Starting phenix.real_space_refine on Sun Mar 10 21:24:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcq_30639/03_2024/7dcq_30639.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcq_30639/03_2024/7dcq_30639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcq_30639/03_2024/7dcq_30639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcq_30639/03_2024/7dcq_30639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcq_30639/03_2024/7dcq_30639.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcq_30639/03_2024/7dcq_30639.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 33 5.16 5 C 3316 2.51 5 N 892 2.21 5 O 956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "x ASP 391": "OD1" <-> "OD2" Residue "x ARG 465": "NH1" <-> "NH2" Residue "x PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5197 Number of models: 1 Model: "" Number of chains: 1 Chain: "x" Number of atoms: 5197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5197 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 619} Time building chain proxies: 3.33, per 1000 atoms: 0.64 Number of scatterers: 5197 At special positions: 0 Unit cell: (80.1625, 88.1125, 81.4875, 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 33 16.00 O 956 8.00 N 892 7.00 C 3316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 891.0 milliseconds 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 5 sheets defined 51.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'x' and resid 225 through 227 No H-bonds generated for 'chain 'x' and resid 225 through 227' Processing helix chain 'x' and resid 228 through 239 removed outlier: 3.501A pdb=" N LYS x 238 " --> pdb=" O GLN x 234 " (cutoff:3.500A) Processing helix chain 'x' and resid 251 through 263 removed outlier: 3.500A pdb=" N LEU x 256 " --> pdb=" O LYS x 252 " (cutoff:3.500A) Proline residue: x 257 - end of helix Processing helix chain 'x' and resid 279 through 295 removed outlier: 3.558A pdb=" N ALA x 287 " --> pdb=" O ALA x 283 " (cutoff:3.500A) Processing helix chain 'x' and resid 324 through 329 removed outlier: 3.643A pdb=" N LEU x 328 " --> pdb=" O ASP x 324 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG x 329 " --> pdb=" O GLY x 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 324 through 329' Processing helix chain 'x' and resid 329 through 334 removed outlier: 4.076A pdb=" N THR x 333 " --> pdb=" O ARG x 329 " (cutoff:3.500A) Processing helix chain 'x' and resid 347 through 351 Processing helix chain 'x' and resid 352 through 369 removed outlier: 3.693A pdb=" N ASP x 364 " --> pdb=" O GLY x 360 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE x 365 " --> pdb=" O LEU x 361 " (cutoff:3.500A) Proline residue: x 367 - end of helix Processing helix chain 'x' and resid 382 through 390 removed outlier: 3.598A pdb=" N PHE x 386 " --> pdb=" O ASN x 382 " (cutoff:3.500A) Processing helix chain 'x' and resid 416 through 432 removed outlier: 3.517A pdb=" N ILE x 422 " --> pdb=" O ILE x 418 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR x 423 " --> pdb=" O HIS x 419 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR x 431 " --> pdb=" O GLN x 427 " (cutoff:3.500A) Processing helix chain 'x' and resid 444 through 463 removed outlier: 3.839A pdb=" N ILE x 448 " --> pdb=" O GLY x 444 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU x 449 " --> pdb=" O GLN x 445 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU x 457 " --> pdb=" O THR x 453 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE x 458 " --> pdb=" O LYS x 454 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS x 461 " --> pdb=" O GLU x 457 " (cutoff:3.500A) Processing helix chain 'x' and resid 479 through 487 removed outlier: 3.684A pdb=" N LYS x 485 " --> pdb=" O GLU x 481 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE x 487 " --> pdb=" O GLN x 483 " (cutoff:3.500A) Processing helix chain 'x' and resid 542 through 551 Processing helix chain 'x' and resid 566 through 572 Processing helix chain 'x' and resid 580 through 584 Processing helix chain 'x' and resid 587 through 598 Processing helix chain 'x' and resid 612 through 626 Processing helix chain 'x' and resid 636 through 643 Processing helix chain 'x' and resid 648 through 661 