Starting phenix.real_space_refine on Tue Feb 11 09:51:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dcq_30639/02_2025/7dcq_30639.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dcq_30639/02_2025/7dcq_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/cci-nas-00/data/ceres_data/7dcq_30639/02_2025/7dcq_30639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dcq_30639/02_2025/7dcq_30639.map" model { file = "/net/cci-nas-00/data/ceres_data/7dcq_30639/02_2025/7dcq_30639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dcq_30639/02_2025/7dcq_30639.cif" } 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. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.60, per 1000 atoms: 0.89 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 - 3.00 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 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 621.9 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: 0.64 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: 1.52 Time building geometry restraints manager: 1.53 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: 0.00 - 2.57: 6984 2.57 - 5.14: 143 5.14 - 7.71: 25 7.71 - 10.28: 5 10.28 - 12.86: 2 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 3.120 nonbonded pdb=" O LEU x 337 " pdb=" NH1 ARG x 369 " model vdw 2.383 3.120 nonbonded pdb=" OE1 GLN x 834 " pdb=" NH2 ARG x 844 " model vdw 2.386 3.120 nonbonded pdb=" OG1 THR x 266 " pdb=" N ASP x 267 " model vdw 2.397 3.120 nonbonded pdb=" OE2 GLU x 449 " pdb=" OH TYR x 475 " model vdw 2.397 3.040 ... (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: 1.950 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.490 Find NCS groups from input model: 0.050 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.090 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.605 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: 1.3376 time to fit residues: 207.9903 Evaluate side-chains 79 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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: 0.9990 chunk 27 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 477 ASN x 630 ASN x 725 GLN x 743 GLN x 834 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.150919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129947 restraints weight = 6791.751| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.18 r_work: 0.3554 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5294 Z= 0.195 Angle : 0.615 7.425 7159 Z= 0.313 Chirality : 0.044 0.185 832 Planarity : 0.006 0.065 909 Dihedral : 5.004 40.345 707 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.56 % Allowed : 14.65 % Favored : 82.79 % 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: -1.37 (0.30), residues: 651 helix: -0.84 (0.26), residues: 293 sheet: -0.42 (0.46), residues: 116 loop : -0.99 (0.38), residues: 242 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 0.017 0.002 PHE x 863 TYR 0.009 0.001 TYR x 409 ARG 0.007 0.001 ARG x 401 *********************** 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 to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: x 301 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.6820 (mt-10) REVERT: x 305 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: x 320 LYS cc_start: 0.8621 (ptmt) cc_final: 0.8290 (ptpt) REVERT: x 427 GLN cc_start: 0.8056 (tp40) cc_final: 0.7798 (tp40) REVERT: x 454 LYS cc_start: 0.7574 (tptp) cc_final: 0.7090 (tttt) REVERT: x 483 GLN cc_start: 0.7423 (mm110) cc_final: 0.7222 (mm110) REVERT: x 700 VAL cc_start: 0.7106 (t) cc_final: 0.6887 (p) REVERT: x 762 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7098 (ptm) REVERT: x 763 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7364 (tttp) outliers start: 15 outliers final: 8 residues processed: 107 average time/residue: 1.3158 time to fit residues: 146.5954 Evaluate side-chains 86 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 301 GLU 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 Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 762 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126003 restraints weight = 6894.809| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.20 r_work: 0.3504 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5294 Z= 0.278 Angle : 0.613 6.527 7159 Z= 0.310 Chirality : 0.045 0.213 832 Planarity : 0.005 0.060 909 Dihedral : 4.830 36.179 707 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.60 % Allowed : 15.16 % Favored : 80.24 % 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: -0.38 (0.32), residues: 651 helix: 0.34 (0.29), residues: 293 sheet: -0.08 (0.47), residues: 119 loop : -0.93 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP x 723 HIS 0.003 0.001 HIS x 572 PHE 0.019 0.002 PHE x 863 TYR 0.010 0.002 TYR x 228 ARG 0.008 0.001 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 105 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: x 301 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.6710 (mt-10) REVERT: x 320 LYS cc_start: 0.8667 (ptmt) cc_final: 0.8311 (ptpt) REVERT: x 427 GLN cc_start: 0.8085 (tp40) cc_final: 0.7759 (tp-100) REVERT: x 454 LYS cc_start: 0.7769 (tptp) cc_final: 0.7335 (tttt) REVERT: x 604 LYS cc_start: 0.8810 (mmmm) cc_final: 0.8548 (mmtm) REVERT: x 700 VAL cc_start: 0.7260 (t) cc_final: 0.6997 (p) REVERT: x 762 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7116 (ptm) REVERT: x 767 ILE cc_start: 0.6189 (OUTLIER) cc_final: 0.5732 (mt) outliers start: 27 outliers final: 12 residues processed: 96 average time/residue: 1.2403 time to fit residues: 124.2390 Evaluate side-chains 88 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 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 531 THR Chi-restraints excluded: chain x residue 576 LEU 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 720 SER Chi-restraints excluded: chain x residue 762 MET 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 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127063 restraints weight = 6958.413| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.20 r_work: 0.3513 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5294 Z= 0.220 Angle : 0.559 6.199 7159 Z= 0.282 Chirality : 0.044 0.197 832 Planarity : 0.005 0.058 909 Dihedral : 4.716 40.944 707 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.43 % Allowed : 16.70 % Favored : 78.88 % 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: 0.14 (0.33), residues: 651 helix: 1.04 (0.30), residues: 293 sheet: -0.16 (0.48), residues: 120 loop : -0.89 (0.40), residues: 238 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 0.015 0.002 PHE x 426 TYR 0.009 0.001 TYR x 832 ARG 0.003 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 105 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: x 320 LYS cc_start: 0.8639 (ptmt) cc_final: 0.8361 (ptpt) REVERT: x 427 GLN cc_start: 0.8020 (tp40) cc_final: 0.7684 (tp-100) REVERT: x 454 LYS cc_start: 0.7747 (tptp) cc_final: 0.7317 (tttt) REVERT: x 604 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8601 (tptm) REVERT: x 762 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7123 (ptm) REVERT: x 764 ILE cc_start: 0.7916 (tp) cc_final: 0.7529 (pp) REVERT: x 767 ILE cc_start: 0.6215 (OUTLIER) cc_final: 0.5740 (mt) outliers start: 26 outliers final: 11 residues processed: 97 average time/residue: 1.0914 time to fit residues: 111.0808 Evaluate side-chains 86 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 355 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 576 LEU 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 762 MET 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 56 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 480 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.149213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128228 restraints weight = 6917.143| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.19 r_work: 0.3528 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3173 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= 0.180 Angle : 0.540 6.170 7159 Z= 0.271 Chirality : 0.043 0.189 832 Planarity : 0.004 0.054 909 Dihedral : 4.534 38.203 707 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.77 % Allowed : 16.18 % 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: 0.43 (0.33), residues: 651 helix: 1.40 (0.31), residues: 293 sheet: -0.13 (0.48), residues: 120 loop : -0.83 (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 419 PHE 0.012 0.002 PHE x 426 TYR 0.009 0.001 TYR x 832 ARG 0.003 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 103 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 221 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7765 (mttt) REVERT: x 232 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7838 (mt) REVERT: x 320 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8387 (ptpt) REVERT: x 427 GLN cc_start: 0.8034 (tp40) cc_final: 0.7764 (tp-100) REVERT: x 454 LYS cc_start: 0.7569 (tptp) cc_final: 0.7176 (tttt) REVERT: x 469 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6669 (tmm) REVERT: x 762 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7140 (ptm) REVERT: x 764 ILE cc_start: 0.7949 (tp) cc_final: 0.7580 (pp) REVERT: x 767 ILE cc_start: 0.6159 (OUTLIER) cc_final: 0.5688 (mt) outliers start: 28 outliers final: 12 residues processed: 94 average time/residue: 1.1555 time to fit residues: 113.9441 Evaluate side-chains 85 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 221 LYS 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 355 THR Chi-restraints excluded: chain x residue 456 GLU Chi-restraints excluded: chain x residue 469 MET Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 576 LEU Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 613 ILE 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 762 MET Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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 x 834 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.148946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127364 restraints weight = 6860.834| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.20 r_work: 0.3519 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5294 Z= 0.174 Angle : 0.532 6.575 7159 Z= 0.266 