Starting phenix.real_space_refine on Sun Apr 27 17:57:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwe_60524/04_2025/8zwe_60524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwe_60524/04_2025/8zwe_60524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zwe_60524/04_2025/8zwe_60524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwe_60524/04_2025/8zwe_60524.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwe_60524/04_2025/8zwe_60524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwe_60524/04_2025/8zwe_60524.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4125 2.51 5 N 1072 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6465 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1556 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 13, 'TRANS': 187} Chain: "B" Number of atoms: 4881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4881 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 30, 'TRANS': 562} Chain: "B" 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 Time building chain proxies: 5.38, per 1000 atoms: 0.83 Number of scatterers: 6465 At special positions: 0 Unit cell: (72.812, 85.504, 116.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1227 8.00 N 1072 7.00 C 4125 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 445 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " 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 B1001 " - " ASN B 53 " " NAG B1002 " - " ASN B 322 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 980.5 milliseconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 53.8% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.740A pdb=" N LEU A 397 " --> pdb=" O PHE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 425 removed outlier: 3.705A pdb=" N LEU A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'B' and resid 21 through 53 removed outlier: 3.545A pdb=" N PHE B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 removed outlier: 4.041A pdb=" N ILE B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.556A pdb=" N ALA B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 157 through 172 Processing helix chain 'B' and resid 176 through 193 removed outlier: 3.561A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 218 through 249 removed outlier: 3.771A pdb=" N LEU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 282 Proline residue: B 280 - end of helix Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 303 through 317 removed outlier: 3.980A pdb=" N ILE B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 3.930A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.690A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.879A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 433 through 443 Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.954A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.581A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 575 removed outlier: 3.763A pdb=" N VAL B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 removed outlier: 3.610A pdb=" N PHE B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 412 removed outlier: 3.505A pdb=" N MET A 571 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 417 Processing sheet with id=AA3, first strand: chain 'A' and resid 518 through 521 removed outlier: 3.867A pdb=" N GLY A 518 " --> pdb=" O THR A 515 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 515 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR A 559 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N CYS A 511 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 557 " --> pdb=" O CYS A 511 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS A 513 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR A 555 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 554 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 263 removed outlier: 5.799A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 350 293 hydrogen bonds defined for protein. 