Starting phenix.real_space_refine on Sat Aug 23 02:12:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gry_34217/08_2025/8gry_34217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gry_34217/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gry_34217/08_2025/8gry_34217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gry_34217/08_2025/8gry_34217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gry_34217/08_2025/8gry_34217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gry_34217/08_2025/8gry_34217.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.83, per 1000 atoms: 0.28 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: 0.61 Conformation dependent library (CDL) restraints added in 422.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.22 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: 0.95 Time building geometry restraints manager: 0.82 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: 11.510 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- 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 : 6.03 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 aren 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 covalent geometry : bond 0.00253 ( 6625) covalent geometry : angle 0.57822 ( 9003) SS BOND : bond 0.00096 ( 7) SS BOND : angle 0.63690 ( 14) hydrogen bonds : bond 0.13587 ( 294) hydrogen bonds : angle 5.51249 ( 843) metal coordination : bond 0.20094 ( 2) link_NAG-ASN : bond 0.00652 ( 1) link_NAG-ASN : angle 1.62800 ( 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 : 0.237 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: 0.1027 time to fit residues: 27.4456 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 : 0.250 ------------------------------------------------------------------------------- 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... 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 ** 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 = 0.3671 r_free = 0.3671 target = 0.129235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116804 restraints weight = 10140.666| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.34 r_work: 0.3375 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2306 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 : 0.610 10.021 9020 Z= 0.311 Chirality : 0.044 0.243 941 Planarity : 0.005 0.054 1169 Dihedral : 5.526 57.056 885 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.58 % Allowed : 9.35 % Favored : 89.06 % 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 aren not related in a simple way. whole: 0.61 (0.31), residues: 788 helix: 1.93 (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 A 340 TYR 0.020 0.001 TYR A 385 PHE 0.017 0.002 PHE A 592 TRP 0.012 0.001 TRP A 610 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 6625) covalent geometry : angle 0.60609 ( 9003) SS BOND : bond 0.00344 ( 7) SS BOND : angle 1.31567 ( 14) hydrogen bonds : bond 0.06127 ( 294) hydrogen bonds : angle 4.11048 ( 843) metal coordination : bond 0.00722 ( 2) link_NAG-ASN : bond 0.00592 ( 1) link_NAG-ASN : angle 2.63808 ( 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 213 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8090 (tp30) cc_final: 0.7581 (tp30) REVERT: A 113 ASN cc_start: 0.8674 (t0) cc_final: 0.8471 (t0) REVERT: A 123 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7902 (ttm) REVERT: A 126 ILE cc_start: 0.9027 (tp) cc_final: 0.8641 (tt) REVERT: A 150 GLU cc_start: 0.7204 (pp20) cc_final: 0.6993 (tm-30) REVERT: A 175 GLN cc_start: 0.8107 (mt0) cc_final: 0.7904 (mt0) REVERT: A 206 ASP cc_start: 0.8297 (t0) cc_final: 0.8055 (t0) REVERT: A 213 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7434 (mm-30) REVERT: A 347 THR cc_start: 0.8422 (m) cc_final: 0.7998 (p) REVERT: A 475 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8284 (ttpt) REVERT: A 482 