Starting phenix.real_space_refine on Wed Jul 30 02:22:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xci_33121/07_2025/7xci_33121.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xci_33121/07_2025/7xci_33121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xci_33121/07_2025/7xci_33121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xci_33121/07_2025/7xci_33121.map" model { file = "/net/cci-nas-00/data/ceres_data/7xci_33121/07_2025/7xci_33121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xci_33121/07_2025/7xci_33121.cif" } resolution = 3.2 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= 0.038 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 6463 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 37 5.16 5 C 4189 2.51 5 N 1079 2.21 5 O 1241 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: 6547 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 8.42, per 1000 atoms: 1.29 Number of scatterers: 6547 At special positions: 0 Unit cell: (77.22, 99.66, 114.84, 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 37 16.00 O 1241 8.00 N 1079 7.00 C 4189 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=2.02 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=2.04 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 702 " - " ASN A 432 " " NAG A 703 " - " ASN A 53 " " NAG A 704 " - " ASN A 90 " " NAG A 705 " - " ASN A 322 " " NAG A 706 " - " ASN A 103 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 546 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 38 helices and 6 sheets defined 56.5% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.598A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.847A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.531A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.807A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix 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 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.718A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.708A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.601A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.737A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.919A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.650A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 466 removed outlier: 3.831A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.531A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.854A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.564A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.866A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.680A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.087A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.872A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.887A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 305 hydrogen bonds defined for protein. 872 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: 1.84 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.24: 670 1.24 - 1.39: 2133 1.39 - 1.54: 3845 1.54 - 1.69: 25 1.69 - 1.85: 59 Bond restraints: 6732 Sorted by residual: bond pdb=" CG PRO A 469 " pdb=" CD PRO A 469 " ideal model delta sigma weight residual 1.503 1.084 0.419 3.40e-02 8.65e+02 1.52e+02 bond pdb=" CG PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.503 1.103 0.400 3.40e-02 8.65e+02 1.39e+02 bond pdb=" N PRO A 469 " pdb=" CD PRO A 469 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.92e+01 bond pdb=" N PRO A 263 " pdb=" CD PRO A 263 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.34e+01 bond pdb=" CB PRO A 469 " pdb=" CG PRO A 469 " ideal model delta sigma weight residual 1.492 1.704 -0.212 5.00e-02 4.00e+02 1.81e+01 ... (remaining 6727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 9124 4.17 - 8.34: 24 8.34 - 12.51: 1 12.51 - 16.69: 2 16.69 - 20.86: 2 Bond angle restraints: 9153 Sorted by residual: angle pdb=" N PRO A 263 " pdb=" CD PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 103.20 82.34 20.86 1.50e+00 4.44e-01 1.93e+02 angle pdb=" N PRO A 469 " pdb=" CD PRO A 469 " pdb=" CG PRO A 469 " ideal model delta sigma weight residual 103.20 82.45 20.75 1.50e+00 4.44e-01 1.91e+02 angle pdb=" CA PRO A 263 " pdb=" CB PRO A 263 " pdb=" CG PRO A 263 " ideal model