840 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: 1.74 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2074 1.34 - 1.46: 1656 1.46 - 1.58: 2853 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 6649 Sorted by residual: bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" C5 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" C5 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C3 NAG B1001 " pdb=" O3 NAG B1001 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.02e+00 ... (remaining 6644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 8684 1.17 - 2.34: 273 2.34 - 3.50: 58 3.50 - 4.67: 13 4.67 - 5.84: 9 Bond angle restraints: 9037 Sorted by residual: angle pdb=" N ASP A 582 " pdb=" CA ASP A 582 " pdb=" C ASP A 582 " ideal model delta sigma weight residual 107.99 113.83 -5.84 1.76e+00 3.23e-01 1.10e+01 angle pdb=" C ASP A 582 " pdb=" N THR A 583 " pdb=" CA THR A 583 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 angle pdb=" N THR A 583 " pdb=" CA THR A 583 " pdb=" C THR A 583 " ideal model delta sigma weight residual 110.80 116.03 -5.23 2.13e+00 2.20e-01 6.02e+00 angle pdb=" N LYS B 234 " pdb=" CA LYS B 234 " pdb=" C LYS B 234 " ideal model delta sigma weight residual 113.25 116.36 -3.11 1.30e+00 5.92e-01 5.71e+00 angle pdb=" N GLY A 580 " pdb=" CA GLY A 580 " pdb=" C GLY A 580 " ideal model delta sigma weight residual 113.18 118.71 -5.53 2.37e+00 1.78e-01 5.44e+00 ... (remaining 9032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 3490 17.78 - 35.56: 368 35.56 - 53.34: 90 53.34 - 71.11: 16 71.11 - 88.89: 12 Dihedral angle restraints: 3976 sinusoidal: 1637 harmonic: 2339 Sorted by residual: dihedral pdb=" CA THR A 581 " pdb=" C THR A 581 " pdb=" N ASP A 582 " pdb=" CA ASP A 582 " ideal model delta harmonic sigma weight residual -180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA TYR A 579 " pdb=" C TYR A 579 " pdb=" N GLY A 580 " pdb=" CA GLY A 580 " ideal model delta harmonic sigma weight residual 180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CB CYS A 445 " pdb=" SG CYS A 445 " pdb=" SG CYS A 587 " pdb=" CB CYS A 587 " ideal model delta sinusoidal sigma weight residual 93.00 125.20 -32.20 1 1.00e+01 1.00e-02 1.48e+01 ... (remaining 3973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 467 0.024 - 0.047: 293 0.047 - 0.071: 118 0.071 - 0.095: 35 0.095 - 0.118: 38 Chirality restraints: 951 Sorted by residual: chirality pdb=" CA ILE A 574 " pdb=" N ILE A 574 " pdb=" C ILE A 574 " pdb=" CB ILE A 574 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA VAL B 487 " pdb=" N VAL B 487 " pdb=" C VAL B 487 " pdb=" CB VAL B 487 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA LYS B 234 " pdb=" N LYS B 234 " pdb=" C LYS B 234 " pdb=" CB LYS B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 948 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 530 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO A 531 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 531 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 531 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 459 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C TRP B 459 " -0.030 2.00e-02 2.50e+03 pdb=" O TRP B 459 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 460 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 458 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C LYS B 458 " -0.029 2.00e-02 2.50e+03 pdb=" O LYS B 458 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP B 459 " 0.010 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 916 2.76 - 3.29: 5898 3.29 - 3.83: 10727 3.83 - 4.36: 12818 4.36 - 4.90: 22468 Nonbonded interactions: 52827 Sorted by model distance: nonbonded pdb=" OH TYR B 183 " pdb=" OD1 ASP B 509 " model vdw 2.221 3.040 nonbonded pdb=" OG SER B 331 " pdb=" O ILE B 358 " model vdw 2.243 3.040 nonbonded pdb=" O ILE B 59 " pdb=" ND2 ASN B 63 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR B 237 " pdb=" O VAL B 485 " model vdw 2.267 3.040 nonbonded pdb=" NH2 ARG B 245 " pdb=" O PHE B 603 " model vdw 2.316 3.120 ... (remaining 52822 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.250 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:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6657 Z= 0.129 Angle : 0.543 5.839 9055 Z= 0.294 Chirality : 0.040 0.118 951 Planarity : 0.004 0.062 1168 Dihedral : 16.061 88.892 2456 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.30), residues: 790 helix: 0.44 (0.27), residues: 391 sheet: 