrogen bonds : angle 5.51249 ( 843) metal coordination : bond 0.20094 ( 2) SS BOND : bond 0.00096 ( 7) SS BOND : angle 0.63690 ( 14) covalent geometry : bond 0.00253 ( 6625) covalent geometry : angle 0.57822 ( 9003) *********************** 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 : 0.640 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: 0.6569 (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: 0.7491 (tpp) cc_final: 0.7275 (ttp) REVERT: A 475 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7691 (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: 0.7313 (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: 0.6160 (ptm-80) REVERT: B 469 SER cc_start: 0.8276 (t) cc_final: 0.8068 (t) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2052 time to fit residues: 54.8103 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 : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 chunk 37 optimal weight: 0.0770 chunk 45 optimal weight: 0.0980 chunk 70 optimal weight: 0.0470 overall best weight: 0.0650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 81 GLN ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN B 422 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122909 restraints weight = 10115.385| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.48 r_work: 0.3475 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6635 Z= 0.107 Angle : 0.554 9.725 9020 Z= 0.275 Chirality : 0.041 0.212 941 Planarity : 0.004 0.053 1169 Dihedral : 5.341 56.725 885 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.44 % Allowed : 8.78 % Favored : 89.78 % 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: 0.86 (0.31), residues: 788 helix: 2.02 (0.28), residues: 372 sheet: 1.87 (0.94), residues: 39 loop : -1.14 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.003 0.001 HIS A 401 PHE 0.010 0.001 PHE A 592 TYR 0.020 0.001 TYR A 385 ARG 0.003 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 1) link_NAG-ASN : angle 2.40512 ( 3) hydrogen bonds : bond 0.04138 ( 294) hydrogen bonds : angle 3.85354 ( 843) metal coordination : bond 0.00224 ( 2) SS BOND : bond 0.00151 ( 7) SS BOND : angle 1.03317 ( 14) covalent geometry : bond 0.00224 ( 6625) covalent geometry : angle 0.55142 ( 9003) *********************** 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 191 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7798 (tp30) cc_final: 0.7389 (tp30) REVERT: A 126 ILE cc_start: 0.8878 (tp) cc_final: 0.8545 (tt) REVERT: A 150 GLU cc_start: 0.6816 (pp20) cc_final: 0.6588 (tm-30) REVERT: A 181 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: A 182 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 197 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6795 (tm-30) REVERT: A 206 ASP cc_start: 0.8135 (t0) cc_final: 0.7858 (t0) REVERT: A 313 LYS cc_start: 0.7896 (tttt) cc_final: 0.7540 (ttmm) REVERT: A 341 LYS cc_start: 0.7952 (mttp) cc_final: 0.7668 (mttp) REVERT: A 347 THR cc_start: 0.8285 (m) cc_final: 0.7976 (p) REVERT: A 472 GLN cc_start: 0.8012 (mp10) cc_final: 0.7730 (mp10) REVERT: A 475 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7969 (ttpt) REVERT: A 476 LYS cc_start: 0.8085 (tppt) cc_final: 0.7850 (tppp) REVERT: A 482 ARG cc_start: 0.7672 (ttm170) cc_final: 0.7317 (ttm-80) REVERT: A 517 THR cc_start: 0.7286 (p) cc_final: 0.6900 (p) REVERT: A 557 MET cc_start: 0.8301 (tmm) cc_final: 0.7965 (ttp) REVERT: A 562 ASN cc_start: 0.7643 (t0) cc_final: 0.7230 (t0) REVERT: A 574 VAL cc_start: 0.8335 (m) cc_final: 0.8124 (p) REVERT: B 336 CYS cc_start: 0.5510 (m) cc_final: 0.4954 (m) REVERT: B 357 ARG cc_start: 0.6979 (ptm-80) cc_final: 0.6629 (ptm-80) REVERT: B 469 SER cc_start: 