Starting phenix.real_space_refine on Sat May 10 13:17:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwe_60524/05_2025/8zwe_60524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwe_60524/05_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_60524/05_2025/8zwe_60524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwe_60524/05_2025/8zwe_60524.map" model { file = "/net/cci-nas-00/data/ceres_data/8zwe_60524/05_2025/8zwe_60524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwe_60524/05_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-5687/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: 4.16, per 1000 atoms: 0.64 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: 1.38 Conformation dependent library (CDL) restraints added in 840.1 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: 0.62 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: 1.71 Time building geometry restraints manager: 1.67 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.580 Find NCS groups from input model: 0.050 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:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.300 ------------------------------------------------------------------------------- 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 : 0.725 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: 1.1629 time to fit residues: 105.3521 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 : 0.654 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.170661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125449 restraints weight = 7375.654| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.54 r_work: 0.3001 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 5.329 9055 Z= 0.262 Chirality : 0.040 0.125 951 Planarity : 0.004 0.053 1168 Dihedral : 5.051 38.141 912 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 0.00013 ( 2) link_NAG-ASN : angle 2.91616 ( 6) hydrogen bonds : bond 0.04724 ( 293) hydrogen bonds : angle 4.51010 ( 840) SS BOND : bond 0.00274 ( 6) SS BOND : angle 0.64985 ( 12) covalent geometry : bond 0.00259 ( 6649) covalent geometry : angle 0.49814 ( 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 : 0.705 Fit side-chains REVERT: A 460 MET cc_start: 0.6946 (mtt) cc_final: 0.6562 (mtp) REVERT: B 150 ASP cc_start: 0.8172 (t0) cc_final: 0.7720 (t0) outliers start: 14 outliers final: 4 residues processed: 94 average time/residue: 1.0825 time to fit residues: 107.6042 Evaluate side-chains 82 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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: 10.0000 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.167292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.121857 restraints weight = 7507.326| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.75 r_work: 0.2931 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6657 Z= 0.179 Angle : 0.552 6.284 9055 Z= 0.283 Chirality : 0.042 0.141 951 Planarity : 0.004 0.052 1168 Dihedral : 4.934 40.025 910 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.85 % Allowed : 13.69 % Favored : 83.45 % 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: 0.38 (0.30), residues: 790 helix: 1.04 (0.27), residues: 392 sheet: 0.38 (0.53), residues: 79 loop : -0.72 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 163 HIS 0.006 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 0.00145 ( 2) link_NAG-ASN : angle 3.36092 ( 6) hydrogen bonds : bond 0.05201 ( 293) hydrogen bonds : angle 4.40896 ( 840) SS BOND : bond 0.00360 ( 6) SS BOND : angle 0.70747 ( 12) covalent geometry : bond 0.00431 ( 6649) covalent geometry : angle 0.54477 ( 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: 20 poor density : 85 time to evaluate : 0.816 Fit side-chains REVERT: A 460 MET cc_start: 0.7032 (mtt) cc_final: 0.6588 (mtp) REVERT: B 150 ASP cc_start: 0.8189 (t0) cc_final: 0.7690 (t0) REVERT: B 288 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7652 (mttm) outliers start: 20 outliers final: 10 residues processed: 96 average time/residue: 1.0828 time to fit residues: 110.0311 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 : 0.767 ------------------------------------------------------------------------------- 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 288 LYS 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: 8.