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7897 (ttm-80) REVERT: A 527 GLU cc_start: 0.8336 (tt0) cc_final: 0.7975 (tt0) REVERT: A 543 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: A 557 MET cc_start: 0.8475 (tmm) cc_final: 0.8227 (ttp) REVERT: B 336 CYS cc_start: 0.6441 (m) cc_final: 0.5950 (m) REVERT: B 357 ARG cc_start: 0.7224 (ptm-80) cc_final: 0.6887 (ptm-80) REVERT: B 393 THR cc_start: 0.7254 (m) cc_final: 0.6844 (p) REVERT: B 433 VAL cc_start: 0.8408 (t) cc_final: 0.8064 (m) REVERT: B 469 SER cc_start: 0.8640 (t) cc_final: 0.8402 (t) outliers start: 11 outliers final: 5 residues processed: 205 average time/residue: 0.1009 time to fit residues: 26.3768 Evaluate side-chains 189 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 21 optimal weight: 0.0980 chunk 42 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 A 562 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.127609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115355 restraints weight = 10029.225| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.30 r_work: 0.3360 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2703 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= 0.156 Angle : 0.581 9.768 9020 Z= 0.296 Chirality : 0.043 0.250 941 Planarity : 0.004 0.049 1169 Dihedral : 5.124 55.090 885 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.73 % Allowed : 14.53 % Favored : 83.74 % 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 aren not related in a simple way. whole: 0.58 (0.30), residues: 788 helix: 1.93 (0.28), residues: 368 sheet: 0.77 (0.86), residues: 49 loop : -1.34 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.028 0.001 TYR A 158 PHE 0.016 0.001 PHE A 369 TRP 0.011 0.001 TRP A 610 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6625) covalent geometry : angle 0.57796 ( 9003) SS BOND : bond 0.00214 ( 7) SS BOND : angle 1.35952 ( 14) hydrogen bonds : bond 0.05808 ( 294) hydrogen bonds : angle 4.03725 ( 843) metal coordination : bond 0.00472 ( 2) link_NAG-ASN : bond 0.00304 ( 1) link_NAG-ASN : angle 1.56908 ( 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 194 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8093 (tp30) cc_final: 0.7649 (tp30) REVERT: A 113 ASN cc_start: 0.8700 (t0) cc_final: 0.8460 (t0) REVERT: A 123 MET cc_start: 0.8173 (ttp) cc_final: 0.7898 (ttm) REVERT: A 126 ILE cc_start: 0.9080 (tp) cc_final: 0.8692 (tt) REVERT: A 150 GLU cc_start: 0.7218 (pp20) cc_final: 0.6473 (tp30) REVERT: A 168 TRP cc_start: 0.8420 (t-100) cc_final: 0.8133 (t-100) REVERT: A 171 GLU cc_start: 0.6246 (tm-30) cc_final: 0.6024 (pp20) REVERT: A 182 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8045 (tp30) REVERT: A 206 ASP cc_start: 0.8249 (t0) cc_final: 0.7938 (t0) REVERT: A 213 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 225 ASP cc_start: 0.7429 (m-30) cc_final: 0.7069 (m-30) REVERT: A 475 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8292 (ttpt) REVERT: A 482 ARG cc_start: 0.8177 (ttm170) cc_final: 0.7896 (ttm-80) REVERT: A 517 THR cc_start: 0.7596 (p) cc_final: 0.7347 (p) REVERT: A 557 MET cc_start: 0.8454 (tmm) cc_final: 0.8118 (ttp) REVERT: B 357 ARG cc_start: 0.7241 (ptm-80) cc_final: 0.6879 (ptm-80) outliers start: 12 outliers final: 7 residues processed: 185 average time/residue: 0.1074 time to fit residues: 25.1024 Evaluate side-chains 187 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 0.0470 chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 0.0670 chunk 50 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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 B 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114970 restraints weight = 10037.014| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.29 r_work: 0.3356 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3028 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= 0.157 Angle : 0.565 