delta sigma weight residual 104.50 90.21 14.29 1.90e+00 2.77e-01 5.65e+01 angle pdb=" CA PRO A 469 " pdb=" CB PRO A 469 " pdb=" CG PRO A 469 " ideal model delta sigma weight residual 104.50 91.08 13.42 1.90e+00 2.77e-01 4.99e+01 angle pdb=" CA PRO A 469 " pdb=" N PRO A 469 " pdb=" CD PRO A 469 " ideal model delta sigma weight residual 112.00 102.73 9.27 1.40e+00 5.10e-01 4.38e+01 ... (remaining 9148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 3698 17.63 - 35.26: 299 35.26 - 52.89: 66 52.89 - 70.52: 9 70.52 - 88.15: 8 Dihedral angle restraints: 4080 sinusoidal: 1750 harmonic: 2330 Sorted by residual: dihedral pdb=" CA PRO B 337 " pdb=" C PRO B 337 " pdb=" N PHE B 338 " pdb=" CA PHE B 338 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 135.79 -42.79 1 1.00e+01 1.00e-02 2.56e+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 56.69 36.31 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 4077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 669 0.038 - 0.076: 232 0.076 - 0.114: 63 0.114 - 0.152: 12 0.152 - 0.190: 4 Chirality restraints: 980 Sorted by residual: chirality pdb=" C1 NAG A 705 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 705 " pdb=" O5 NAG A 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA PRO B 373 " pdb=" N PRO B 373 " pdb=" C PRO B 373 " pdb=" CB PRO B 373 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 977 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " -0.072 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO A 469 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 262 " -0.059 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO A 263 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 415 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.031 5.00e-02 4.00e+02 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 43 2.58 - 3.16: 5341 3.16 - 3.74: 9924 3.74 - 4.32: 13728 4.32 - 4.90: 23220 Nonbonded interactions: 52256 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.000 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.265 3.040 nonbonded pdb=" OG SER A 607 " pdb=" OD1 ASP A 609 " model vdw 2.272 3.040 nonbonded pdb=" OG SER A 77 " pdb=" O GLN A 101 " model vdw 2.304 3.040 nonbonded pdb=" OE1 GLU A 189 " pdb=" NH2 ARG A 192 " model vdw 2.310 3.120 ... (remaining 52251 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=0.49 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: 9.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.330 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:3.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.419 6749 Z= 0.313 Angle : 0.759 20.857 9191 Z= 0.447 Chirality : 0.043 0.190 980 Planarity : 0.006 0.102 1176 Dihedral : 13.674 88.150 2563 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.30 % Favored : 96.44 % Rotamer: Outliers : 0.14 % Allowed : 0.57 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.57 (0.30), residues: 788 helix: 1.09 (0.27), residues: 387 sheet: 1.23 (0.73), residues: 50 loop : -0.50 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 165 HIS 0.006 0.001 HIS A 378 PHE 0.022 0.001 PHE A 504 TYR 0.018 0.001 TYR A 202 ARG 0.007 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 7) link_NAG-ASN : angle 1.81815 ( 21) link_BETA1-4 : bond 0.00183 ( 1) link_BETA1-4 : angle 0.70087 ( 3) hydrogen bonds : bond 0.16052 ( 305) hydrogen bonds : angle 6.30357 ( 872) metal coordination : bond 0.20318 ( 2) SS BOND : bond 0.00551 ( 7) SS BOND : angle 1.52376 ( 14) covalent geometry : bond 0.00865 ( 6732) covalent geometry : angle 0.75317 ( 9153) *********************** 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 100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.711 Fit side-chains REVERT: A 383 MET cc_start: 0.8242 (mtp) cc_final: 0.7894 (mtp) REVERT: B 420 ASP cc_start: 0.8031 (m-30) cc_final: 0.7576 (m-30) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.1661 time to fit residues: 22.9330 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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: 0.6980 chunk 59 optimal weight: 0.0570 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 0.0010 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.178211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121105 restraints weight = 