0.8513 (t) cc_final: 0.8138 (t) REVERT: B 515 PHE cc_start: 0.7943 (m-80) cc_final: 0.7722 (m-80) outliers start: 10 outliers final: 5 residues processed: 184 average time/residue: 0.1976 time to fit residues: 46.4558 Evaluate side-chains 175 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 231 LYS 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 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 0 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 64 optimal weight: 0.0570 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3687 r_free = 0.3687 target = 0.129396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116633 restraints weight = 10075.929| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.46 r_work: 0.3380 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2506 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= 0.147 Angle : 0.565 9.960 9020 Z= 0.288 Chirality : 0.043 0.260 941 Planarity : 0.004 0.048 1169 Dihedral : 5.177 54.593 885 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.44 % Allowed : 12.66 % Favored : 85.90 % 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: 0.76 (0.31), residues: 788 helix: 2.04 (0.28), residues: 367 sheet: 0.77 (0.86), residues: 49 loop : -1.18 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.006 0.001 HIS A 374 PHE 0.014 0.001 PHE A 592 TYR 0.020 0.001 TYR A 385 ARG 0.004 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 1) link_NAG-ASN : angle 1.55616 ( 3) hydrogen bonds : bond 0.05615 ( 294) hydrogen bonds : angle 3.94305 ( 843) metal coordination : bond 0.00384 ( 2) SS BOND : bond 0.00371 ( 7) SS BOND : angle 1.17095 ( 14) covalent geometry : bond 0.00330 ( 6625) covalent geometry : angle 0.56305 ( 9003) *********************** 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 196 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7837 (tp30) cc_final: 0.7410 (tp30) REVERT: A 77 SER cc_start: 0.8343 (t) cc_final: 0.8073 (m) REVERT: A 126 ILE cc_start: 0.9011 (tp) cc_final: 0.8648 (tt) REVERT: A 181 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: A 182 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7848 (pp20) REVERT: A 206 ASP cc_start: 0.8099 (t0) cc_final: 0.7812 (t0) REVERT: A 213 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7307 (mm-30) REVERT: A 225 ASP cc_start: 0.7155 (m-30) cc_final: 0.6799 (m-30) REVERT: A 250 GLU cc_start: 0.8232 (tp30) cc_final: 0.8017 (tp30) REVERT: A 347 THR cc_start: 0.8414 (m) cc_final: 0.7930 (p) REVERT: A 462 MET cc_start: 0.8449 (mtp) cc_final: 0.8190 (mtm) REVERT: A 475 LYS cc_start: 0.8346 (ttpt) cc_final: 0.8125 (ttpt) REVERT: A 482 ARG cc_start: 0.7909 (ttm170) cc_final: 0.7607 (ttm-80) REVERT: A 517 THR cc_start: 0.7481 (p) cc_final: 0.7254 (p) REVERT: A 557 MET cc_start: 0.8365 (tmm) cc_final: 0.7998 (ttp) REVERT: A 562 ASN cc_start: 0.7792 (t0) cc_final: 0.7407 (t0) REVERT: A 610 TRP cc_start: 0.8424 (t60) cc_final: 0.8057 (t60) REVERT: B 357 ARG cc_start: 0.7041 (ptm-80) cc_final: 0.6664 (ptm-80) REVERT: B 393 THR cc_start: 0.7092 (m) cc_final: 0.6747 (p) REVERT: B 469 SER cc_start: 0.8515 (t) cc_final: 0.8227 (t) outliers start: 10 outliers final: 8 residues processed: 190 average time/residue: 0.2761 time to fit residues: 66.2296 Evaluate side-chains 192 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 148 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 363 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 5 optimal weight: 0.1980 chunk 19 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.0170 chunk 76 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 77 optimal weight: 0.0980 chunk 8 optimal weight: 0.0870 overall best weight: 0.