9.650 9020 Z= 0.290 Chirality : 0.043 0.241 941 Planarity : 0.004 0.044 1169 Dihedral : 4.813 55.480 885 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.30 % Allowed : 15.83 % Favored : 81.87 % 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 aren not related in a simple way. whole: 0.61 (0.30), residues: 788 helix: 1.99 (0.28), residues: 366 sheet: 1.73 (0.92), residues: 41 loop : -1.44 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 466 TYR 0.024 0.001 TYR A 158 PHE 0.013 0.001 PHE A 142 TRP 0.010 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6625) covalent geometry : angle 0.56314 ( 9003) SS BOND : bond 0.00271 ( 7) SS BOND : angle 1.17745 ( 14) hydrogen bonds : bond 0.05792 ( 294) hydrogen bonds : angle 4.00389 ( 843) metal coordination : bond 0.00473 ( 2) link_NAG-ASN : bond 0.00363 ( 1) link_NAG-ASN : angle 1.79304 ( 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 203 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8091 (tp30) cc_final: 0.7720 (tp30) REVERT: A 77 SER cc_start: 0.8394 (t) cc_final: 0.8096 (m) REVERT: A 87 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7897 (tp30) REVERT: A 123 MET cc_start: 0.8154 (ttp) cc_final: 0.7869 (ttm) REVERT: A 126 ILE cc_start: 0.9074 (tp) cc_final: 0.8695 (tt) REVERT: A 152 MET cc_start: 0.7439 (mmm) cc_final: 0.7207 (mmm) REVERT: A 181 GLU cc_start: 0.8127 (tt0) cc_final: 0.7747 (tt0) REVERT: A 182 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8258 (tm-30) REVERT: A 206 ASP cc_start: 0.8356 (t0) cc_final: 0.7943 (t0) REVERT: A 213 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 225 ASP cc_start: 0.7472 (m-30) cc_final: 0.7098 (m-30) REVERT: A 250 GLU cc_start: 0.8541 (tp30) cc_final: 0.8145 (tm-30) REVERT: A 269 ASP cc_start: 0.7968 (t0) cc_final: 0.7722 (t0) REVERT: A 475 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8294 (ttpt) REVERT: A 482 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7935 (ttm-80) REVERT: A 517 THR cc_start: 0.7671 (p) cc_final: 0.7371 (p) REVERT: A 527 GLU cc_start: 0.8275 (tt0) cc_final: 0.7901 (tt0) REVERT: A 557 MET cc_start: 0.8509 (tmm) cc_final: 0.8121 (ttp) REVERT: A 562 ASN cc_start: 0.8024 (t0) cc_final: 0.7747 (t0) REVERT: B 357 ARG cc_start: 0.7261 (ptm-80) cc_final: 0.6884 (ptm-80) REVERT: B 501 TYR cc_start: 0.8298 (m-10) cc_final: 0.7828 (m-10) outliers start: 16 outliers final: 7 residues processed: 192 average time/residue: 0.1066 time to fit residues: 25.9127 Evaluate side-chains 180 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 173 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 231 LYS Chi-restraints excluded: chain A residue 251 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: 0.4980 chunk 65 optimal weight: 0.0980 chunk 32 optimal weight: 0.0970 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.0870 chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 57 optimal weight: 0.0970 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.1554 ------------------------------------------------------------------------------- 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 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.128949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116734 restraints weight = 10169.378| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.33 r_work: 0.3387 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3102 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= 0.117 Angle : 0.553 9.649 9020 Z= 0.279 Chirality : 0.041 0.231 941 Planarity : 0.004 0.041 1169 Dihedral : 4.570 55.110 885 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.44 % Allowed : 16.98 % 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 aren not related in a simple way. whole: 0.65 (0.31), residues: 788 helix: 2.01 (0.28), residues: 366 sheet: 1.62 (0.91), residues: 41 loop : -1.38 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 