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.168583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122716 restraints weight = 7497.107| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.90 r_work: 0.2917 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6657 Z= 0.138 Angle : 0.510 5.705 9055 Z= 0.262 Chirality : 0.041 0.127 951 Planarity : 0.004 0.048 1168 Dihedral : 4.692 37.734 910 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.85 % Allowed : 15.12 % Favored : 82.03 % 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: 0.51 (0.30), residues: 790 helix: 1.19 (0.27), residues: 392 sheet: 0.34 (0.52), residues: 84 loop : -0.69 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 163 HIS 0.005 0.001 HIS B 241 PHE 0.021 0.002 PHE A 407 TYR 0.013 0.001 TYR B 385 ARG 0.002 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00064 ( 2) link_NAG-ASN : angle 3.13424 ( 6) hydrogen bonds : bond 0.04545 ( 293) hydrogen bonds : angle 4.31019 ( 840) SS BOND : bond 0.00292 ( 6) SS BOND : angle 0.66124 ( 12) covalent geometry : bond 0.00328 ( 6649) covalent geometry : angle 0.50388 ( 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 106 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.777 Fit side-chains REVERT: A 460 MET cc_start: 0.6831 (mtt) cc_final: 0.6388 (mtp) REVERT: B 150 ASP cc_start: 0.8098 (t0) cc_final: 0.7528 (t0) REVERT: B 288 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7603 (mttm) outliers start: 20 outliers final: 11 residues processed: 97 average time/residue: 1.1098 time to fit residues: 113.8319 Evaluate side-chains 88 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 288 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 351 LEU 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=3.50 ------------------------------------------------------------------------------- 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: 5.9990 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 57 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.165690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.120153 restraints weight = 7508.638| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.67 r_work: 0.2896 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6657 Z= 0.211 Angle : 0.580 6.824 9055 Z= 0.296 Chirality : 0.044 0.127 951 Planarity : 0.004 0.051 1168 Dihedral : 4.974 42.098 910 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.42 % Allowed : 14.84 % 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: 0.35 (0.30), residues: 790 helix: 1.07 (0.27), residues: 392 sheet: 0.29 (0.52), residues: 84 loop : -0.79 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 163 HIS 0.006 0.001 HIS B 241 PHE 0.024 0.002 PHE A 407 TYR 0.017 0.002 TYR B 385 ARG 0.002 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 2) link_NAG-ASN : angle 3.59087 ( 6) hydrogen bonds : bond 0.05465 ( 293) hydrogen bonds : angle 4.40758 ( 840) SS BOND : bond 0.00391 ( 6) SS BOND : angle 0.75244 ( 12) covalent geometry : bond 0.00514 ( 6649) covalent geometry : angle 0.57260 ( 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 109 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.660 Fit side-chains REVERT: A 396 MET cc_start: 0.4522 (OUTLIER) cc_final: 0.4032 (mpt) REVERT: A 460 MET cc_start: 0.6963 (mtt) cc_final: 0.6555 (mtp) REVERT: B 150 ASP cc_start: 0.8150 (t0) cc_final: 0.7580 (t0) REVERT: B 288 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7606 (mttm) outliers start: 24 outliers final: 13 residues processed: 101 average time/residue: 1.0574 time to fit residues: 112.9931 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 : 0.738 ------------------------------------------------------------------------------- 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 59 ILE Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 288 LYS 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=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: 0.6980 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.167393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123571 restraints weight = 7473.779| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.14 r_work: 0.2952 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1514 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= 0.110 Angle : 0.489 5.409 9055 Z= 0.252 Chirality : 0.040 0.129 951 Planarity : 0.004 0.046 1168 Dihedral : 4.566 35.964 910 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.00 % Allowed : 16.83 % Favored : 81.17 % 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: 0.59 (0.30), residues: 790 helix: 1.34 (0.27), residues: 385 sheet: 0.32 (0.52), residues: 84 loop : -0.72 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 163 HIS 0.003 0.001 HIS B 241 PHE 0.023 0.001 PHE A 407 TYR 0.010 0.001 TYR B 385 ARG 0.002 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 2) link_NAG-ASN : angle 3.02296 ( 6) hydrogen bonds : bond 0.04099 ( 293) hydrogen bonds : angle 4.23994 ( 840) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.62861 ( 12) covalent geometry : bond 0.00248 ( 6649) covalent geometry : angle 0.48232 ( 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 103 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.757 Fit side-chains REVERT: A 396 MET cc_start: 0.4539 (OUTLIER) cc_final: 0.4094 (mpt) REVERT: A 460 MET cc_start: 0.6940 (mtt) cc_final: 0.6559 (mtp) REVERT: B 150 ASP cc_start: 0.8134 (t0) cc_final: 0.7561 (t0) REVERT: B 288 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7633 (mttm) REVERT: B 531 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7956 (tm-30) outliers start: 14 outliers final: 9 residues processed: 98 average time/residue: 1.0847 time to fit residues: 112.5569 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 : 0.728 ------------------------------------------------------------------------------- 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 B residue 59 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 288 LYS 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 531 GLN Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 0.0000 chunk 67 optimal weight: 2.