Starting phenix.real_space_refine (version: dev) on Thu May 12 15:33:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcq_30639/05_2022/7dcq_30639.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcq_30639/05_2022/7dcq_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_30639/05_2022/7dcq_30639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcq_30639/05_2022/7dcq_30639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcq_30639/05_2022/7dcq_30639.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcq_30639/05_2022/7dcq_30639.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped 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-4597/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: {'PTRANS': 32, 'TRANS': 619, 'PCIS': 1} Time building chain proxies: 3.87, per 1000 atoms: 0.74 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: 1.98 Conformation dependent library (CDL) restraints added in 746.1 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: 0.36 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: 1.53 Time building geometry restraints manager: 2.18 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 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. 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: 1.150 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: 6.050 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 18.970 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.85 % 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 *********************** 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 : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 150 average time/residue: 1.2146 time to fit residues: 189.6243 Evaluate side-chains 78 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.602 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.8179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.2390 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= 0.216 Angle : 0.619 7.089 7159 Z= 0.315 Chirality : 0.044 0.181 832 Planarity : 0.006 0.065 909 Dihedral : 4.778 20.198 706 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 2.56 % 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: -1.32 (0.30), residues: 651 helix: -0.82 (0.26), residues: 293 sheet: -0.12 (0.47), residues: 121 loop : -1.10 (0.39), residues: 237 *********************** 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 109 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.657 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 104 average time/residue: 1.0274 time to fit residues: 112.2804 Evaluate side-chains 82 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 5 average time/residue: 0.1129 time to fit residues: 1.6809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** x 725 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 5294 Z= 0.302 Angle : 0.626 6.473 7159 Z= 0.316 Chirality : 0.046 0.216 832 Planarity : 0.005 0.060 909 Dihedral : 4.667 19.553 706 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 4.60 % 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: -0.03 (0.48), residues: 119 loop : -0.97 (0.40), residues: 239 *********************** 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 103 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 76 time to evaluate : 0.655 Fit side-chains outliers start: 27 outliers final: 11 residues processed: 95 average time/residue: 1.0535 time to fit residues: 105.6648 Evaluate side-chains 84 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 3 average time/residue: 0.1095 time to fit residues: 1.3360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** x 834 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3085 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= 0.239 Angle : 0.581 6.211 7159 Z= 0.292 Chirality : 0.045 0.205 832 Planarity : 0.005 0.058 909 Dihedral : 4.515 19.200 706 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 4.60 % 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: 0.15 (0.33), residues: 651 helix: 1.02 (0.31), residues: 293 sheet: -0.02 (0.49), residues: 119 loop : -0.89 (0.40), residues: 239 *********************** 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 102 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 0.609 Fit side-chains outliers start: 27 outliers final: 10 residues processed: 97 average time/residue: 0.9588 time to fit residues: 98.2323 Evaluate side-chains 81 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 0.1116 time to fit residues: 1.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.129 5294 Z= 0.279 Angle : 0.625 11.909 7159 Z= 0.319 Chirality : 0.045 0.209 832 Planarity : 0.005 0.056 909 Dihedral : 4.452 23.254 706 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 4.94 % 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 (0.34), residues: 651 helix: 1.33 (0.31), residues: 293 sheet: 0.00 (0.49), residues: 119 loop : -0.82 (0.40), residues: 239 *********************** 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 102 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 0.638 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 92 average time/residue: 0.9518 time to fit residues: 92.5921 Evaluate side-chains 79 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 3 average time/residue: 0.1113 time to fit residues: 1.3888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8131 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 5294 Z= 0.235 Angle : 0.565 6.710 7159 Z= 0.293 Chirality : 0.044 0.187 832 Planarity : 0.006 