493 TYR 0.024 0.001 TYR A 158 PHE 0.010 0.001 PHE A 142 TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6625) covalent geometry : angle 0.55100 ( 9003) SS BOND : bond 0.00228 ( 7) SS BOND : angle 1.09824 ( 14) hydrogen bonds : bond 0.04786 ( 294) hydrogen bonds : angle 3.88475 ( 843) metal coordination : bond 0.00261 ( 2) link_NAG-ASN : bond 0.00377 ( 1) link_NAG-ASN : angle 1.74432 ( 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 180 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8084 (tp30) cc_final: 0.7724 (tp30) REVERT: A 77 SER cc_start: 0.8407 (t) cc_final: 0.8102 (m) REVERT: A 87 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7858 (tp30) REVERT: A 123 MET cc_start: 0.8132 (ttp) cc_final: 0.7901 (ttm) REVERT: A 126 ILE cc_start: 0.9038 (tp) cc_final: 0.8663 (tt) REVERT: A 181 GLU cc_start: 0.8129 (tt0) cc_final: 0.7897 (tt0) REVERT: A 206 ASP cc_start: 0.8394 (t0) cc_final: 0.7986 (t0) REVERT: A 213 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7528 (mm-30) REVERT: A 225 ASP cc_start: 0.7453 (m-30) cc_final: 0.7079 (m-30) REVERT: A 250 GLU cc_start: 0.8462 (tp30) cc_final: 0.8034 (tm-30) REVERT: A 288 LYS cc_start: 0.7937 (pttm) cc_final: 0.7659 (pttt) REVERT: A 313 LYS cc_start: 0.8086 (tttt) cc_final: 0.7589 (ttmm) REVERT: A 475 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8273 (ttpt) REVERT: A 482 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7980 (ttm-80) REVERT: A 517 THR cc_start: 0.7547 (p) cc_final: 0.7257 (p) REVERT: A 557 MET cc_start: 0.8473 (tmm) cc_final: 0.8067 (ttp) REVERT: A 563 SER cc_start: 0.8735 (t) cc_final: 0.8232 (p) REVERT: A 598 GLN cc_start: 0.8393 (tp40) cc_final: 0.8140 (tp40) REVERT: B 357 ARG cc_start: 0.7245 (ptm-80) cc_final: 0.6865 (ptm-80) REVERT: B 501 TYR cc_start: 0.8238 (m-10) cc_final: 0.7790 (m-80) outliers start: 10 outliers final: 7 residues processed: 174 average time/residue: 0.0854 time to fit residues: 19.3760 Evaluate side-chains 173 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 64 optimal weight: 0.0010 chunk 12 optimal weight: 0.4980 chunk 3 optimal weight: 0.3980 chunk 31 optimal weight: 0.0570 chunk 19 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 overall best weight: 0.1904 ------------------------------------------------------------------------------- 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 B 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116601 restraints weight = 10106.303| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.34 r_work: 0.3377 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3228 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= 0.122 Angle : 0.565 9.662 9020 Z= 0.282 Chirality : 0.042 0.233 941 Planarity : 0.004 0.040 1169 Dihedral : 4.607 55.247 885 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.01 % Allowed : 16.69 % 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 aren not related in a simple way. whole: 0.65 (0.31), residues: 788 helix: 2.03 (0.28), residues: 366 sheet: 1.57 (0.92), residues: 41 loop : -1.40 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.020 0.001 TYR A 158 PHE 0.015 0.001 PHE B 456 TRP 0.010 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6625) covalent geometry : angle 0.56108 ( 9003) SS BOND : bond 0.00201 ( 7) SS BOND : angle 1.65155 ( 14) hydrogen bonds : bond 0.04888 ( 294) hydrogen bonds : angle 3.83842 ( 843) metal coordination : bond 0.00311 ( 2) link_NAG-ASN : bond 0.00357 ( 1) link_NAG-ASN : angle 1.59617 ( 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 175 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8073 (tp30) cc_final: 0.7633 (tp30) REVERT: A 77 SER cc_start: 0.8414 (t) cc_final: 0.8105 (m) REVERT: A 87 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7872 (tp30) REVERT: A 123 MET cc_start: 0.8120 (ttp) cc_final: 0.7854 (ttm) REVERT: A 126 ILE cc_start: 0.9037 (tp) cc_final: 0.8664 (tt) REVERT: A 181 GLU cc_start: 0.8188 (tt0) cc_final: 0.7872 (tt0) REVERT: A 206 ASP cc_start: 0.8420 (t0) cc_final: 0.8014 (t0) REVERT: A 213 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7530 (mm-30) REVERT: A 250 GLU cc_start: 0.8435 (tp30) cc_final: 0.7998 (tm-30) REVERT: A 269 ASP cc_start: 0.8077 (t0) cc_final: 0.7835 (t0) REVERT: A 288 LYS cc_start: 0.7920 (pttm) cc_final: 0.7635 (pttt) REVERT: A 313 LYS cc_start: 0.8083 (tttt) cc_final: 0.7590 (ttmm) REVERT: A 475 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8322 (ttpt) REVERT: A 482 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7984 (ttm-80) REVERT: A 557 MET cc_start: 0.8480 (tmm) cc_final: 0.8079 (ttp) REVERT: A 563 SER cc_start: 0.8771 (t) cc_final: 0.8242 (p) REVERT: A 598 GLN cc_start: 0.8434 (tp40) cc_final: 0.8189 (tp40) REVERT: B 357 ARG cc_start: 0.7251 (ptm-80) cc_final: 0.6856 (ptm-80) REVERT: B 501 TYR cc_start: 0.8287 (m-10) cc_final: 0.7937 (m-80) outliers start: 14 outliers final: 12 residues processed: 168 average time/residue: 0.0902 time to fit residues: 19.7035 Evaluate side-chains 172 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 59 optimal weight: 0.0670 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 45 optimal weight: 0.0040 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 3 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 overall best weight: 0.1930 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.128434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116294 restraints weight = 10113.320| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.31 r_work: 0.3382 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3313 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= 0.124 Angle : 0.572 9.653 9020 Z= 0.285 Chirality : 0.042 0.233 941 Planarity : 0.004 0.040 1169 Dihedral : 4.571 55.361 885 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.01 % Allowed : 18.13 % 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 aren not related in a simple way. whole: 0.58 (0.31), residues: 788 helix: 1.93 (0.28), residues: 368 sheet: 1.54 (0.91), residues: 41 loop : -1.41 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.019 0.001 TYR A 158 PHE 0.014 0.001 PHE B 456 TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6625) covalent geometry : angle 0.56816 ( 9003) SS BOND : bond 0.00131 ( 7) SS BOND : angle 1.54613 ( 14) hydrogen bonds : bond 0.04930 ( 294) hydrogen bonds : angle 3.90554 ( 843) metal coordination : bond 0.00318 ( 2) link_NAG-ASN : bond 0.00354 ( 1) link_NAG-ASN : angle 1.53820 ( 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 180 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8058 (tp30) cc_final: 0.7622 (tp30) REVERT: A 77 SER cc_start: 0.8415 (t) cc_final: 0.8112 (m) REVERT: A 87 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7867 (tp30) REVERT: A 123 MET cc_start: 0.8183 (ttp) cc_final: 0.7953 (ttm) REVERT: A 126 ILE cc_start: 0.9031 (tp) cc_final: 0.8649 (tt) REVERT: A 181 GLU cc_start: 0.8173 (tt0) cc_final: 0.7836 (tt0) REVERT: A 206 ASP cc_start: 0.8425 (t0) cc_final: 0.8029 (t0) REVERT: A 213 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7531 (mm-30) REVERT: A 225 ASP cc_start: 0.7441 (m-30) cc_final: 0.7093 (m-30) REVERT: A 250 GLU cc_start: 0.8425 (tp30) cc_final: 0.7939 (tm-30) REVERT: A 269 ASP cc_start: 0.8128 (t0) cc_final: 0.7857 (t0) REVERT: A 288 LYS cc_start: 0.7889 (pttm) cc_final: 0.7617 (pttt) REVERT: A 313 LYS cc_start: 0.8107 (tttt) cc_final: 0.7610 (ttmm) REVERT: A 347 THR cc_start: 0.8516 (m) cc_final: 0.8100 (p) REVERT: A 475 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8303 (ttpt) REVERT: A 482 ARG cc_start: 0.8187 (ttm170) cc_final: 0.7964 (ttm-80) REVERT: A 557 MET cc_start: 0.8511 (tmm) cc_final: 0.8041 (ttp) REVERT: A 563 SER cc_start: 0.8762 (t) cc_final: 0.8234 (p) REVERT: A 598 GLN