0.14 (0.51), residues: 79 loop : -0.53 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 165 HIS 0.002 0.001 HIS A 507 PHE 0.023 0.001 PHE A 407 TYR 0.009 0.001 TYR B 497 ARG 0.002 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 2) link_NAG-ASN : angle 3.16313 ( 6) hydrogen bonds : bond 0.17652 ( 293) hydrogen bonds : angle 6.40669 ( 840) SS BOND : bond 0.00163 ( 6) SS BOND : angle 0.61787 ( 12) covalent geometry : bond 0.00267 ( 6649) covalent geometry : angle 0.53654 ( 9037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.726 Fit side-chains REVERT: A 460 MET cc_start: 0.7008 (mtt) cc_final: 0.6666 (mtp) REVERT: B 150 ASP cc_start: 0.7939 (t0) cc_final: 0.7601 (t0) outliers start: 0 outliers final: 1 residues processed: 86 average time/residue: 1.4966 time to fit residues: 134.2723 Evaluate side-chains 78 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.0980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN A 524 ASN B 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.167702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.121122 restraints weight = 7400.288| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.83 r_work: 0.2968 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6657 Z= 0.117 Angle : 0.504 5.331 9055 Z= 0.262 Chirality : 0.040 0.125 951 Planarity : 0.004 0.053 1168 Dihedral : 5.051 38.144 912 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.29 % Favored : 96.58 % Rotamer: Outliers : 2.00 % Allowed : 14.12 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.30), residues: 790 helix: 0.92 (0.27), residues: 399 sheet: 0.34 (0.54), residues: 79 loop : -0.56 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 163 HIS 0.003 0.001 HIS B 241 PHE 0.009 0.001 PHE A 573 TYR 0.011 0.001 TYR B 385 ARG 0.003 0.000 ARG B 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00014 ( 2) link_NAG-ASN : angle 2.91758 ( 6) hydrogen bonds : bond 0.04719 ( 293) hydrogen bonds : angle 4.50938 ( 840) SS BOND : bond 0.00274 ( 6) SS BOND : angle 0.65102 ( 12) covalent geometry : bond 0.00259 ( 6649) covalent geometry : angle 0.49810 ( 9037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.692 Fit side-chains REVERT: A 460 MET cc_start: 0.6818 (mtt) cc_final: 0.6441 (mtp) REVERT: B 150 ASP cc_start: 0.8138 (t0) cc_final: 0.7664 (t0) REVERT: B 288 LYS cc_start: 0.7714 (mmtp) cc_final: 0.7507 (mttm) outliers start: 14 outliers final: 4 residues processed: 94 average time/residue: 1.9833 time to fit residues: 193.6034 Evaluate side-chains 83 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 578 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN A 584 ASN B 420 ASN B 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.168144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122182 restraints weight = 7503.695| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.52 r_work: 0.2963 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6657 Z= 0.164 Angle : 0.538 6.093 9055 Z= 0.277 Chirality : 0.042 0.141 951 Planarity : 0.004 0.051 1168 Dihedral : 4.880 39.305 910 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.71 % Allowed : 13.55 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.42 (0.30), residues: 790 helix: 1.08 (0.27), residues: 392 sheet: 0.39 (0.53), residues: 79 loop : -0.70 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 163 HIS 0.005 0.001 HIS B 241 PHE 0.020 0.002 PHE A 407 TYR 0.016 0.001 TYR B 385 ARG 0.002 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 2) link_NAG-ASN : angle 3.27881 ( 6) hydrogen bonds : bond 0.05026 ( 293) hydrogen bonds : angle 4.38702 ( 840) SS BOND : bond 0.00336 ( 6) SS BOND : angle 0.68886 ( 12) covalent geometry : bond 0.00393 ( 6649) covalent geometry : angle 0.53174 ( 9037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.731 Fit side-chains REVERT: A 460 MET cc_start: 0.7073 (mtt) cc_final: 0.6661 (mtp) REVERT: B 150 ASP cc_start: 0.8199 (t0) cc_final: 0.7713 (t0) REVERT: B 288 LYS cc_start: 0.7750 (mmtp) cc_final: 0.7538 (mttm) outliers start: 19 outliers final: 10 residues processed: 96 average time/residue: 1.1357 time to fit residues: 115.2720 Evaluate side-chains 89 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 597 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 