Starting phenix.real_space_refine on Tue Nov 14 03:02:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/11_2023/7w88_32353.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/11_2023/7w88_32353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/11_2023/7w88_32353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/11_2023/7w88_32353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/11_2023/7w88_32353.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w88_32353/11_2023/7w88_32353.pdb" } resolution = 3.5 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 45 5.16 5 C 4541 2.51 5 N 1241 2.21 5 O 1311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 125": "OE1" <-> "OE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A ASP 682": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 730": "OD1" <-> "OD2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A PHE 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A ASP 844": "OD1" <-> "OD2" Residue "A ASP 877": "OD1" <-> "OD2" Residue "A ASP 914": "OD1" <-> "OD2" Residue "A PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 935": "OD1" <-> "OD2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A ASP 1035": "OD1" <-> "OD2" Residue "A TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1044": "OD1" <-> "OD2" Residue "A ASP 1051": "OD1" <-> "OD2" Residue "A TYR 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A GLU 1088": "OE1" <-> "OE2" Residue "A PHE 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 7138 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7138 Classifications: {'peptide': 896} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 854} Chain breaks: 7 Time building chain proxies: 4.32, per 1000 atoms: 0.61 Number of scatterers: 7138 At special positions: 0 Unit cell: (79.18, 94.72, 105.08, 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 45 16.00 O 1311 8.00 N 1241 7.00 C 4541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 728 " - pdb=" SG CYS A 805 " distance=2.04 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: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 31.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.525A pdb=" N LEU A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.790A pdb=" N LEU A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 395 through 401 Processing helix chain 'A' and resid 402 through 408 removed outlier: 4.260A pdb=" N SER A 406 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 removed outlier: 3.781A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 422 through 427' Processing helix chain 'A' and resid 441 through 453 removed outlier: 4.075A pdb=" N HIS A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.948A pdb=" N GLY A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.647A pdb=" N CYS A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 554 through 566 removed outlier: 3.771A pdb=" N LYS A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 641 through 651 removed outlier: 4.990A pdb=" N MET A 647 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLN A 648 " --> pdb=" O PHE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 694 through 715 Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 794 through 800 Processing helix chain 'A' and resid 815 through 821 removed outlier: 4.410A pdb=" N SER A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 874 removed outlier: 3.673A pdb=" N MET A 874 " --> pdb=" O PHE A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 removed outlier: 3.503A pdb=" N ILE A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 909 removed outlier: 3.807A pdb=" N VAL A 903 " --> pdb=" O SER A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 956 Processing helix chain 'A' and resid 997 through 1009 Processing helix chain 'A' and resid 1017 through 1022 Processing helix chain 'A' and resid 1039 through 1060 Processing helix chain 'A' and resid 1073 through 1078 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 131 removed outlier: 3.562A pdb=" N ALA A 129 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 117 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER A 131 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 115 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 238 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 removed outlier: 7.266A pdb=" N GLN A 183 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.567A pdb=" N GLU A 390 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 384 through 386 removed outlier: 7.036A pdb=" N TRP A 478 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 455 " --> pdb=" O TYR A 462 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA8, first strand: chain 'A' and resid 537 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 575 through 576 removed outlier: 3.504A pdb=" N PHE A 576 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 726 through 727 removed outlier: 7.404A pdb=" N ILE A 726 " --> pdb=" O VAL A 806 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 740 removed outlier: 3.599A pdb=" N VAL A 740 " --> pdb=" O GLU A 790 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 789 " --> pdb=" O VAL A 773 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 776 " --> pdb=" O PHE A 831 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 744 through 745 removed outlier: 3.618A pdb=" N ILE A 744 " --> pdb=" O ALA A 767 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 540 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: 2.35 Time building geometry restraints manager: 2.95 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: 2334 1.34 - 1.46: 1638 1.46 - 1.58: 3252 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 7293 Sorted by residual: bond pdb=" N GLU A 391 " pdb=" CA GLU A 391 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.43e+00 bond pdb=" N GLU A 390 " pdb=" CA GLU A 390 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.58e+00 