cc_start: 0.8412 (tp40) cc_final: 0.8147 (tp40) REVERT: B 357 ARG cc_start: 0.7248 (ptm-80) cc_final: 0.6855 (ptm-80) REVERT: B 501 TYR cc_start: 0.8282 (m-10) cc_final: 0.7936 (m-80) outliers start: 14 outliers final: 13 residues processed: 172 average time/residue: 0.0821 time to fit residues: 18.5065 Evaluate side-chains 177 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 472 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 chunk 76 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 74 optimal weight: 0.0370 chunk 60 optimal weight: 0.0870 chunk 33 optimal weight: 0.1980 overall best weight: 0.1434 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.129192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.117063 restraints weight = 10052.323| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.30 r_work: 0.3399 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3362 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= 0.112 Angle : 0.572 9.632 9020 Z= 0.285 Chirality : 0.042 0.232 941 Planarity : 0.004 0.040 1169 Dihedral : 4.485 55.329 885 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.16 % Allowed : 18.13 % Favored : 79.71 % 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 aren not related in a simple way. whole: 0.63 (0.31), residues: 788 helix: 1.98 (0.28), residues: 368 sheet: 1.54 (0.92), residues: 41 loop : -1.39 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.018 0.001 TYR A 158 PHE 0.014 0.001 PHE B 456 TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6625) covalent geometry : angle 0.56927 ( 9003) SS BOND : bond 0.00145 ( 7) SS BOND : angle 1.36809 ( 14) hydrogen bonds : bond 0.04451 ( 294) hydrogen bonds : angle 3.83982 ( 843) metal coordination : bond 0.00238 ( 2) link_NAG-ASN : bond 0.00359 ( 1) link_NAG-ASN : angle 1.47376 ( 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 177 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8046 (tp30) cc_final: 0.7612 (tp30) REVERT: A 77 SER cc_start: 0.8403 (t) cc_final: 0.8097 (m) REVERT: A 87 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7854 (tp30) REVERT: A 123 MET cc_start: 0.8151 (ttp) cc_final: 0.7921 (ttm) REVERT: A 126 ILE cc_start: 0.9012 (tp) cc_final: 0.8632 (tt) REVERT: A 181 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: A 206 ASP cc_start: 0.8439 (t0) cc_final: 0.8073 (t0) REVERT: A 213 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 250 GLU cc_start: 0.8377 (tp30) cc_final: 0.7845 (tm-30) REVERT: A 269 ASP cc_start: 0.8125 (t0) cc_final: 0.7839 (t0) REVERT: A 288 LYS cc_start: 0.7858 (pttm) cc_final: 0.7583 (pttt) REVERT: A 313 LYS cc_start: 0.8054 (tttt) cc_final: 0.7561 (ttmm) REVERT: A 347 THR cc_start: 0.8496 (m) cc_final: 0.8017 (p) REVERT: A 358 ILE cc_start: 0.8743 (mt) cc_final: 0.8360 (tt) REVERT: A 475 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8288 (ttpt) REVERT: A 482 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7999 (ttm-80) REVERT: A 557 MET cc_start: 0.8481 (tmm) cc_final: 0.8011 (ttp) REVERT: A 563 SER cc_start: 0.8787 (t) cc_final: 0.8238 (p) REVERT: A 598 GLN cc_start: 0.8406 (tp40) cc_final: 0.8131 (tp40) REVERT: B 501 TYR cc_start: 0.8255 (m-10) cc_final: 0.7915 (m-80) outliers start: 15 outliers final: 12 residues processed: 168 average time/residue: 0.0936 time to fit residues: 20.5179 Evaluate side-chains 173 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 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 382 VAL 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: 0.9980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 74 optimal weight: 0.0370 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.0020 chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 68 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 overall best weight: 0.1442 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.129315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117009 restraints weight = 10277.367| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.37 r_work: 0.3386 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3409 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 : 0.563 9.625 9020 Z= 0.281 Chirality : 0.042 0.232 941 Planarity : 0.004 0.040 1169 Dihedral : 4.470 55.418 885 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.01 % Allowed : 17.