65 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 420 ASN B 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.168833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122452 restraints weight = 7490.379| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.01 r_work: 0.2930 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6657 Z= 0.117 Angle : 0.493 5.408 9055 Z= 0.254 Chirality : 0.040 0.127 951 Planarity : 0.004 0.047 1168 Dihedral : 4.609 36.754 910 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.28 % Allowed : 15.55 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.30), residues: 790 helix: 1.30 (0.27), residues: 386 sheet: 0.35 (0.52), residues: 84 loop : -0.66 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 163 HIS 0.004 0.001 HIS B 241 PHE 0.022 0.001 PHE A 573 TYR 0.011 0.001 TYR B 385 ARG 0.002 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00032 ( 2) link_NAG-ASN : angle 3.00503 ( 6) hydrogen bonds : bond 0.04307 ( 293) hydrogen bonds : angle 4.28660 ( 840) SS BOND : bond 0.00253 ( 6) SS BOND : angle 0.62814 ( 12) covalent geometry : bond 0.00269 ( 6649) covalent geometry : angle 0.48732 ( 9037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.663 Fit side-chains REVERT: A 460 MET cc_start: 0.6815 (mtt) cc_final: 0.6428 (mtp) REVERT: B 150 ASP cc_start: 0.8119 (t0) cc_final: 0.7561 (t0) outliers start: 16 outliers final: 10 residues processed: 95 average time/residue: 1.1570 time to fit residues: 115.9730 Evaluate side-chains 88 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 420 ASN B 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.163008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109757 restraints weight = 7551.486| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.48 r_work: 0.2881 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6657 Z= 0.220 Angle : 0.594 6.954 9055 Z= 0.304 Chirality : 0.044 0.130 951 Planarity : 0.005 0.051 1168 Dihedral : 5.033 42.985 910 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.00 % Allowed : 15.26 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.30), residues: 790 helix: 1.07 (0.27), residues: 392 sheet: 0.32 (0.52), residues: 84 loop : -0.78 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 478 HIS 0.007 0.001 HIS B 241 PHE 0.025 0.002 PHE A 407 TYR 0.018 0.002 TYR B 385 ARG 0.003 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 2) link_NAG-ASN : angle 3.63360 ( 6) hydrogen bonds : bond 0.05692 ( 293) hydrogen bonds : angle 4.42585 ( 840) SS BOND : bond 0.00441 ( 6) SS BOND : angle 0.78015 ( 12) covalent geometry : bond 0.00535 ( 6649) covalent geometry : angle 0.58660 ( 9037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.639 Fit side-chains REVERT: A 396 MET cc_start: 0.4422 (OUTLIER) cc_final: 0.3961 (mpt) REVERT: A 460 MET cc_start: 0.6907 (mtt) cc_final: 0.6485 (mtp) REVERT: B 150 ASP cc_start: 0.8156 (t0) cc_final: 0.7578 (t0) REVERT: B 531 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7839 (tm-30) outliers start: 21 outliers final: 11 residues processed: 98 average time/residue: 1.1332 time to fit residues: 117.2791 Evaluate side-chains 96 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 597 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 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 504 ASN A 524 ASN B 420 ASN B 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.169641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125483 restraints weight = 7475.627| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.15 r_work: 0.2968 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6657 Z= 0.107 Angle : 0.486 5.288 9055 Z= 0.252 Chirality : 0.040 0.127 951 Planarity : 0.004 0.045 1168 Dihedral : 4.570 35.518 910 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.57 % Allowed : 16.41 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 790 helix: 1.32 (0.27), residues: 391 sheet: 0.24 (0.53), residues: 85 loop : -0.62 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 163 HIS 0.003 0.001 HIS B 79 PHE 0.025 0.001 PHE A 407 TYR 0.009 0.001 TYR B 385 ARG 0.002 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00059 ( 2) link_NAG-ASN : angle 2.97639 ( 6) hydrogen bonds : bond 