Chirality : 0.043 0.199 832 Planarity : 0.004 0.053 909 Dihedral : 4.470 39.034 707 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.77 % Allowed : 15.84 % Favored : 79.39 % 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: 0.66 (0.34), residues: 651 helix: 1.64 (0.31), residues: 293 sheet: 0.01 (0.49), residues: 119 loop : -0.81 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 723 HIS 0.001 0.001 HIS x 429 PHE 0.012 0.001 PHE x 426 TYR 0.011 0.001 TYR x 795 ARG 0.002 0.000 ARG x 289 *********************** 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 103 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: x 221 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7702 (mttt) REVERT: x 232 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7845 (mt) REVERT: x 305 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: x 320 LYS cc_start: 0.8651 (ptmt) cc_final: 0.8363 (ptpt) REVERT: x 422 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7498 (pt) REVERT: x 427 GLN cc_start: 0.8000 (tp40) cc_final: 0.7750 (tp-100) REVERT: x 454 LYS cc_start: 0.7553 (tptp) cc_final: 0.7190 (tttt) REVERT: x 469 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6770 (tmm) REVERT: x 762 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.7091 (ptm) REVERT: x 764 ILE cc_start: 0.7980 (tp) cc_final: 0.7591 (pp) REVERT: x 767 ILE cc_start: 0.6248 (OUTLIER) cc_final: 0.5777 (mt) outliers start: 28 outliers final: 12 residues processed: 95 average time/residue: 1.0988 time to fit residues: 109.6664 Evaluate side-chains 89 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 221 LYS 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 422 ILE Chi-restraints excluded: chain x residue 469 MET Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 576 LEU 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 613 ILE 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 762 MET Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 18 optimal weight: 0.3980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.151404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130064 restraints weight = 6757.837| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.19 r_work: 0.3553 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5294 Z= 0.141 Angle : 0.520 8.012 7159 Z= 0.258 Chirality : 0.043 0.188 832 Planarity : 0.004 0.051 909 Dihedral : 4.309 37.490 707 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.58 % Allowed : 16.87 % Favored : 79.56 % 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: 0.87 (0.34), residues: 651 helix: 1.85 (0.31), residues: 293 sheet: 0.05 (0.50), residues: 119 loop : -0.72 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP x 723 HIS 0.002 0.000 HIS x 429 PHE 0.017 0.001 PHE x 816 TYR 0.008 0.001 TYR x 832 ARG 0.002 0.000 ARG x 289 *********************** 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 100 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: x 305 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: x 320 LYS cc_start: 0.8623 (ptmt) cc_final: 0.8325 (ptpt) REVERT: x 422 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7509 (pt) REVERT: x 427 GLN cc_start: 0.7952 (tp40) cc_final: 0.7730 (tp-100) REVERT: x 454 LYS cc_start: 0.7435 (tptp) cc_final: 0.7099 (tttt) REVERT: x 767 ILE cc_start: 0.6159 (OUTLIER) cc_final: 0.5678 (mt) outliers start: 21 outliers final: 8 residues processed: 93 average time/residue: 1.1813 time to fit residues: 115.2589 Evaluate side-chains 86 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 319 LEU Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 422 ILE 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 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 46 optimal weight: 0.4980 chunk 48 optimal weight: 0.0770 chunk 34 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1144 ------------------------------------------------------------------------------- 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 727 HIS x 796 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.148117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126410 restraints weight = 6837.130| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.21 r_work: 0.3506 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5294 Z= 0.219 Angle : 0.567 8.449 7159 Z= 0.283 Chirality : 0.045 0.227 832 Planarity : 0.004 0.051 909 Dihedral : 4.444 38.093 707 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.56 % Allowed : 18.57 % Favored : 78.88 % 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: 1.78 (0.31), residues: 292 sheet: -0.14 (0.49), residues: 119 loop : -0.65 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 723 HIS 0.004 0.001 HIS x 429 PHE 0.012 0.002 PHE x 863 TYR 0.010 0.001 TYR x 832 ARG 0.003 0.000 ARG x 289 *********************** 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 87 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.629 Fit side-chains REVERT: x 320 LYS cc_start: 0.8610 (ptmt) cc_final: 0.8365 (ptpt) REVERT: x 330 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8580 (mt-10) REVERT: x 422 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7504 (pt) REVERT: x 427 GLN cc_start: 0.8016 (tp40) cc_final: 0.7777 (tp-100) REVERT: x 454 LYS cc_start: 0.7540 (tptp) cc_final: 0.7173 (tttt) REVERT: x 764 ILE cc_start: 0.8010 (tp) cc_final: 0.7637 (pp) REVERT: x 767 ILE cc_start: 0.6193 (OUTLIER) cc_final: 0.5711 (mt) outliers start: 15 outliers final: 9 residues processed: 83 average time/residue: 1.1868 time to fit residues: 103.2185 Evaluate side-chains 81 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 422 ILE Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR 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 18 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128200 restraints weight = 6745.630| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.20 r_work: 0.3527 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3582 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= 0.177 Angle : 0.559 8.442 7159 Z= 0.275 Chirality : 0.044 0.209 832 Planarity : 0.004 0.050 909 Dihedral : 4.392 37.465 707 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.56 % Allowed : 18.57 % Favored : 78.88 % 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: 0.84 (0.34), residues: 651 helix: 1.90 (0.31), residues: 292 sheet: -0.31 (0.48), residues: 124 loop : -0.61 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 PHE 0.011 0.001 PHE x 816 TYR 0.010 0.001 TYR x 624 ARG 0.008 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 86 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.586 Fit side-chains REVERT: x 305 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: x 422 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7517 (pt) REVERT: x 427 GLN cc_start: 0.7978 (tp40) cc_final: 0.7746 (tp-100) REVERT: x 454 LYS cc_start: 0.7546 (tptp) cc_final: 0.7162 (tttt) REVERT: x 767 ILE cc_start: 0.6172 (OUTLIER) cc_final: 0.5689 (mt) outliers start: 15 outliers final: 9 residues processed: 82 average time/residue: 1.1478 time to fit residues: 98.7502 Evaluate side-chains 84 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 422 ILE Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 613 ILE 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 42 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.148036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126467 restraints weight = 6845.311| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.22 r_work: 0.3502 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5294 Z= 0.236 Angle : 0.595 9.431 7159 Z= 0.294 Chirality : 0.046 0.250 832 Planarity : 0.005 0.051 909 Dihedral : 4.552 38.286 707 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.90 % Allowed : 18.57 % Favored : 78.53 % 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: 0.75 (0.34), residues: 651 helix: 1.79 (0.31), residues: 292 sheet: -0.39 (0.48), residues: 124 loop : -0.57 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 723 HIS 0.004 0.001 HIS x 429 PHE 0.014 0.002 PHE x 426 TYR 0.010 0.001 TYR x 475 ARG 0.012 0.001 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 89 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: x 305 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: x 320 LYS cc_start: 0.8672 (ptmt) cc_final: 0.8430 (ptpt) REVERT: x 422 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7531 (pt) REVERT: x 427 GLN cc_start: 0.8008 (tp40) cc_final: 0.7767 (tp-100) REVERT: x 454 LYS cc_start: 0.7646 (tptp) cc_final: 0.7239 (tttt) REVERT: x 469 MET cc_start: 0.7751 (tmm) cc_final: 0.6190 (ttm) REVERT: x 762 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7100 (ptm) REVERT: x 764 ILE cc_start: 0.8016 (tp) cc_final: 0.7673 (pp) REVERT: x 767 ILE cc_start: 0.6196 (OUTLIER) cc_final: 0.5708 (mt) outliers start: 17 outliers final: 12 residues processed: 83 average time/residue: 1.2446 time to fit residues: 108.1615 Evaluate side-chains 87 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 319 LEU 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 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 613 ILE 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 762 MET 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 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 0.0040 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.150448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128965 restraints weight = 6889.519| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.23 r_work: 0.3543 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5294 Z= 0.156 Angle : 0.563 10.014 7159 Z= 0.276 Chirality : 0.044 0.202 832 Planarity : 0.004 0.050 909 Dihedral : 4.401 36.983 707 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.39 % Allowed : 19.59 % Favored : 78.02 % 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: 0.96 (0.34), residues: 651 helix: 2.01 (0.31), residues: 292 sheet: -0.09 (0.51), residues: 103 loop : -0.65 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 PHE 0.012 0.001 PHE x 816 TYR 0.017 0.001 TYR x 304 ARG 0.009 0.000 ARG x 844 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4108.94 seconds wall clock time: 73 minutes 12.62 seconds (4392.62 seconds total)