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.31), residues: 788 helix: 1.98 (0.28), residues: 368 sheet: 1.97 (0.93), residues: 39 loop : -1.29 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.017 0.001 TYR A 158 PHE 0.017 0.001 PHE A 142 TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6625) covalent geometry : angle 0.56075 ( 9003) SS BOND : bond 0.00110 ( 7) SS BOND : angle 1.29586 ( 14) hydrogen bonds : bond 0.04441 ( 294) hydrogen bonds : angle 3.82034 ( 843) metal coordination : bond 0.00237 ( 2) link_NAG-ASN : bond 0.00355 ( 1) link_NAG-ASN : angle 1.44095 ( 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 177 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8212 (m-40) cc_final: 0.7975 (m-40) REVERT: A 75 GLU cc_start: 0.8061 (tp30) cc_final: 0.7632 (tp30) REVERT: A 77 SER cc_start: 0.8419 (t) cc_final: 0.8121 (m) REVERT: A 87 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7872 (tp30) REVERT: A 123 MET cc_start: 0.8164 (ttp) cc_final: 0.7934 (ttm) REVERT: A 126 ILE cc_start: 0.9015 (tp) cc_final: 0.8767 (tp) REVERT: A 165 TRP cc_start: 0.7678 (t60) cc_final: 0.7328 (t60) REVERT: A 181 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: A 206 ASP cc_start: 0.8457 (t0) cc_final: 0.8088 (t0) REVERT: A 213 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7561 (mm-30) REVERT: A 250 GLU cc_start: 0.8395 (tp30) cc_final: 0.7853 (tm-30) REVERT: A 269 ASP cc_start: 0.8146 (t0) cc_final: 0.7895 (t0) REVERT: A 288 LYS cc_start: 0.7840 (pttm) cc_final: 0.7577 (pttt) REVERT: A 313 LYS cc_start: 0.8083 (tttt) cc_final: 0.7572 (ttmm) REVERT: A 341 LYS cc_start: 0.8080 (mttm) cc_final: 0.7866 (mttm) REVERT: A 347 THR cc_start: 0.8477 (m) cc_final: 0.8019 (p) REVERT: A 358 ILE cc_start: 0.8749 (mt) cc_final: 0.8443 (tt) REVERT: A 369 PHE cc_start: 0.6575 (t80) cc_final: 0.5698 (t80) REVERT: A 475 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8319 (ttpt) REVERT: A 482 ARG cc_start: 0.8262 (ttm170) cc_final: 0.8040 (ttm-80) REVERT: A 557 MET cc_start: 0.8492 (tmm) cc_final: 0.8029 (ttp) REVERT: A 563 SER cc_start: 0.8785 (t) cc_final: 0.8239 (p) REVERT: A 598 GLN cc_start: 0.8412 (tp40) cc_final: 0.8135 (tp40) REVERT: B 501 TYR cc_start: 0.8245 (m-10) cc_final: 0.7934 (m-80) outliers start: 14 outliers final: 11 residues processed: 168 average time/residue: 0.0896 time to fit residues: 19.7552 Evaluate side-chains 172 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 251 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 376 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.0060 chunk 65 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 0.0470 chunk 43 optimal weight: 0.4980 overall best weight: 0.2294 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.128169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115851 restraints weight = 9927.767| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.40 r_work: 0.3364 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6635 Z= 0.136 Angle : 0.591 9.633 9020 Z= 0.297 Chirality : 0.043 0.235 941 Planarity : 0.004 0.040 1169 Dihedral : 4.580 55.524 885 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.16 % Allowed : 17.84 % Favored : 80.00 % 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 aren not related in a simple way. whole: 0.67 (0.31), residues: 788 helix: 1.92 (0.28), residues: 369 sheet: 1.93 (0.93), residues: 39 loop : -1.30 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.017 