removed outlier: 3.698A pdb=" N ALA x 659 " --> pdb=" O LEU x 655 " (cutoff:3.500A) Processing helix chain 'x' and resid 667 through 680 removed outlier: 3.560A pdb=" N THR x 673 " --> pdb=" O GLU x 669 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS x 679 " --> pdb=" O VAL x 675 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU x 680 " --> pdb=" O SER x 676 " (cutoff:3.500A) Processing helix chain 'x' and resid 681 through 684 Processing helix chain 'x' and resid 688 through 697 removed outlier: 3.587A pdb=" N ALA x 692 " --> pdb=" O GLN x 688 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER x 695 " --> pdb=" O ASP x 691 " (cutoff:3.500A) Processing helix chain 'x' and resid 702 through 717 removed outlier: 3.609A pdb=" N PHE x 711 " --> pdb=" O TYR x 707 " (cutoff:3.500A) Processing helix chain 'x' and resid 720 through 727 removed outlier: 3.936A pdb=" N CYS x 724 " --> pdb=" O SER x 720 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP x 726 " --> pdb=" O SER x 722 " (cutoff:3.500A) Processing helix chain 'x' and resid 730 through 752 Processing helix chain 'x' and resid 752 through 764 removed outlier: 3.544A pdb=" N LYS x 756 " --> pdb=" O GLY x 752 " (cutoff:3.500A) Processing helix chain 'x' and resid 770 through 783 removed outlier: 3.847A pdb=" N ILE x 775 " --> pdb=" O ILE x 771 " (cutoff:3.500A) Processing helix chain 'x' and resid 813 through 821 removed outlier: 3.621A pdb=" N VAL x 817 " --> pdb=" O SER x 813 " (cutoff:3.500A) Processing helix chain 'x' and resid 852 through 859 removed outlier: 3.643A pdb=" N ILE x 856 " --> pdb=" O GLU x 852 " (cutoff:3.500A) Processing helix chain 'x' and resid 859 through 867 removed outlier: 4.837A pdb=" N ASP x 865 " --> pdb=" O GLN x 861 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU x 866 " --> pdb=" O ILE x 862 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 310 through 311 removed outlier: 6.874A pdb=" N GLY x 303 " --> pdb=" O TYR x 321 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR x 323 " --> pdb=" O GLY x 303 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLN x 305 " --> pdb=" O THR x 323 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE x 273 " --> pdb=" O LYS x 320 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET x 322 " --> pdb=" O ILE x 273 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE x 275 " --> pdb=" O MET x 322 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN x 272 " --> pdb=" O SER x 341 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE x 343 " --> pdb=" O GLN x 272 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA x 274 " --> pdb=" O ILE x 343 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE x 345 " --> pdb=" O ALA x 274 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR x 276 " --> pdb=" O ILE x 345 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER x 378 " --> pdb=" O ILE x 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 405 through 409 removed outlier: 6.115A pdb=" N ASP x 406 " --> pdb=" O CYS x 561 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ARG x 563 " --> pdb=" O ASP x 406 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N HIS x 408 " --> pdb=" O ARG x 563 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS x 560 " --> pdb=" O ARG x 514 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASP x 437 " --> pdb=" O TYR x 515 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE x 517 " --> pdb=" O ASP x 437 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU x 439 " --> pdb=" O ILE x 517 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE x 438 " --> pdb=" O VAL x 498 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA x 500 " --> pdb=" O ILE x 438 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL x 440 " --> pdb=" O ALA x 500 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN x 468 " --> pdb=" O ARG x 495 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL x 497 " --> pdb=" O GLN x 468 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE x 470 " --> pdb=" O VAL x 497 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU x 499 " --> pdb=" O ILE x 470 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR x 472 " --> pdb=" O LEU x 