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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 472 GLN B 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.168335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115500 restraints weight = 7415.759| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.18 r_work: 0.2995 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1571 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= 0.132 Angle : 0.511 6.125 9055 Z= 0.262 Chirality : 0.041 0.128 951 Planarity : 0.004 0.044 1168 Dihedral : 4.562 36.939 910 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.43 % Allowed : 16.98 % Favored : 80.60 % 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: 1.37 (0.27), residues: 386 sheet: 0.35 (0.52), residues: 84 loop : -0.70 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 163 HIS 0.004 0.001 HIS B 241 PHE 0.023 0.002 PHE A 573 TYR 0.012 0.001 TYR B 385 ARG 0.001 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00046 ( 2) link_NAG-ASN : angle 3.10900 ( 6) hydrogen bonds : bond 0.04361 ( 293) hydrogen bonds : angle 4.21932 ( 840) SS BOND : bond 0.00269 ( 6) SS BOND : angle 0.61978 ( 12) covalent geometry : bond 0.00312 ( 6649) covalent geometry : angle 0.50491 ( 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 104 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.734 Fit side-chains REVERT: A 396 MET cc_start: 0.4590 (OUTLIER) cc_final: 0.4153 (mpt) REVERT: A 460 MET cc_start: 0.6987 (mtt) cc_final: 0.6619 (mtp) REVERT: B 150 ASP cc_start: 0.8138 (t0) cc_final: 0.7580 (t0) REVERT: B 288 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7636 (mttm) outliers start: 17 outliers final: 9 residues processed: 98 average time/residue: 1.0693 time to fit residues: 110.7960 Evaluate side-chains 96 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 288 LYS 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 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: 7.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 472 GLN B 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.166812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.116636 restraints weight = 7420.121| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.29 r_work: 0.2944 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6657 Z= 0.140 Angle : 0.525 7.305 9055 Z= 0.269 Chirality : 0.041 0.125 951 Planarity : 0.004 0.044 1168 Dihedral : 4.608 38.226 910 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.14 % Allowed : 17.55 % Favored : 80.31 % 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: 0.60 (0.30), residues: 790 helix: 1.31 (0.27), residues: 392 sheet: 0.32 (0.52), residues: 84 loop : -0.71 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 163 HIS 0.005 0.001 HIS B 241 PHE 0.023 0.002 PHE A 407 TYR 0.013 0.001 TYR B 385 ARG 0.001 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 2) link_NAG-ASN : angle 3.16932 ( 6) hydrogen bonds : bond 0.04514 ( 293) hydrogen bonds : angle 4.21708 ( 840) SS BOND : bond 0.00291 ( 6) SS BOND : angle 0.64484 ( 12) covalent geometry : bond 0.00333 ( 6649) covalent geometry : angle 0.51898 ( 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: 15 poor density : 88 time to evaluate : 0.724 Fit side-chains REVERT: A 396 MET cc_start: 0.4678 (OUTLIER) cc_final: 0.4289 (mpt) REVERT: A 460 MET cc_start: 0.6910 (mtt) cc_final: 0.6538 (mtp) REVERT: B 150 ASP cc_start: 0.8127 (t0) cc_final: 0.7581 (t0) REVERT: B 288 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7606 (mttm) outliers start: 15 outliers final: 9 residues processed: 98 average time/residue: 1.1123 time to fit residues: 115.2591 Evaluate side-chains 94 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 589 MET Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 574 VAL 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: 9.