0.001 TYR A 158 PHE 0.015 0.001 PHE B 456 TRP 0.010 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6625) covalent geometry : angle 0.58894 ( 9003) SS BOND : bond 0.00122 ( 7) SS BOND : angle 1.38438 ( 14) hydrogen bonds : bond 0.05101 ( 294) hydrogen bonds : angle 3.90248 ( 843) metal coordination : bond 0.00386 ( 2) link_NAG-ASN : bond 0.00305 ( 1) link_NAG-ASN : angle 1.43255 ( 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 175 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8094 (tp30) cc_final: 0.7656 (tp30) REVERT: A 77 SER cc_start: 0.8418 (t) cc_final: 0.8125 (m) REVERT: A 87 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7856 (mp0) REVERT: A 123 MET cc_start: 0.8177 (ttp) cc_final: 0.7919 (ttm) REVERT: A 126 ILE cc_start: 0.9010 (tp) cc_final: 0.8789 (tp) REVERT: A 155 SER cc_start: 0.8880 (t) cc_final: 0.8102 (m) REVERT: A 165 TRP cc_start: 0.7696 (t60) cc_final: 0.7382 (t60) REVERT: A 181 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: A 182 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 186 LEU cc_start: 0.7868 (mm) cc_final: 0.7514 (mm) REVERT: A 206 ASP cc_start: 0.8443 (t0) cc_final: 0.8114 (t0) REVERT: A 213 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 225 ASP cc_start: 0.7531 (m-30) cc_final: 0.7185 (m-30) REVERT: A 250 GLU cc_start: 0.8400 (tp30) cc_final: 0.7861 (tm-30) REVERT: A 269 ASP cc_start: 0.8154 (t0) cc_final: 0.7848 (t0) REVERT: A 288 LYS cc_start: 0.7931 (pttm) cc_final: 0.7609 (mttp) REVERT: A 313 LYS cc_start: 0.8033 (tttt) cc_final: 0.7625 (ttmm) REVERT: A 341 LYS cc_start: 0.8091 (mttm) cc_final: 0.7873 (mttm) REVERT: A 347 THR cc_start: 0.8466 (m) cc_final: 0.7994 (p) REVERT: A 475 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8333 (ttpt) REVERT: A 482 ARG cc_start: 0.8274 (ttm170) cc_final: 0.8044 (ttm-80) REVERT: A 557 MET cc_start: 0.8509 (tmm) cc_final: 0.8047 (ttp) REVERT: A 563 SER cc_start: 0.8823 (t) cc_final: 0.8273 (p) REVERT: B 501 TYR cc_start: 0.8271 (m-10) cc_final: 0.7954 (m-80) outliers start: 15 outliers final: 11 residues processed: 166 average time/residue: 0.0801 time to fit residues: 17.5147 Evaluate side-chains 172 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 251 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain B residue 382 VAL 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 66 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 74 optimal weight: 0.0470 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 5 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 overall best weight: 0.2056 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.127709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115736 restraints weight = 10106.743| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.29 r_work: 0.3375 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 6635 Z= 0.186 Angle : 1.049 59.185 9020 Z= 0.609 Chirality : 0.042 0.235 941 Planarity : 0.004 0.040 1169 Dihedral : 4.591 55.523 885 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.73 % Allowed : 17.99 % Favored : 80.29 % Cbeta Deviations : 0.13 % 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 aren not related in a simple way. whole: 0.67 (0.31), residues: 788 helix: 1.93 (0.28), residues: 369 sheet: 1.87 (0.93), residues: 39 loop : -1.30 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.016 0.001 TYR A 158 PHE 0.013 0.001 PHE B 456 TRP 0.010 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6625) covalent geometry : angle 1.04785 ( 9003) SS BOND : bond 0.00113 ( 7) SS BOND : angle 1.36175 ( 14) hydrogen bonds : bond 0.05111 ( 294) hydrogen bonds : angle 3.90864 ( 843) metal coordination : bond 0.00353 ( 2) link_NAG-ASN : bond 0.00303 ( 1) link_NAG-ASN : angle 1.43144 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.69 seconds wall clock time: 35 minutes 54.25 seconds (2154.25 seconds total)