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3706 r_free = 0.3706 target = 0.129225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116546 restraints weight = 10208.582| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.46 r_work: 0.3444 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6635 Z= 0.109 Angle : 0.551 9.639 9020 Z= 0.274 Chirality : 0.041 0.232 941 Planarity : 0.004 0.065 1169 Dihedral : 5.103 55.404 885 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.44 % Allowed : 15.68 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.31), residues: 788 helix: 2.07 (0.28), residues: 365 sheet: 0.53 (0.83), residues: 51 loop : -1.16 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.002 0.001 HIS A 373 PHE 0.009 0.001 PHE A 369 TYR 0.025 0.001 TYR A 158 ARG 0.004 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 1) link_NAG-ASN : angle 1.55816 ( 3) hydrogen bonds : bond 0.04216 ( 294) hydrogen bonds : angle 3.82779 ( 843) metal coordination : bond 0.00184 ( 2) SS BOND : bond 0.00157 ( 7) SS BOND : angle 1.11522 ( 14) covalent geometry : bond 0.00236 ( 6625) covalent geometry : angle 0.54865 ( 9003) *********************** 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 181 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7813 (tp30) cc_final: 0.7398 (tp30) REVERT: A 77 SER cc_start: 0.8345 (t) cc_final: 0.8060 (m) REVERT: A 126 ILE cc_start: 0.8980 (tp) cc_final: 0.8598 (tt) REVERT: A 151 ILE cc_start: 0.5978 (tp) cc_final: 0.5581 (tp) REVERT: A 160 ARG cc_start: 0.7185 (ttp80) cc_final: 0.6625 (ttt90) REVERT: A 182 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7834 (pp20) REVERT: A 206 ASP cc_start: 0.8181 (t0) cc_final: 0.7912 (t0) REVERT: A 213 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 225 ASP cc_start: 0.7139 (m-30) cc_final: 0.6821 (m-30) REVERT: A 250 GLU cc_start: 0.8168 (tp30) cc_final: 0.7882 (tm-30) REVERT: A 462 MET cc_start: 0.8398 (mtp) cc_final: 0.8142 (mtm) REVERT: A 475 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7996 (ttpt) REVERT: A 482 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7547 (ttm-80) REVERT: A 517 THR cc_start: 0.7329 (p) cc_final: 0.6950 (p) REVERT: A 557 MET cc_start: 0.8318 (tmm) cc_final: 0.7908 (ttp) REVERT: A 610 TRP cc_start: 0.8327 (t60) cc_final: 0.7906 (t60) REVERT: B 350 VAL cc_start: 0.8309 (t) cc_final: 0.7173 (m) REVERT: B 357 ARG cc_start: 0.6975 (ptm-80) cc_final: 0.6603 (ptm-80) REVERT: B 393 THR cc_start: 0.7076 (m) cc_final: 0.6712 (p) REVERT: B 469 SER cc_start: 0.8536 (t) cc_final: 0.8305 (t) outliers start: 10 outliers final: 9 residues processed: 175 average time/residue: 0.2957 time to fit residues: 67.6204 Evaluate side-chains 182 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 543 ASP 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 67 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 70 optimal weight: 0.0050 chunk 60 optimal weight: 0.0870 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 59 optimal weight: 0.0170 overall best weight: 0.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117792 restraints weight = 10042.631| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.32 r_work: 0.3403 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2949 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= 0.125 Angle : 0.556 9.619 9020 Z= 0.278 Chirality : 0.042 0.241 941 Planarity : 0.004 0.052 1169 Dihedral : 4.598 55.520 885 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.16 % Allowed : 15.83 % 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 (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: 0.68 (0.31), residues: 788 helix: 2.04 (0.28), residues: 366 sheet: 