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 0.0000 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN B 472 GLN B 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.165605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.120026 restraints weight = 7575.117| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.76 r_work: 0.2935 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6657 Z= 0.205 Angle : 0.585 8.314 9055 Z= 0.298 Chirality : 0.043 0.124 951 Planarity : 0.005 0.048 1168 Dihedral : 4.895 41.644 910 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.28 % Allowed : 17.55 % 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: 0.43 (0.30), residues: 790 helix: 1.17 (0.27), residues: 392 sheet: 0.30 (0.52), residues: 84 loop : -0.80 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 163 HIS 0.006 0.001 HIS B 241 PHE 0.026 0.002 PHE A 407 TYR 0.016 0.002 TYR B 385 ARG 0.005 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 2) link_NAG-ASN : angle 3.54864 ( 6) hydrogen bonds : bond 0.05273 ( 293) hydrogen bonds : angle 4.31798 ( 840) SS BOND : bond 0.00378 ( 6) SS BOND : angle 0.72877 ( 12) covalent geometry : bond 0.00498 ( 6649) covalent geometry : angle 0.57751 ( 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 96 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.755 Fit side-chains REVERT: A 396 MET cc_start: 0.4764 (OUTLIER) cc_final: 0.4308 (mpt) REVERT: A 460 MET cc_start: 0.7063 (mtt) cc_final: 0.6494 (mtp) REVERT: B 150 ASP cc_start: 0.8174 (t0) cc_final: 0.7624 (t0) REVERT: B 288 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7594 (mttm) outliers start: 16 outliers final: 9 residues processed: 92 average time/residue: 1.1199 time to fit residues: 108.7615 Evaluate side-chains 89 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 288 LYS 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 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: 5.9990 chunk 62 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 47 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 524 ASN B 472 GLN B 552 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.169351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125997 restraints weight = 7493.024| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.13 r_work: 0.2993 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6657 Z= 0.106 Angle : 0.514 8.381 9055 Z= 0.263 Chirality : 0.040 0.127 951 Planarity : 0.004 0.043 1168 Dihedral : 4.537 35.858 910 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.57 % Allowed : 18.12 % Favored : 80.31 % 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: 0.64 (0.30), residues: 790 helix: 1.34 (0.27), residues: 392 sheet: 0.31 (0.53), residues: 84 loop : -0.67 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 163 HIS 0.003 0.001 HIS B 241 PHE 0.026 0.001 PHE A 407 TYR 0.009 0.001 TYR A 505 ARG 0.005 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 2) link_NAG-ASN : angle 2.96844 ( 6) hydrogen bonds : bond 0.03983 ( 293) hydrogen bonds : angle 4.17751 ( 840) SS BOND : bond 0.00211 ( 6) SS BOND : angle 0.60929 ( 12) covalent geometry : bond 0.00237 ( 6649) covalent geometry : angle 0.50862 ( 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 101 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.697 Fit side-chains REVERT: A 396 MET cc_start: 0.5090 (OUTLIER) cc_final: 0.4681 (mpt) REVERT: A 458 THR cc_start: 0.7079 (m) cc_final: 0.6871 (m) REVERT: A 460 MET cc_start: 0.7142 (mtt) cc_final: 0.6718 (mtp) REVERT: B 150 ASP cc_start: 0.8134 (t0) cc_final: 0.7634 (t0) REVERT: B 288 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7647 (mttm) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 1.1444 time to fit residues: 118.8444 Evaluate side-chains 98 residues out of total 701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 288 LYS 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 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: 0.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 472 GLN B 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.163676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.114208 restraints weight = 7634.025| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.67 r_work: 0.2899 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1840 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= 0.186 Angle : 0.579 8.727 9055 Z= 0.293 Chirality : 0.043 0.125 951 Planarity : 0.004 0.050 1168 Dihedral : 4.788 40.465 910 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.28 % Allowed : 17.69 % Favored : 80.03 % 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: 0.53 (0.30), residues: 790 helix: 1.24 (0.27), residues: 392 sheet: 0.32 (0.53), residues: 84 loop : -0.72 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 163 HIS 0.006 0.001 HIS B 241 PHE 0.028 0.002 PHE A 407 TYR 0.015 0.002 TYR B 385 ARG 0.005 0.000 ARG B 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 2) link_NAG-ASN : angle 3.40890 ( 6) hydrogen bonds : bond 0.05008 ( 293) hydrogen bonds : angle 4.24911 ( 840) SS BOND : bond 0.00345 ( 6) SS BOND : angle 0.67086 ( 12) covalent geometry : bond 0.00453 ( 6649) covalent geometry : angle 0.57251 ( 9037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5149.84 seconds wall clock time: 89 minutes 31.03 seconds (5371.03 seconds total)