16767.149| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.73 r_work: 0.3182 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6749 Z= 0.126 Angle : 0.564 9.471 9191 Z= 0.288 Chirality : 0.043 0.233 980 Planarity : 0.004 0.056 1176 Dihedral : 5.889 57.241 1031 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.80 % Favored : 96.95 % Rotamer: Outliers : 0.57 % Allowed : 6.31 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.69 (0.30), residues: 788 helix: 1.18 (0.26), residues: 387 sheet: 1.20 (0.72), residues: 50 loop : -0.41 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 165 HIS 0.004 0.001 HIS A 378 PHE 0.028 0.001 PHE A 504 TYR 0.014 0.001 TYR A 385 ARG 0.006 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 7) link_NAG-ASN : angle 2.11009 ( 21) link_BETA1-4 : bond 0.00073 ( 1) link_BETA1-4 : angle 1.17841 ( 3) hydrogen bonds : bond 0.04921 ( 305) hydrogen bonds : angle 4.83283 ( 872) metal coordination : bond 0.00516 ( 2) SS BOND : bond 0.00351 ( 7) SS BOND : angle 1.04115 ( 14) covalent geometry : bond 0.00288 ( 6732) covalent geometry : angle 0.55366 ( 9153) *********************** 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 99 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.721 Fit side-chains REVERT: A 265 HIS cc_start: 0.6042 (p90) cc_final: 0.5797 (p-80) REVERT: A 435 GLU cc_start: 0.7276 (mp0) cc_final: 0.7034 (mp0) REVERT: B 420 ASP cc_start: 0.8568 (m-30) cc_final: 0.8173 (m-30) outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 0.1748 time to fit residues: 23.5294 Evaluate side-chains 90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.176491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117608 restraints weight = 10801.658| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.75 r_work: 0.3227 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6749 Z= 0.134 Angle : 0.549 9.452 9191 Z= 0.278 Chirality : 0.042 0.237 980 Planarity : 0.004 0.046 1176 Dihedral : 5.395 55.864 1031 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 1.43 % Allowed : 8.32 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.77 (0.30), residues: 788 helix: 1.33 (0.27), residues: 383 sheet: 0.62 (0.67), residues: 60 loop : -0.38 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.022 0.001 PHE A 504 TYR 0.021 0.001 TYR A 381 ARG 0.008 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 7) link_NAG-ASN : angle 2.12742 ( 21) link_BETA1-4 : bond 0.00250 ( 1) link_BETA1-4 : angle 1.40205 ( 3) hydrogen bonds : bond 0.05092 ( 305) hydrogen bonds : angle 4.61607 ( 872) metal coordination : bond 0.00303 ( 2) SS BOND : bond 0.00352 ( 7) SS BOND : angle 1.04841 ( 14) covalent geometry : bond 0.00301 ( 6732) covalent geometry : angle 0.53857 ( 9153) *********************** 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 101 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 435 GLU cc_start: 0.7436 (mp0) cc_final: 0.7161 (mp0) REVERT: B 420 ASP cc_start: 0.8701 (m-30) cc_final: 0.8410 (m-30) REVERT: B 443 SER cc_start: 0.8837 (m) cc_final: 0.8410 (m) outliers start: 10 outliers final: 5 residues processed: 96 average time/residue: 0.1865 time to fit residues: 24.1427 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 0.0670 chunk 14 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.176614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117137 restraints weight = 12457.396| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.01 r_work: 0.3207 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6749 Z= 0.121 Angle : 0.544 9.485 9191 Z= 0.272 Chirality : 0.042 0.254 980 Planarity : 0.004 0.045 1176 Dihedral : 5.150 55.838 1031 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 1.00 % Allowed : 9.76 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.78 (0.30), residues: 788 helix: 1.37 (0.27), residues: 383 sheet: 0.57 (0.66), residues: 60 loop : -0.40 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.022 0.001 PHE A 504 TYR 0.016 0.001 TYR A 381 ARG 0.005 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 7) link_NAG-ASN : angle 2.05470 ( 21) link_BETA1-4 : bond 0.00263 ( 1) link_BETA1-4 : angle 1.29100 ( 3) hydrogen bonds : bond 0.04781 ( 305) hydrogen bonds : angle 4.56210 ( 872) metal coordination : bond 0.00218 ( 2) SS BOND : bond 0.00397 ( 7) SS BOND : angle 0.99776 ( 14) covalent geometry : bond 0.00268 ( 6732) covalent geometry : angle 0.53437 ( 9153) *********************** 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 97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.700 Fit side-chains REVERT: A 435 GLU cc_start: 0.7350 (mp0) cc_final: 0.6852 (mp0) REVERT: B 360 ASN cc_start: 0.7520 (m-40) cc_final: 0.7232 (m-40) REVERT: B 420 ASP cc_start: 0.8484 (m-30) cc_final: 0.8178 (m-30) REVERT: B 443 SER cc_start: 0.8690 (m) cc_final: 0.8289 (m) REVERT: B 517 LEU cc_start: 0.8282 (mt) cc_final: 0.8063 (mm) outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 0.1758 time to fit residues: 23.1552 Evaluate side-chains 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 72 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.183045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129419 restraints weight = 17041.456| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.74 r_work: 0.3352 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6749 Z= 0.131 Angle : 0.552 9.503 9191 Z= 0.279 Chirality : 0.042 0.240 980 Planarity : 0.004 0.044 1176 Dihedral : 5.091 55.759 1031 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.15 % Allowed : 10.62 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.30), residues: 788 helix: 1.42 (0.27), residues: 383 sheet: 0.53 (0.67), residues: 60 loop : -0.45 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.022 0.001 PHE A 504 TYR 0.018 0.001 TYR A 381 ARG 0.006 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 7) link_NAG-ASN : angle 2.08183 ( 21) link_BETA1-4 : bond 0.00168 ( 1) link_BETA1-4 : angle 1.36093 ( 3) hydrogen bonds : bond 0.04863 ( 305) hydrogen bonds : angle 4.53742 ( 872) metal coordination : bond 0.00211 ( 2) SS BOND : bond 0.00461 ( 7) SS BOND : angle 1.95175 ( 14) covalent geometry : bond 0.00292 ( 6732) covalent geometry : angle 0.53777 ( 9153) *********************** 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 97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.956 Fit side-chains REVERT: A 435 GLU cc_start: 0.7450 (mp0) cc_final: 0.7128 (mp0) REVERT: B 360 ASN cc_start: 0.7608 (m-40) cc_final: 0.7026 (t0) REVERT: B 420 ASP cc_start: 0.8359 (m-30) cc_final: 0.8085 (m-30) REVERT: B 443 SER cc_start: 0.8631 (m) cc_final: 0.8242 (m) REVERT: B 517 LEU cc_start: 0.8206 (mt) cc_final: 0.8005 (mm) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.2483 time to fit residues: 33.0635 Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 59 optimal weight: 0.0570 chunk 48 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.175956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119559 restraints weight = 15403.837| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.46 r_work: 0.3222 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6749 Z= 0.132 Angle : 0.547 9.569 9191 Z= 0.278 Chirality : 0.042 0.238 980 Planarity : 0.004 0.046 1176 Dihedral : 5.029 55.598 1031 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 1.15 % Allowed : 11.05 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.83 (0.30), residues: 788 helix: 1.46 (0.27), residues: 383 sheet: 0.54 (0.67), residues: 60 loop : -0.43 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.007 0.001 HIS A 265 PHE 0.022 0.001 PHE A 504 TYR 0.021 0.001 TYR A 381 ARG 0.008 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 7) link_NAG-ASN : angle 2.05564 ( 21) link_BETA1-4 : bond 0.00188 ( 1) link_BETA1-4 : angle 1.39639 ( 3) hydrogen bonds : bond 0.04931 ( 305) hydrogen bonds : angle 4.50185 ( 872) metal coordination : bond 0.00266 ( 2) SS BOND : bond 0.00420 ( 7) SS BOND : angle 1.25524 ( 14) covalent geometry : bond 0.00299 ( 6732) covalent geometry : angle 0.53652 ( 9153) *********************** 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 97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.685 Fit side-chains REVERT: A 435 GLU cc_start: 0.7394 (mp0) cc_final: 0.7004 (mp0) REVERT: B 360 ASN cc_start: 0.7624 (m-40) cc_final: 0.7018 (t0) REVERT: B 420 ASP cc_start: 0.8450 (m-30) cc_final: 0.8177 (m-30) REVERT: B 443 SER cc_start: 0.8668 (m) cc_final: 0.8267 (m) outliers start: 8 outliers final: 8 residues processed: 92 average time/residue: 0.1789 time