0.69 (0.85), residues: 49 loop : -1.28 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.011 0.001 PHE A 592 TYR 0.022 0.001 TYR A 158 ARG 0.002 0.000 ARG A 470 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 1) link_NAG-ASN : angle 1.78352 ( 3) hydrogen bonds : bond 0.04943 ( 294) hydrogen bonds : angle 3.84420 ( 843) metal coordination : bond 0.00320 ( 2) SS BOND : bond 0.00283 ( 7) SS BOND : angle 1.00487 ( 14) covalent geometry : bond 0.00280 ( 6625) covalent geometry : angle 0.55456 ( 9003) *********************** 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 191 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8094 (tp30) cc_final: 0.7643 (tp30) REVERT: A 77 SER cc_start: 0.8469 (t) cc_final: 0.8197 (m) REVERT: A 126 ILE cc_start: 0.9063 (tp) cc_final: 0.8693 (tt) REVERT: A 151 ILE cc_start: 0.6145 (tp) cc_final: 0.5776 (tp) REVERT: A 160 ARG cc_start: 0.7460 (ttp80) cc_final: 0.6910 (ttt90) REVERT: A 182 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7970 (pp20) REVERT: A 206 ASP cc_start: 0.8331 (t0) cc_final: 0.7972 (t0) REVERT: A 213 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 225 ASP cc_start: 0.7427 (m-30) cc_final: 0.7063 (m-30) REVERT: A 250 GLU cc_start: 0.8403 (tp30) cc_final: 0.8039 (tm-30) REVERT: A 358 ILE cc_start: 0.8696 (mt) cc_final: 0.8323 (tt) REVERT: A 475 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8197 (ttpt) REVERT: A 482 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7907 (ttm-80) REVERT: A 509 ASP cc_start: 0.8665 (t0) cc_final: 0.8427 (t70) REVERT: A 517 THR cc_start: 0.7578 (p) cc_final: 0.7284 (p) REVERT: A 557 MET cc_start: 0.8482 (tmm) cc_final: 0.8074 (ttp) REVERT: A 610 TRP cc_start: 0.8464 (t60) cc_final: 0.7985 (t60) REVERT: B 357 ARG cc_start: 0.7255 (ptm-80) cc_final: 0.7039 (ptm-80) REVERT: B 466 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8106 (mtp85) REVERT: B 469 SER cc_start: 0.8575 (t) cc_final: 0.8311 (t) REVERT: B 501 TYR cc_start: 0.8212 (m-10) cc_final: 0.7824 (m-80) outliers start: 15 outliers final: 11 residues processed: 184 average time/residue: 0.2275 time to fit residues: 53.8187 Evaluate side-chains 184 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 148 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.0040 chunk 72 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 overall best weight: 0.2890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112124 restraints weight = 10002.643| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.39 r_work: 0.3362 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6635 Z= 0.154 Angle : 0.587 9.677 9020 Z= 0.295 Chirality : 0.043 0.243 941 Planarity : 0.004 0.047 1169 Dihedral : 4.704 55.537 885 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.87 % Allowed : 16.69 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.30), residues: 788 helix: 2.01 (0.28), residues: 366 sheet: 0.66 (0.85), residues: 49 loop : -1.35 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.013 0.001 PHE A 592 TYR 0.019 0.001 TYR A 158 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 1) link_NAG-ASN : angle 1.49875 ( 3) hydrogen bonds : bond 0.05515 ( 294) hydrogen bonds : angle 3.99192 ( 843) metal coordination : bond 0.00439 ( 2) SS BOND : bond 0.00229 ( 7) SS BOND : angle 1.71965 ( 14) covalent geometry : bond 0.00349 ( 6625) covalent geometry : angle 0.58325 ( 9003) *********************** 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 186 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8108 (tp30) cc_final: 0.7658 (tp30) REVERT: A 77 SER cc_start: 0.8500 (t) cc_final: 0.8257 (m) REVERT: A 87 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7792 (tp30) REVERT: A 126 ILE cc_start: 0.9082 (tp) cc_final: 0.8702 (tt) REVERT: A 151 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.6047 (tp) REVERT: A 182 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8053 (pp20) REVERT: A 206 ASP cc_start: 0.8375 (t0) cc_final: 0.7971 (t0) REVERT: A 213 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 225 ASP cc_start: 0.7472 (m-30) cc_final: 0.7098 (m-30) REVERT: A 250 GLU cc_start: 0.8380 (tp30) cc_final: 0.8055 (tm-30) REVERT: A 257 SER cc_start: 0.8572 (p) cc_final: 0.8130 (p) REVERT: A 313 LYS cc_start: 0.8077 (tttm) cc_final: 0.7669 (ttmm) REVERT: A 347 THR cc_start: 0.8451 (m) cc_final: 0.8055 (p) REVERT: A 358 ILE cc_start: 0.8721 (mt) cc_final: 0.8370 (tt) REVERT: A 476 LYS cc_start: 0.8374 (tppt) cc_final: 0.8137 (tppp) REVERT: A 482 ARG cc_start: 0.8199 (ttm170) cc_final: 0.7986 (ttm-80) REVERT: A 509 ASP cc_start: 0.8708 (t0) cc_final: 0.8482 (t70) REVERT: A 517 THR cc_start: 0.7670 (p) cc_final: 0.7446 (p) REVERT: A 557 MET cc_start: 0.8521 (tmm) cc_final: 0.8112 (ttp) REVERT: A 610 TRP cc_start: 0.8509 (t60) cc_final: 0.8095 (t60) REVERT: B 357 ARG cc_start: 0.7285 (ptm-80) cc_final: 0.6907 (ptm-80) REVERT: B 466 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8261 (mtp85) REVERT: B 469 SER cc_start: 0.8703 (t) cc_final: 0.8485 (t) REVERT: B 501 TYR cc_start: 0.8283 (m-10) cc_final: 0.7898 (m-80) outliers start: 13 outliers final: 10 residues processed: 176 average time/residue: 0.1948 time to fit residues: 44.4578 Evaluate side-chains 181 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 0.0010 chunk 59 optimal weight: 0.0040 chunk 74 optimal weight: 0.0570 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 overall best weight: 0.1716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3666 r_free = 0.3666 target = 0.126218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113799 restraints weight = 10053.219| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.40 r_work: 0.3394 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6635 Z= 0.119 Angle : 0.572 9.646 9020 Z= 0.282 Chirality : 0.042 0.235 941 Planarity : 0.004 0.039 1169 Dihedral : 4.556 55.302 885 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.01 % Allowed : 17.12 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.30), residues: 788 helix: 2.01 (0.28), residues: 367 sheet: 0.56 (0.84), residues: 49 loop : -1.35 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.009 0.001 PHE A 452 TYR 0.017 0.001 TYR A 158 ARG 0.006 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 1) link_NAG-ASN : angle 1.52569 ( 3) hydrogen bonds : bond 0.04634 ( 294) hydrogen bonds : angle 3.89602 ( 843) metal coordination : bond 0.00294 ( 2) SS BOND : bond 0.00146 ( 7) SS BOND : angle 1.50380 ( 14) covalent geometry : bond 0.00267 ( 6625) covalent geometry : angle 0.56921 ( 9003) *********************** 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 179 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8090 (tp30) cc_final: 0.7651 (tp30) REVERT: A 77 SER cc_start: 0.8490 (t) cc_final: 0.8207 (m) REVERT: A 87 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7759 (tp30) REVERT: A 126 ILE cc_start: 0.9022 (tp) cc_final: 0.8642 (tt) REVERT: A 181 GLU cc_start: 0.8259 (tt0) cc_final: 0.7968 (mm-30) REVERT: A 182 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8009 (pp20) REVERT: A 206 ASP cc_start: 0.8426 (t0) cc_final: 0.8088 (t0) REVERT: A 213 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 225 ASP cc_start: 0.7408 (m-30) cc_final: 0.7039 (m-30) REVERT: A 250 GLU cc_start: 0.8343 (tp30) cc_final: 0.7965 (tm-30) REVERT: A 313 LYS cc_start: 0.8062 (tttm) cc_final: 0.7653 (ttmm) REVERT: A 358 ILE cc_start: 0.8702 (mt) cc_final: 0.8361 (tt) REVERT: A 482 ARG cc_start: 0.8175 (ttm170) cc_final: 0.7972 (ttm-80) REVERT: A 509 ASP cc_start: 0.8718 (t0) cc_final: 0.8492 (t70) REVERT: A 557 MET cc_start: 0.8474 (tmm) cc_final: 0.8074 (ttp) REVERT: B 357 ARG cc_start: 0.7246 (ptm-80) cc_final: 0.6859 (ptm-80) REVERT: B 501 TYR cc_start: 0.8276 (m-10) cc_final: 0.7894 (m-80) outliers start: 14 outliers final: 10 residues processed: 171 average time/residue: 0.2020 time to fit residues: 45.3315 Evaluate side-chains 171 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 MET 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 15 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 0.0070 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.0770 chunk 45 optimal weight: 0.2980 chunk 36 optimal weight: 0.0770 chunk 54 optimal weight: 0.5980 overall best weight: 0.1714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3667 r_free = 0.3667 target = 0.126323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113959 restraints weight = 10068.430| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.41 r_work: 0.3389 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6635 Z= 0.121 Angle : 0.577 9.641 9020 Z= 0.286 Chirality : 0.042 0.236 941 Planarity : 0.004 0.039 1169 Dihedral : 4.543 55.403 885 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.73 % Allowed : 17.27 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.30), residues: 788 helix: 2.01 (0.28), residues: 367 sheet: 0.52 (0.84), residues: 49 loop : -1.33 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 PHE 0.016 0.001 PHE A 142 TYR 0.017 0.001 TYR A 385 ARG 0.010 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 1) link_NAG-ASN : angle 1.42828 ( 3) hydrogen bonds : bond 0.04683 ( 294) hydrogen bonds : angle 3.84051 ( 843) metal coordination : bond 0.00282 ( 2) SS BOND : bond 0.00130 ( 7) SS BOND : angle 1.36847 ( 14) covalent geometry : bond 0.00273 ( 6625) covalent geometry : angle 0.57394 ( 9003) *********************** 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 175 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8242 (m-40) cc_final: 0.8000 (m-40) REVERT: A 75 GLU cc_start: 0.8107 (tp30) cc_final: 0.7664 (tp30) REVERT: A 77 SER cc_start: 0.8495 (t) cc_final: 0.8237 (m) REVERT: A 87 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7796 (tp30) REVERT: A 126 ILE cc_start: 0.9038 (tp) cc_final: 0.8798 (tp) REVERT: A 181 GLU cc_start: 0.8256 (tt0) cc_final: 0.7953 (mm-30) REVERT: A 182 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8005 (pp20) REVERT: A 206 ASP cc_start: 0.8413 (t0) cc_final: 0.8056 (t0) REVERT: A 213 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 225 ASP cc_start: 0.7440 (m-30) cc_final: 0.7102 (m-30) REVERT: A 250 GLU cc_start: 0.8315 (tp30) cc_final: 0.7911 (tm-30) REVERT: A 313 LYS cc_start: 0.8072 (tttm) cc_final: 0.7663 (ttmm) REVERT: A 358 ILE cc_start: 0.8714 (mt) cc_final: 0.8401 (tt) REVERT: A 482 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7995 (ttm-80) REVERT: A 509 ASP cc_start: 0.8706 (t0) cc_final: 0.8465 (t70) REVERT: A 557 MET cc_start: 0.8491 (tmm) cc_final: 0.8026 (ttp) REVERT: B 501 TYR cc_start: 0.8267 (m-10) cc_final: 0.7898 (m-80) outliers start: 12 outliers final: 9 residues processed: 168 average time/residue: 0.2303 time to fit residues: 51.2294 Evaluate side-chains 170 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.0670 chunk 73 optimal weight: 0.0010 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.0870 chunk 5 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.0040 chunk 4 optimal weight: 0.2980 chunk 45 optimal weight: 