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'x' and resid 521 through 527 Processing sheet with id=AA4, first strand: chain 'x' and resid 795 through 797 removed outlier: 4.091A pdb=" N TYR x 829 " --> pdb=" O ILE x 849 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'x' and resid 808 through 809 removed outlier: 3.557A pdb=" N GLN x 834 " --> pdb=" O ARG x 844 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 615 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: 1.56 Time building geometry restraints manager: 1.99 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: 1637 1.34 - 1.45: 649 1.45 - 1.57: 2954 1.57 - 1.69: 1 1.69 - 1.81: 53 Bond restraints: 5294 Sorted by residual: bond pdb=" CA ARG x 584 " pdb=" CB ARG x 584 " ideal model delta sigma weight residual 1.531 1.610 -0.079 3.12e-02 1.03e+03 6.42e+00 bond pdb=" N GLN x 412 " pdb=" CA GLN x 412 " ideal model delta sigma weight residual 1.455 1.470 -0.015 7.00e-03 2.04e+04 4.45e+00 bond pdb=" C GLN x 412 " pdb=" N PRO x 413 " ideal model delta sigma weight residual 1.332 1.354 -0.022 1.32e-02 5.74e+03 2.83e+00 bond pdb=" CB ARG x 584 " pdb=" CG ARG x 584 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.72e+00 bond pdb=" CA LEU x 411 " pdb=" C LEU x 411 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.30e-02 5.92e+03 2.56e+00 ... (remaining 5289 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.14: 124 105.14 - 112.35: 2683 112.35 - 119.56: 1755 119.56 - 126.77: 2540 126.77 - 133.99: 57 Bond angle restraints: 7159 Sorted by residual: angle pdb=" N LEU x 411 " pdb=" CA LEU x 411 " pdb=" C LEU x 411 " ideal model delta sigma weight residual 111.28 120.48 -9.20 1.09e+00 8.42e-01 7.12e+01 angle pdb=" N GLU x 414 " pdb=" CA GLU x 414 " pdb=" C GLU x 414 " ideal model delta sigma weight residual 107.62 120.48 -12.86 1.97e+00 2.58e-01 4.26e+01 angle pdb=" C GLN x 412 " pdb=" N PRO x 413 " pdb=" CA PRO x 413 " ideal model delta sigma weight residual 119.76 113.74 6.02 1.00e+00 1.00e+00 3.62e+01 angle pdb=" C THR x 266 " pdb=" N ASP x 267 " pdb=" CA ASP x 267 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C THR x 838 " pdb=" N SER x 839 " pdb=" CA SER x 839 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 ... (remaining 7154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 3074 14.73 - 29.45: 131 29.45 - 44.18: 52 44.18 - 58.90: 5 58.90 - 73.63: 5 Dihedral angle restraints: 3267 sinusoidal: 1360 harmonic: 1907 Sorted by residual: dihedral pdb=" C ASP x 391 " pdb=" N ASP x 391 " pdb=" CA ASP x 391 " pdb=" CB ASP x 391 " ideal model delta harmonic sigma weight residual -122.60 -134.75 12.15 0 2.50e+00 1.60e-01 2.36e+01 dihedral pdb=" N ASP x 391 " pdb=" C ASP x 391 " pdb=" CA ASP x 391 " pdb=" CB ASP x 391 " ideal model delta harmonic sigma weight residual 122.80 134.26 -11.46 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" CA ILE x 862 " pdb=" C ILE x 862 " pdb=" N PHE x 863 " pdb=" CA PHE x 863 " ideal model delta harmonic sigma weight residual -180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 3264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 737 0.092 - 0.183: 86 0.183 - 0.275: 4 0.275 - 0.366: 4 0.366 - 0.458: 1 Chirality restraints: 832 Sorted by residual: chirality pdb=" CA ASP x 391 " pdb=" N ASP x 391 " pdb=" C ASP x 391 " pdb=" CB ASP x 391 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CB THR x 585 " pdb=" CA THR x 585 " pdb=" OG1 THR x 585 " pdb=" CG2 THR x 585 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA GLU x 414 " pdb=" N GLU x 414 " pdb=" C GLU x 414 " pdb=" CB GLU x 414 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 829 not shown) Planarity restraints: 909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE x 605 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.35e+00 pdb=" N PRO x 606 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO x 606 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO x 606 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU x 434 " 0.047 5.00e-02 4.00e+02 7.19e-02 8.26e+00 pdb=" N PRO x 435 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO x 435 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO x 435 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR x 409 