0.04044 ( 293) hydrogen bonds : angle 4.23047 ( 840) SS BOND : bond 0.00207 ( 6) SS BOND : angle 0.61854 ( 12) covalent geometry : bond 0.00240 ( 6649) covalent geometry : angle 0.47963 ( 9037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.727 Fit side-chains REVERT: A 396 MET cc_start: 0.4568 (OUTLIER) cc_final: 0.4104 (mpt) REVERT: A 460 MET cc_start: 0.6975 (mtt) cc_final: 0.6603 (mtp) REVERT: B 150 ASP cc_start: 0.8157 (t0) cc_final: 0.7603 (t0) outliers start: 18 outliers final: 13 residues processed: 101 average time/residue: 1.0728 time to fit residues: 114.6478 Evaluate side-chains 97 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 597 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 6.9990 chunk 68 optimal weight: 0.1980 chunk 19 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN A 524 ASN B 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.169859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126319 restraints weight = 7409.117| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.02 r_work: 0.3012 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6657 Z= 0.104 Angle : 0.490 6.059 9055 Z= 0.252 Chirality : 0.040 0.129 951 Planarity : 0.004 0.042 1168 Dihedral : 4.442 34.988 910 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.28 % Allowed : 16.98 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.30), residues: 790 helix: 1.42 (0.27), residues: 391 sheet: 0.36 (0.53), residues: 85 loop : -0.57 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 163 HIS 0.003 0.001 HIS B 241 PHE 0.024 0.001 PHE A 407 TYR 0.009 0.001 TYR B 385 ARG 0.001 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 2) link_NAG-ASN : angle 2.89258 ( 6) hydrogen bonds : bond 0.03972 ( 293) hydrogen bonds : angle 4.18325 ( 840) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.59053 ( 12) covalent geometry : bond 0.00233 ( 6649) covalent geometry : angle 0.48417 ( 9037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.658 Fit side-chains REVERT: A 396 MET cc_start: 0.4622 (OUTLIER) cc_final: 0.4142 (mpt) REVERT: A 460 MET cc_start: 0.7051 (mtt) cc_final: 0.6686 (mtp) REVERT: B 150 ASP cc_start: 0.8136 (t0) cc_final: 0.7631 (t0) REVERT: B 552 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7703 (mp10) outliers start: 16 outliers final: 11 residues processed: 96 average time/residue: 0.9728 time to fit residues: 99.3406 Evaluate side-chains 97 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 597 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN A 524 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.170725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126718 restraints weight = 7441.356| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.00 r_work: 0.3022 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6657 Z= 0.101 Angle : 0.484 7.244 9055 Z= 0.248 Chirality : 0.039 0.127 951 Planarity : 0.004 0.038 1168 Dihedral : 4.307 34.228 910 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.71 % Allowed : 18.12 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.31), residues: 790 helix: 1.46 (0.27), residues: 392 sheet: 0.39 (0.54), residues: 85 loop : -0.50 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 163 HIS 0.003 0.001 HIS A 507 PHE 0.025 0.001 PHE A 573 TYR 0.009 0.001 TYR B 385 ARG 0.002 0.000 ARG B 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00067 ( 2) link_NAG-ASN : angle 2.75817 ( 6) hydrogen bonds : bond 0.03829 ( 293) hydrogen bonds : angle 4.11439 ( 840) SS BOND : bond 0.00210 ( 6) SS BOND : angle 0.58682 ( 12) covalent geometry : bond 0.00227 ( 6649) covalent geometry : angle 0.47919 ( 9037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.658 Fit side-chains REVERT: A 396 MET cc_start: 0.4740 (OUTLIER) cc_final: 0.4268 (mpt) REVERT: A 460 MET cc_start: 0.7133 (mtt) cc_final: 0.6762 (mtp) REVERT: B 150 ASP cc_start: 0.8156 (t0) cc_final: 0.7689 (t0) outliers start: 12 outliers final: 10 residues processed: 98 average time/residue: 1.0239 time to fit residues: 106.4210 Evaluate side-chains 97 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 597 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 524 ASN B 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.165562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.122307 