0.112 909 Dihedral : 4.390 30.114 706 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 3.92 % 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: 0.64 (0.34), residues: 651 helix: 1.58 (0.32), residues: 293 sheet: 0.10 (0.50), residues: 119 loop : -0.81 (0.41), residues: 239 *********************** 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 97 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 0.669 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 89 average time/residue: 0.9194 time to fit residues: 86.6664 Evaluate side-chains 79 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 0.3612 time to fit residues: 2.4869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.8148 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 5294 Z= 0.276 Angle : 0.590 8.226 7159 Z= 0.301 Chirality : 0.045 0.216 832 Planarity : 0.006 0.078 909 Dihedral : 4.444 32.583 706 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 4.09 % 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: 0.66 (0.34), residues: 651 helix: 1.63 (0.32), residues: 291 sheet: 0.11 (0.50), residues: 119 loop : -0.82 (0.41), residues: 241 *********************** 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 96 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 0.674 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 91 average time/residue: 0.9758 time to fit residues: 93.8959 Evaluate side-chains 83 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 0.1409 time to fit residues: 1.2284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 5294 Z= 0.222 Angle : 0.569 8.020 7159 Z= 0.287 Chirality : 0.044 0.210 832 Planarity : 0.005 0.067 909 Dihedral : 4.350 32.170 706 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 3.24 % 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: 0.79 (0.35), residues: 651 helix: 1.73 (0.32), residues: 292 sheet: 0.23 (0.51), residues: 117 loop : -0.81 (0.41), residues: 242 *********************** 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 96 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.589 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 91 average time/residue: 0.9150 time to fit residues: 88.2133 Evaluate side-chains 83 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 4 average time/residue: 0.1374 time to fit residues: 1.6383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8168 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 5294 Z= 0.295 Angle : 0.625 9.174 7159 Z= 0.314 Chirality : 0.047 0.240 832 Planarity : 0.005 0.061 909 Dihedral : 4.539 29.237 706 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 2.90 % 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: 0.61 (0.34), residues: 651 helix: 1.57 (0.31), residues: 291 sheet: -0.03 (0.49), residues: 119 loop : -0.77 (0.41), residues: 241 *********************** 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 87 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.615 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 85 average time/residue: 0.9651 time to fit residues: 86.8493 Evaluate side-chains 78 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.646 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 1 average time/residue: 0.2146 time to fit residues: 1.1666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 5294 Z= 0.234 Angle : 0.608 10.540 7159 Z= 0.311 Chirality : 0.046 0.215 832 Planarity : 0.006 0.142 909 Dihedral : 4.430 37.711 706 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 2.90 % 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: 0.81 (0.35), residues: 651 helix: 1.86 (0.32), residues: 292 sheet: 0.04 (0.51), residues: 117 loop : -0.84 (0.42), residues: 242 ********************** 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 87 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.630 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 85 average time/residue: 0.9863 time to fit residues: 88.4185 Evaluate side-chains 76 residues out of total 587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 1 average time/residue: 0.2561 time to fit residues: 1.2447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 x 630 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127082 restraints weight = 6787.845| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.18 r_work: 0.3617 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.3591 rms_B_bonded: 2.03 restraints_weight: 0.1250 r_work: 0.3577 rms_B_bonded: 2.15 restraints_weight: 0.0625 r_work: 0.3562 rms_B_bonded: 2.32 restraints_weight: 0.0312 r_work: 0.3546 rms_B_bonded: 2.54 restraints_weight: 0.0156 r_work: 0.3528 rms_B_bonded: 2.81 restraints_weight: 0.0078 r_work: 0.3508 rms_B_bonded: 3.13 restraints_weight: 0.0039 r_work: 0.3486 rms_B_bonded: 3.51 restraints_weight: 0.0020 r_work: 0.3462 rms_B_bonded: 3.96 restraints_weight: 0.0010 r_work: 0.3435 rms_B_bonded: 4.49 restraints_weight: 0.0005 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 5294 Z= 0.240 Angle : 0.620 11.078 7159 Z= 0.313 Chirality : 0.046 0.237 832 Planarity : 0.006 0.122 909 Dihedral : 4.402 35.648 706 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 2.39 % 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: 0.78 (0.35), residues: 651 helix: 1.87 (0.31), residues: 292 sheet: -0.01 (0.51), residues: 117 loop : -0.88 (0.42), residues: 242 =============================================================================== Job complete usr+sys time: 2177.07 seconds wall clock time: 39 minutes 21.55 seconds (2361.55 seconds total)