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C TYR x 409 " 0.044 2.00e-02 2.50e+03 pdb=" O TYR x 409 " -0.017 2.00e-02 2.50e+03 pdb=" N THR x 410 " -0.015 2.00e-02 2.50e+03 ... (remaining 906 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1785 2.88 - 3.39: 4953 3.39 - 3.89: 8352 3.89 - 4.40: 9688 4.40 - 4.90: 16503 Nonbonded interactions: 41281 Sorted by model distance: nonbonded pdb=" OE1 GLU x 644 " pdb=" NZ LYS x 750 " model vdw 2.378 2.520 nonbonded pdb=" O LEU x 337 " pdb=" NH1 ARG x 369 " model vdw 2.383 2.520 nonbonded pdb=" OE1 GLN x 834 " pdb=" NH2 ARG x 844 " model vdw 2.386 2.520 nonbonded pdb=" OG1 THR x 266 " pdb=" N ASP x 267 " model vdw 2.397 2.520 nonbonded pdb=" OE2 GLU x 449 " pdb=" OH TYR x 475 " model vdw 2.397 2.440 ... (remaining 41276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.580 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: 0.010 Extract box with map and model: 6.070 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.450 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.006 0.079 5294 Z= 0.391 Angle : 0.949 12.856 7159 Z= 0.516 Chirality : 0.061 0.458 832 Planarity : 0.008 0.072 909 Dihedral : 10.613 73.626 2031 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.85 % Allowed : 2.73 % Favored : 96.42 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 3.03 % 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: -3.49 (0.26), residues: 651 helix: -3.36 (0.17), residues: 277 sheet: -0.46 (0.45), residues: 123 loop : -1.75 (0.34), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP x 723 HIS 0.004 0.001 HIS x 572 PHE 0.028 0.003 PHE x 863 TYR 0.023 0.003 TYR x 321 ARG 0.010 0.001 ARG x 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 454 LYS cc_start: 0.7709 (tptp) cc_final: 0.7309 (tttt) REVERT: x 494 CYS cc_start: 0.7814 (m) cc_final: 0.7509 (m) outliers start: 5 outliers final: 1 residues processed: 150 average time/residue: 1.3224 time to fit residues: 205.5010 Evaluate side-chains 79 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 585 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 295 ASN x 408 HIS x 477 ASN x 586 ASN ** x 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 743 GLN x 834 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5294 Z= 0.208 Angle : 0.616 7.233 7159 Z= 0.314 Chirality : 0.044 0.186 832 Planarity : 0.006 0.065 909 Dihedral : 5.042 42.887 707 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.90 % Allowed : 14.65 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.31 (0.30), residues: 651 helix: -0.82 (0.26), residues: 293 sheet: -0.11 (0.47), residues: 121 loop : -1.10 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 PHE 0.018 0.002 PHE x 863 TYR 0.009 0.002 TYR x 409 ARG 0.007 0.001 ARG x 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: x 305 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: x 320 LYS cc_start: 0.8295 (ptmt) cc_final: 0.7984 (ptpt) REVERT: x 454 LYS cc_start: 0.7667 (tptp) cc_final: 0.7251 (tttt) outliers start: 17 outliers final: 8 residues processed: 105 average time/residue: 1.1358 time to fit residues: 124.6692 Evaluate side-chains 86 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 292 ASP Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 342 CYS Chi-restraints excluded: chain x residue 382 ASN Chi-restraints excluded: chain x residue 443 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 0.0570 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5294 Z= 0.184 Angle : 0.557 6.214 7159 Z= 0.281 Chirality : 0.043 0.178 832 Planarity : 0.005 0.056 909 Dihedral : 4.721 44.612 707 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.41 % Allowed : 17.55 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.21 (0.32), residues: 651 helix: 0.47 (0.29), residues: 293 sheet: 0.17 (0.48), residues: 121 loop : -0.95 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP x 723 HIS 0.002 0.001 HIS x 419 PHE 0.014 0.002 PHE x 863 TYR 0.008 0.001 TYR x 832 ARG 0.004 0.000 ARG x 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: x 320 LYS cc_start: 0.8295 (ptmt) cc_final: 0.7981 (ptpt) REVERT: x 422 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7626 (pt) REVERT: x 454 LYS cc_start: 0.7717 (tptp) cc_final: 0.7394 (tttt) REVERT: x 604 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8236 (tptm) REVERT: x 703 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: x 767 ILE cc_start: 0.5411 (OUTLIER) cc_final: 0.4932 (mt) outliers start: 20 outliers final: 10 residues processed: 104 average time/residue: 1.1532 time to fit residues: 125.3242 Evaluate side-chains 89 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 342 CYS Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 422 ILE Chi-restraints excluded: chain x residue 424 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 685 PHE Chi-restraints excluded: chain x residue 703 ASP Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 725 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5294 Z= 0.200 Angle : 0.548 6.184 7159 Z= 0.277 Chirality : 0.043 0.205 832 Planarity : 0.005 0.055 909 Dihedral : 4.697 47.451 707 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.94 % Allowed : 17.04 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.25 (0.33), residues: 651 helix: 1.08 (0.31), residues: 293 sheet: 0.09 (0.48), residues: 122 loop : -0.86 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 PHE 0.014 0.002 PHE x 863 TYR 0.011 0.001 TYR x 795 ARG 0.008 0.000 ARG x 401 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 83 time to evaluate : 0.669 Fit side-chains REVERT: x 454 LYS cc_start: 0.7738 (tptp) cc_final: 0.7419 (tttt) REVERT: x 604 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8337 (tptm) REVERT: x 767 ILE cc_start: 0.5530 (OUTLIER) cc_final: 0.5011 (mt) outliers start: 29 outliers final: 12 residues processed: 100 average time/residue: 0.9424 time to fit residues: 99.5273 Evaluate side-chains 90 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 424 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 685 PHE Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 727 HIS x 834 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5294 Z= 0.162 Angle : 0.522 6.416 7159 Z= 0.262 Chirality : 0.043 0.156 832 Planarity : 0.004 0.052 909 Dihedral : 4.549 47.175 707 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.77 % Allowed : 16.87 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.34), residues: 651 helix: 1.50 (0.31), residues: 292 sheet: 0.18 (0.49), residues: 121 loop : -0.84 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 723 HIS 0.002 0.001 HIS x 408 PHE 0.015 0.002 PHE x 816 TYR 0.008 0.001 TYR x 832 ARG 0.005 0.000 ARG x 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 76 time to evaluate : 0.623 Fit side-chains REVERT: x 454 LYS cc_start: 0.7587 (tptp) cc_final: 0.7250 (ttpt) REVERT: x 577 MET cc_start: 0.7554 (tpt) cc_final: 0.7286 (tpt) REVERT: x 767 ILE cc_start: 0.5427 (OUTLIER) cc_final: 0.4918 (mt) outliers start: 28 outliers final: 12 residues processed: 95 average time/residue: 0.9248 time to fit residues: 92.7906 Evaluate side-chains 86 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 292 ASP Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 685 PHE Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Chi-restraints excluded: chain x residue 781 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 62 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 480 GLN x 630 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5294 Z= 0.144 Angle : 0.522 6.945 7159 Z= 0.261 Chirality : 0.042 0.144 832 Planarity : 0.004 0.050 909 Dihedral : 4.435 47.781 707 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.92 % Allowed : 17.55 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.82 (0.34), residues: 651 helix: 1.76 (0.32), residues: 292 sheet: 0.13 (0.49), residues: 121 loop : -0.74 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP x 723 HIS 0.002 0.001 HIS x 429 PHE 0.011 0.001 PHE x 426 TYR 0.008 0.001 TYR x 832 ARG 0.004 0.000 ARG x 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 0.583 Fit side-chains REVERT: x 221 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7843 (mttt) REVERT: x 305 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: x 422 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7550 (pt) REVERT: x 454 LYS cc_start: 0.7545 (tptp) cc_final: 0.7242 (tttt) REVERT: x 641 MET cc_start: 