0.2980 chunk 57 optimal weight: 0.4980 overall best weight: 0.0714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3733 r_free = 0.3733 target = 0.132576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119992 restraints weight = 10113.817| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.49 r_work: 0.3431 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3458 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= 0.107 Angle : 0.577 9.602 9020 Z= 0.284 Chirality : 0.041 0.229 941 Planarity : 0.004 0.084 1169 Dihedral : 4.384 55.316 885 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.29 % Allowed : 18.13 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.70 (0.31), residues: 788 helix: 2.08 (0.28), residues: 367 sheet: 0.57 (0.83), residues: 49 loop : -1.29 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.002 0.001 HIS A 265 PHE 0.013 0.001 PHE B 456 TYR 0.017 0.001 TYR A 385 ARG 0.008 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 1) link_NAG-ASN : angle 1.43615 ( 3) hydrogen bonds : bond 0.03810 ( 294) hydrogen bonds : angle 3.76208 ( 843) metal coordination : bond 0.00126 ( 2) SS BOND : bond 0.00086 ( 7) SS BOND : angle 0.98631 ( 14) covalent geometry : bond 0.00236 ( 6625) covalent geometry : angle 0.57556 ( 9003) *********************** 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 170 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8109 (m-40) cc_final: 0.7838 (m-40) REVERT: A 75 GLU cc_start: 0.7818 (tp30) cc_final: 0.7400 (tp30) REVERT: A 77 SER cc_start: 0.8412 (t) cc_final: 0.8109 (m) REVERT: A 87 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7584 (tp30) REVERT: A 126 ILE cc_start: 0.8931 (tp) cc_final: 0.8695 (tp) REVERT: A 165 TRP cc_start: 0.7622 (t60) cc_final: 0.7281 (t60) REVERT: A 179 LEU cc_start: 0.8461 (mt) cc_final: 0.8232 (mp) REVERT: A 181 GLU cc_start: 0.7987 (tt0) cc_final: 0.7712 (mm-30) REVERT: A 182 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 206 ASP cc_start: 0.8192 (t0) cc_final: 0.7863 (t0) REVERT: A 213 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 250 GLU cc_start: 0.8033 (tp30) cc_final: 0.7589 (tm-30) REVERT: A 313 LYS cc_start: 0.7969 (tttm) cc_final: 0.7564 (ttmm) REVERT: A 341 LYS cc_start: 0.7913 (mttp) cc_final: 0.7662 (mttm) REVERT: A 347 THR cc_start: 0.8332 (m) cc_final: 0.7879 (p) REVERT: A 482 ARG cc_start: 0.8034 (ttm170) cc_final: 0.7818 (ttm-80) REVERT: A 509 ASP cc_start: 0.8520 (t0) cc_final: 0.8269 (t70) REVERT: A 557 MET cc_start: 0.8273 (tmm) cc_final: 0.7821 (ttp) REVERT: B 501 TYR cc_start: 0.8058 (m-10) cc_final: 0.7706 (m-80) outliers start: 9 outliers final: 6 residues processed: 165 average time/residue: 0.1963 time to fit residues: 42.5782 Evaluate side-chains 163 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.3980 chunk 67 optimal weight: 0.0970 chunk 68 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 43 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 overall best weight: 0.1174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115986 restraints weight = 10169.990| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.43 r_work: 0.3416 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6635 Z= 0.113 Angle : 0.586 9.605 9020 Z= 0.290 Chirality : 0.042 0.232 941 Planarity : 0.005 0.086 1169 Dihedral : 4.411 55.487 885 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.01 % Allowed : 19.42 % Favored : 79.57 % 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: 0.68 (0.30), residues: 788 helix: 2.04 (0.28), residues: 367 sheet: 0.54 (0.82), residues: 49 loop : -1.27 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 265 PHE 0.020 0.001 PHE A 142 TYR 0.022 0.001 