restraints weight = 7566.369| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.14 r_work: 0.3038 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6657 Z= 0.193 Angle : 0.569 8.548 9055 Z= 0.290 Chirality : 0.043 0.128 951 Planarity : 0.004 0.047 1168 Dihedral : 4.772 41.151 910 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.14 % Allowed : 17.97 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.30), residues: 790 helix: 1.26 (0.27), residues: 392 sheet: 0.43 (0.53), residues: 84 loop : -0.73 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 163 HIS 0.006 0.001 HIS B 241 PHE 0.025 0.002 PHE A 407 TYR 0.016 0.001 TYR B 385 ARG 0.002 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 2) link_NAG-ASN : angle 3.33512 ( 6) hydrogen bonds : bond 0.05088 ( 293) hydrogen bonds : angle 4.25653 ( 840) SS BOND : bond 0.00371 ( 6) SS BOND : angle 0.66555 ( 12) covalent geometry : bond 0.00467 ( 6649) covalent geometry : angle 0.56298 ( 9037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.731 Fit side-chains REVERT: A 396 MET cc_start: 0.4766 (OUTLIER) cc_final: 0.4418 (mpt) REVERT: A 460 MET cc_start: 0.7166 (mtt) cc_final: 0.6587 (mtp) REVERT: B 150 ASP cc_start: 0.8249 (t0) cc_final: 0.7789 (t0) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 1.0858 time to fit residues: 106.8202 Evaluate side-chains 90 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 597 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.168382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124574 restraints weight = 7508.105| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.32 r_work: 0.2964 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6657 Z= 0.136 Angle : 0.522 8.367 9055 Z= 0.267 Chirality : 0.041 0.128 951 Planarity : 0.004 0.040 1168 Dihedral : 4.570 37.710 910 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.00 % Allowed : 18.12 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.30), residues: 790 helix: 1.38 (0.27), residues: 385 sheet: 0.50 (0.53), residues: 84 loop : -0.74 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 163 HIS 0.004 0.001 HIS B 241 PHE 0.025 0.002 PHE A 407 TYR 0.013 0.001 TYR B 385 ARG 0.002 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00040 ( 2) link_NAG-ASN : angle 3.05140 ( 6) hydrogen bonds : bond 0.04370 ( 293) hydrogen bonds : angle 4.19297 ( 840) SS BOND : bond 0.00263 ( 6) SS BOND : angle 0.60595 ( 12) covalent geometry : bond 0.00322 ( 6649) covalent geometry : angle 0.51632 ( 9037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.671 Fit side-chains REVERT: A 396 MET cc_start: 0.4831 (OUTLIER) cc_final: 0.4343 (mpt) REVERT: A 460 MET cc_start: 0.7117 (mtt) cc_final: 0.6764 (mtp) REVERT: B 150 ASP cc_start: 0.8165 (t0) cc_final: 0.7666 (t0) outliers start: 14 outliers final: 11 residues processed: 94 average time/residue: 1.3096 time to fit residues: 131.1769 Evaluate side-chains 95 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 597 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.167188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123233 restraints weight = 7590.465| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.31 r_work: 0.3005 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6657 Z= 0.166 Angle : 0.562 8.638 9055 Z= 0.284 Chirality : 0.042 0.125 951 Planarity : 0.004 0.047 1168 Dihedral : 4.686 39.467 910 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.00 % Allowed : 18.26 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.30), residues: 790 helix: 1.29 (0.27), residues: 392 sheet: 0.48 (0.53), residues: 84 loop : -0.73 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 163 HIS 0.005 0.001 HIS B 241 PHE 0.027 0.002 PHE A 407 TYR 0.015 0.001 TYR B 385 ARG 0.002 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00120 ( 2) link_NAG-ASN : angle 3.25919 ( 6) hydrogen bonds : bond 0.04786 ( 293) hydrogen bonds : angle 4.19150 ( 840) SS BOND : bond 0.00316 ( 6) SS BOND : angle 0.64849 ( 12) covalent geometry : bond 0.00401 ( 6649) covalent geometry : angle 0.55620 ( 9037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6302.03 seconds wall clock time: 112 minutes 3.66 seconds (6723.66 seconds total)