0.7480 (ttp) cc_final: 0.7259 (ttp) REVERT: x 767 ILE cc_start: 0.5470 (OUTLIER) cc_final: 0.4954 (mt) outliers start: 23 outliers final: 11 residues processed: 86 average time/residue: 1.0936 time to fit residues: 98.8961 Evaluate side-chains 84 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 221 LYS Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 322 MET Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 422 ILE Chi-restraints excluded: chain x residue 424 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 685 PHE Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Chi-restraints excluded: chain x residue 781 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5294 Z= 0.173 Angle : 0.540 7.389 7159 Z= 0.270 Chirality : 0.043 0.134 832 Planarity : 0.004 0.050 909 Dihedral : 4.441 47.210 707 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.75 % Allowed : 18.23 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.89 (0.34), residues: 651 helix: 1.85 (0.32), residues: 292 sheet: 0.06 (0.48), residues: 119 loop : -0.68 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 723 HIS 0.002 0.001 HIS x 429 PHE 0.011 0.002 PHE x 863 TYR 0.009 0.001 TYR x 475 ARG 0.005 0.000 ARG x 844 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.621 Fit side-chains REVERT: x 221 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7862 (mttt) REVERT: x 301 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.6183 (mp0) REVERT: x 305 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: x 422 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7560 (pt) REVERT: x 454 LYS cc_start: 0.7590 (tptp) cc_final: 0.7260 (tttt) REVERT: x 641 MET cc_start: 0.7448 (ttp) cc_final: 0.7191 (ttp) REVERT: x 767 ILE cc_start: 0.5430 (OUTLIER) cc_final: 0.4913 (mt) outliers start: 22 outliers final: 11 residues processed: 90 average time/residue: 1.0838 time to fit residues: 102.4295 Evaluate side-chains 90 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 221 LYS Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 301 GLU Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 422 ILE Chi-restraints excluded: chain x residue 424 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 685 PHE Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Chi-restraints excluded: chain x residue 781 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 239 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5294 Z= 0.224 Angle : 0.570 7.199 7159 Z= 0.286 Chirality : 0.044 0.144 832 Planarity : 0.004 0.051 909 Dihedral : 4.596 47.270 707 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.60 % Allowed : 17.89 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.34), residues: 651 helix: 1.76 (0.31), residues: 292 sheet: -0.03 (0.48), residues: 119 loop : -0.68 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP x 723 HIS 0.004 0.001 HIS x 429 PHE 0.018 0.002 PHE x 816 TYR 0.011 0.001 TYR x 475 ARG 0.004 0.000 ARG x 844 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 0.676 Fit side-chains REVERT: x 221 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7913 (mttt) REVERT: x 301 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: x 305 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: x 347 GLU cc_start: 0.7741 (mp0) cc_final: 0.7504 (mm-30) REVERT: x 422 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7551 (pt) REVERT: x 454 LYS cc_start: 0.7656 (tptp) cc_final: 0.7326 (tttt) REVERT: x 564 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8242 (mm) REVERT: x 641 MET cc_start: 0.7465 (ttp) cc_final: 0.7248 (ttp) REVERT: x 767 ILE cc_start: 0.5531 (OUTLIER) cc_final: 0.5006 (mt) outliers start: 27 outliers final: 12 residues processed: 95 average time/residue: 1.0218 time to fit residues: 102.0344 Evaluate side-chains 91 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 221 LYS Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 292 ASP Chi-restraints excluded: chain x residue 301 GLU Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 422 ILE Chi-restraints excluded: chain x residue 424 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 564 ILE Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 685 PHE Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 