to fit residues: 22.4249 Evaluate side-chains 96 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.175334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.117363 restraints weight = 12762.749| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.08 r_work: 0.3183 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6749 Z= 0.141 Angle : 0.556 9.599 9191 Z= 0.282 Chirality : 0.042 0.238 980 Planarity : 0.004 0.048 1176 Dihedral : 5.049 55.467 1031 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.15 % Allowed : 11.91 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.90 (0.30), residues: 788 helix: 1.57 (0.27), residues: 375 sheet: 0.52 (0.68), residues: 60 loop : -0.41 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.005 0.001 HIS A 265 PHE 0.022 0.001 PHE A 504 TYR 0.022 0.001 TYR A 381 ARG 0.009 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 7) link_NAG-ASN : angle 2.12151 ( 21) link_BETA1-4 : bond 0.00134 ( 1) link_BETA1-4 : angle 1.45541 ( 3) hydrogen bonds : bond 0.05092 ( 305) hydrogen bonds : angle 4.51602 ( 872) metal coordination : bond 0.00273 ( 2) SS BOND : bond 0.00477 ( 7) SS BOND : angle 1.24686 ( 14) covalent geometry : bond 0.00325 ( 6732) covalent geometry : angle 0.54537 ( 9153) *********************** 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 94 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.700 Fit side-chains REVERT: A 435 GLU cc_start: 0.7420 (mp0) cc_final: 0.6985 (mp0) REVERT: B 360 ASN cc_start: 0.7569 (m-40) cc_final: 0.6973 (t0) REVERT: B 420 ASP cc_start: 0.8514 (m-30) cc_final: 0.8225 (m-30) REVERT: B 443 SER cc_start: 0.8717 (m) cc_final: 0.8304 (m) outliers start: 8 outliers final: 7 residues processed: 91 average time/residue: 0.1735 time to fit residues: 21.5735 Evaluate side-chains 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117538 restraints weight = 12752.842| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.89 r_work: 0.3184 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6749 Z= 0.143 Angle : 0.558 9.592 9191 Z= 0.283 Chirality : 0.042 0.245 980 Planarity : 0.004 0.049 1176 Dihedral : 5.068 55.417 1031 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 1.29 % Allowed : 12.34 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.90 (0.31), residues: 788 helix: 1.57 (0.27), residues: 375 sheet: 0.56 (0.69), residues: 60 loop : -0.42 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.004 0.001 HIS A 34 PHE 0.022 0.001 PHE A 504 TYR 0.021 0.001 TYR A 381 ARG 0.009 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 7) link_NAG-ASN : angle 2.17166 ( 21) link_BETA1-4 : bond 0.00020 ( 1) link_BETA1-4 : angle 1.40845 ( 3) hydrogen bonds : bond 0.05156 ( 305) hydrogen bonds : angle 4.51680 ( 872) metal coordination : bond 0.00280 ( 2) SS BOND : bond 0.00401 ( 7) SS BOND : angle 1.29989 ( 14) covalent geometry : bond 0.00330 ( 6732) covalent geometry : angle 0.54668 ( 9153) *********************** 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 95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7214 (mp0) REVERT: A 435 GLU cc_start: 0.7455 (mp0) cc_final: 0.7012 (mp0) REVERT: B 360 ASN cc_start: 0.7586 (m-40) cc_final: 0.7023 (t0) REVERT: B 420 ASP cc_start: 0.8461 (m-30) cc_final: 0.8208 (m-30) REVERT: B 443 SER cc_start: 0.8708 (m) cc_final: 0.8299 (m) outliers start: 9 outliers final: 6 residues processed: 90 average time/residue: 0.1751 time to fit residues: 21.6888 Evaluate side-chains 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.174149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115926 restraints weight = 15425.434| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.36 r_work: 0.3158 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6749 Z= 0.155 Angle : 0.576 9.634 9191 Z= 0.290 Chirality : 0.043 0.242 980 Planarity : 0.004 0.050 1176 Dihedral : 5.128 55.321 1031 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.00 % Allowed : 12.48 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.80 (0.31), residues: 788 helix: 1.45 (0.27), residues: 382 sheet: 0.56 (0.69), residues: 60 loop : -0.48 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 165 HIS 0.004 0.001 HIS A 34 PHE 0.021 0.002 PHE A 504 TYR 0.025 0.002 TYR A 381 ARG 0.009 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 