TYR B 473 ARG 0.008 0.001 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 1) link_NAG-ASN : angle 1.39085 ( 3) hydrogen bonds : bond 0.04087 ( 294) hydrogen bonds : angle 3.77772 ( 843) metal coordination : bond 0.00205 ( 2) SS BOND : bond 0.00112 ( 7) SS BOND : angle 0.96230 ( 14) covalent geometry : bond 0.00252 ( 6625) covalent geometry : angle 0.58500 ( 9003) ********************** 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 162 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8243 (m-40) cc_final: 0.7984 (m-40) REVERT: A 75 GLU cc_start: 0.8090 (tp30) cc_final: 0.7659 (tp30) REVERT: A 77 SER cc_start: 0.8505 (t) cc_final: 0.8225 (m) REVERT: A 87 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7765 (tp30) REVERT: A 126 ILE cc_start: 0.9025 (tp) cc_final: 0.8796 (tp) REVERT: A 165 TRP cc_start: 0.7671 (t60) cc_final: 0.7296 (t60) REVERT: A 179 LEU cc_start: 0.8605 (mt) cc_final: 0.8394 (mp) REVERT: A 181 GLU cc_start: 0.8256 (tt0) cc_final: 0.7974 (mm-30) REVERT: A 182 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8103 (tp30) REVERT: A 206 ASP cc_start: 0.8423 (t0) cc_final: 0.8070 (t0) REVERT: A 213 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7585 (mm-30) REVERT: A 250 GLU cc_start: 0.8277 (tp30) cc_final: 0.7781 (tm-30) REVERT: A 297 MET cc_start: 0.8186 (mtt) cc_final: 0.7953 (mtm) REVERT: A 313 LYS cc_start: 0.8063 (tttm) cc_final: 0.7658 (ttmm) REVERT: A 341 LYS cc_start: 0.7983 (mttp) cc_final: 0.7735 (mttm) REVERT: A 347 THR cc_start: 0.8447 (m) cc_final: 0.8025 (p) REVERT: A 482 ARG cc_start: 0.8242 (ttm170) cc_final: 0.8039 (ttm-80) REVERT: A 509 ASP cc_start: 0.8643 (t0) cc_final: 0.8416 (t70) REVERT: A 557 MET cc_start: 0.8458 (tmm) cc_final: 0.7990 (ttp) REVERT: B 350 VAL cc_start: 0.8221 (t) cc_final: 0.7030 (m) REVERT: B 501 TYR cc_start: 0.8208 (m-10) cc_final: 0.7856 (m-80) outliers start: 7 outliers final: 7 residues processed: 157 average time/residue: 0.2733 time to fit residues: 56.7611 Evaluate side-chains 161 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 394 ASN 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 46 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 chunk 77 optimal weight: 0.0970 chunk 22 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 overall best weight: 0.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** 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 = 0.3692 r_free = 0.3692 target = 0.128365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115874 restraints weight = 10315.885| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.46 r_work: 0.3420 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 6635 Z= 0.197 Angle : 1.059 59.199 9020 Z= 0.615 Chirality : 0.042 0.232 941 Planarity : 0.004 0.078 1169 Dihedral : 4.417 55.486 885 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.01 % Allowed : 19.28 % Favored : 79.71 % Cbeta Deviations : 0.13 % 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: 0.68 (0.30), residues: 788 helix: 2.04 (0.28), residues: 367 sheet: 0.49 (0.81), residues: 49 loop : -1.27 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS A 265 PHE 0.016 0.001 PHE B 456 TYR 0.018 0.001 TYR B 473 ARG 0.011 0.001 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 1) link_NAG-ASN : angle 1.39120 ( 3) hydrogen bonds : bond 0.04142 ( 294) hydrogen bonds : angle 3.78692 ( 843) metal coordination : bond 0.00193 ( 2) SS BOND : bond 0.00110 ( 7) SS BOND : angle 0.94263 ( 14) covalent geometry : bond 0.00373 ( 6625) covalent geometry : angle 1.05880 ( 9003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5313.61 seconds wall clock time: 97 minutes 7.30 seconds (5827.30 seconds total)