630 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5294 Z= 0.201 Angle : 0.572 8.370 7159 Z= 0.284 Chirality : 0.044 0.156 832 Planarity : 0.004 0.049 909 Dihedral : 4.581 47.364 707 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.24 % Allowed : 18.91 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.34), residues: 651 helix: 1.81 (0.31), residues: 292 sheet: -0.07 (0.48), residues: 119 loop : -0.64 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 PHE 0.013 0.002 PHE x 426 TYR 0.009 0.001 TYR x 475 ARG 0.005 0.000 ARG x 844 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.590 Fit side-chains REVERT: x 221 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7892 (mttt) REVERT: x 301 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: x 305 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: x 422 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7552 (pt) REVERT: x 454 LYS cc_start: 0.7620 (tptp) cc_final: 0.7294 (tttt) REVERT: x 564 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8209 (mm) REVERT: x 767 ILE cc_start: 0.5493 (OUTLIER) cc_final: 0.4965 (mt) outliers start: 19 outliers final: 10 residues processed: 86 average time/residue: 1.1473 time to fit residues: 103.3980 Evaluate side-chains 87 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 221 LYS Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 301 GLU Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 422 ILE Chi-restraints excluded: chain x residue 424 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 564 ILE Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 685 PHE Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5294 Z= 0.177 Angle : 0.566 9.814 7159 Z= 0.279 Chirality : 0.043 0.153 832 Planarity : 0.004 0.049 909 Dihedral : 4.533 47.672 707 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.24 % Allowed : 19.25 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.93 (0.35), residues: 651 helix: 1.91 (0.32), residues: 292 sheet: -0.06 (0.48), residues: 119 loop : -0.60 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 PHE 0.023 0.002 PHE x 816 TYR 0.010 0.001 TYR x 624 ARG 0.004 0.000 ARG x 844 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.562 Fit side-chains REVERT: x 221 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7877 (mttt) REVERT: x 301 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: x 305 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: x 422 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7561 (pt) REVERT: x 454 LYS cc_start: 0.7547 (tptp) cc_final: 0.7282 (tttt) REVERT: x 564 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8211 (mm) REVERT: x 767 ILE cc_start: 0.5444 (OUTLIER) cc_final: 0.4912 (mt) outliers start: 19 outliers final: 12 residues processed: 84 average time/residue: 1.0527 time to fit residues: 92.8638 Evaluate side-chains 86 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 221 LYS Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 301 GLU Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 382 ASN Chi-restraints excluded: chain x residue 422 ILE Chi-restraints excluded: chain x residue 424 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 564 ILE Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 685 PHE Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.149930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128297 restraints weight = 6704.078| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.18 r_work: 0.3532 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 5294 Z= 0.236 Angle : 1.090 59.200 7159 Z= 0.644 Chirality : 0.057 1.077 832 Planarity : 0.007 0.128 909 Dihedral : 4.501 47.731 707 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.24 % Allowed : 19.25 % Favored : 77.51 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.93 (0.35), residues: 651 helix: 1.91 (0.32), residues: 292 sheet: -0.06 (0.48), residues: 119 loop : -0.61 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 723 HIS 0.002 0.001 HIS x 429 PHE 0.197 0.004 PHE x 685 TYR 0.008 0.001 TYR x 475 ARG 0.003 0.000 ARG x 844 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2509.62 seconds wall clock time: 45 minutes 22.19 seconds (2722.19 seconds total)