7) link_NAG-ASN : angle 2.23282 ( 21) link_BETA1-4 : bond 0.00005 ( 1) link_BETA1-4 : angle 1.54131 ( 3) hydrogen bonds : bond 0.05333 ( 305) hydrogen bonds : angle 4.54186 ( 872) metal coordination : bond 0.00289 ( 2) SS BOND : bond 0.00564 ( 7) SS BOND : angle 1.46469 ( 14) covalent geometry : bond 0.00364 ( 6732) covalent geometry : angle 0.56313 ( 9153) *********************** 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 97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.833 Fit side-chains REVERT: A 435 GLU cc_start: 0.7467 (mp0) cc_final: 0.7014 (mp0) REVERT: B 360 ASN cc_start: 0.7573 (m-40) cc_final: 0.6962 (t0) REVERT: B 420 ASP cc_start: 0.8503 (m-30) cc_final: 0.8253 (m-30) REVERT: B 443 SER cc_start: 0.8744 (m) cc_final: 0.8540 (m) outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 0.1749 time to fit residues: 22.4518 Evaluate side-chains 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.0020 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.174264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116552 restraints weight = 15387.065| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.62 r_work: 0.3105 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6749 Z= 0.134 Angle : 0.556 9.625 9191 Z= 0.281 Chirality : 0.042 0.236 980 Planarity : 0.005 0.051 1176 Dihedral : 5.077 55.369 1031 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 1.00 % Allowed : 12.77 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.78 (0.30), residues: 788 helix: 1.47 (0.27), residues: 382 sheet: 0.52 (0.68), residues: 60 loop : -0.53 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.004 0.001 HIS A 34 PHE 0.022 0.001 PHE A 504 TYR 0.019 0.001 TYR A 381 ARG 0.017 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 7) link_NAG-ASN : angle 2.12973 ( 21) link_BETA1-4 : bond 0.00179 ( 1) link_BETA1-4 : angle 1.32339 ( 3) hydrogen bonds : bond 0.05047 ( 305) hydrogen bonds : angle 4.52179 ( 872) metal coordination : bond 0.00236 ( 2) SS BOND : bond 0.00542 ( 7) SS BOND : angle 1.39062 ( 14) covalent geometry : bond 0.00306 ( 6732) covalent geometry : angle 0.54448 ( 9153) ********************** 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 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 GLU cc_start: 0.7417 (mp0) cc_final: 0.6941 (mp0) REVERT: B 360 ASN cc_start: 0.7562 (m-40) cc_final: 0.6956 (t0) REVERT: B 420 ASP cc_start: 0.8588 (m-30) cc_final: 0.8270 (m-30) REVERT: B 443 SER cc_start: 0.8779 (m) cc_final: 0.8346 (m) outliers start: 7 outliers final: 6 residues processed: 89 average time/residue: 0.1825 time to fit residues: 22.3271 Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 70 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 31 optimal weight: 0.0040 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 16 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 overall best weight: 0.2748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 397 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.176691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132950 restraints weight = 8517.368| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.54 r_work: 0.3181 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6749 Z= 0.107 Angle : 0.532 9.584 9191 Z= 0.268 Chirality : 0.041 0.231 980 Planarity : 0.004 0.051 1176 Dihedral : 4.903 55.566 1031 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 1.00 % Allowed : 13.34 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.90 (0.31), residues: 788 helix: 1.59 (0.27), residues: 382 sheet: 0.52 (0.68), residues: 60 loop : -0.49 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.021 0.001 PHE A 504 TYR 0.019 0.001 TYR A 202 ARG 0.017 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 7) link_NAG-ASN : angle 1.94489 ( 21) link_BETA1-4 : bond 0.00414 ( 1) link_BETA1-4 : angle 0.90534 ( 3) hydrogen bonds : bond 0.04306 ( 305) hydrogen bonds : angle 4.41662 ( 872) metal coordination : bond 0.00102 ( 2) SS BOND : bond 0.00509 ( 7) SS BOND : angle 1.17407 ( 14) covalent geometry : bond 0.00226 ( 6732) covalent geometry : angle 0.52268 ( 9153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4885.99 seconds wall clock time: 85 minutes 28.63 seconds (5128.63 seconds total)