bond pdb=" N ASP A 590 " pdb=" CA ASP A 590 " ideal model delta sigma weight residual 1.457 1.486 -0.030 1.41e-02 5.03e+03 4.40e+00 bond pdb=" N GLU A 938 " pdb=" CA GLU A 938 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.60e+00 bond pdb=" CA VAL A 529 " pdb=" CB VAL A 529 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.34e-02 5.57e+03 1.49e+00 ... (remaining 7288 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.06: 235 107.06 - 113.82: 4022 113.82 - 120.58: 2895 120.58 - 127.34: 2617 127.34 - 134.11: 81 Bond angle restraints: 9850 Sorted by residual: angle pdb=" C ARG A 898 " pdb=" N SER A 899 " pdb=" CA SER A 899 " ideal model delta sigma weight residual 120.49 114.60 5.89 1.42e+00 4.96e-01 1.72e+01 angle pdb=" N VAL A 247 " pdb=" CA VAL A 247 " pdb=" C VAL A 247 " ideal model delta sigma weight residual 113.71 110.18 3.53 9.50e-01 1.11e+00 1.38e+01 angle pdb=" N GLY A 638 " pdb=" CA GLY A 638 " pdb=" C GLY A 638 " ideal model delta sigma weight residual 113.18 120.68 -7.50 2.37e+00 1.78e-01 1.00e+01 angle pdb=" N SER A 339 " pdb=" CA SER A 339 " pdb=" C SER A 339 " ideal model delta sigma weight residual 108.32 113.51 -5.19 1.64e+00 3.72e-01 1.00e+01 angle pdb=" N LYS A 640 " pdb=" CA LYS A 640 " pdb=" C LYS A 640 " ideal model delta sigma weight residual 110.80 117.23 -6.43 2.13e+00 2.20e-01 9.10e+00 ... (remaining 9845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3779 17.99 - 35.98: 492 35.98 - 53.97: 122 53.97 - 71.96: 20 71.96 - 89.95: 5 Dihedral angle restraints: 4418 sinusoidal: 1806 harmonic: 2612 Sorted by residual: dihedral pdb=" CA SER A 547 " pdb=" C SER A 547 " pdb=" N ASP A 548 " pdb=" CA ASP A 548 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA MET A1009 " pdb=" C MET A1009 " pdb=" N THR A1010 " pdb=" CA THR A1010 " ideal model delta harmonic sigma weight residual 180.00 157.54 22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ALA A1108 " pdb=" C ALA A1108 " pdb=" N ARG A1109 " pdb=" CA ARG A1109 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 4415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 738 0.039 - 0.078: 246 0.078 - 0.118: 82 0.118 - 0.157: 17 0.157 - 0.196: 1 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CB VAL A 740 " pdb=" CA VAL A 740 " pdb=" CG1 VAL A 740 " pdb=" CG2 VAL A 740 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CB ILE A 265 " pdb=" CA ILE A 265 " pdb=" CG1 ILE A 265 " pdb=" CG2 ILE A 265 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE A 377 " pdb=" N ILE A 377 " pdb=" C ILE A 377 " pdb=" CB ILE A 377 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1081 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 589 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C ILE A 589 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 589 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP A 590 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 380 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 381 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 933 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO A 934 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 934 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 934 " 0.026 5.00e-02 4.00e+02 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1190 2.76 - 3.29: 6891 3.29 - 3.83: 11142 3.83 - 4.36: 12501 4.36 - 4.90: 21855 Nonbonded interactions: 53579 Sorted by model distance: nonbonded pdb=" O MET A 603 " pdb=" NZ LYS A 605 " model vdw 2.225 2.520 nonbonded pdb=" N ASP A 165 " pdb=" OD1 ASP A 165 " model vdw 2.237 2.520 nonbonded pdb=" OE2 GLU A 642 " pdb=" NZ LYS A 837 " model vdw 2.249 2.520 nonbonded pdb=" O CYS A 624 " pdb=" ND1 HIS A 718 " model vdw 2.258 2.520 nonbonded pdb=" NH2 ARG A 519 " pdb=" O ILE A 565 " model vdw 2.263 2.520 ... (remaining 53574 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 group one per residue 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.180 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.410 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7293 Z= 0.199 Angle : 0.705 8.829 9850 Z= 0.406 Chirality : 0.045 0.196 1084 Planarity : 0.004 0.053 1260 Dihedral : 16.867 89.950 2727 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.23 % Favored : 84.77 % Rotamer: Outliers : 8.23 % Allowed : 23.26 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -5.15 (0.23), residues: 880 helix: -1.89 (0.28), residues: 236 sheet: -4.61 (0.35), residues: 129 loop : -4.04 (0.23), residues: 515 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 114 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 35 residues processed: 166 average time/residue: 0.2304 time to fit residues: 49.8919 Evaluate side-chains 124 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 89 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.0986 time to fit residues: 6.7115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 276 ASN A 560 GLN A 661 ASN A 686 GLN A 739 GLN A 748 HIS A 756 GLN A 778 ASN A1024 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 7293 Z= 0.450 Angle : 0.812 9.040 9850 Z= 0.423 Chirality : 0.050 0.203 1084 Planarity : 0.006 0.064 1260 Dihedral : 6.621 27.977 985 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.25 % Favored : 78.75 % Rotamer: Outliers : 7.97 % Allowed : 25.84 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -4.83 (0.25), residues: 880 helix: -1.55 (0.29), residues: 241 sheet: -4.56 (0.32), residues: 139 loop : -3.81 (0.25), residues: 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 90 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 36 residues processed: 142 average time/residue: 0.1938 time to fit residues: 37.1925 Evaluate side-chains 121 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 85 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.0714 time to fit residues: 5.8265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7293 Z= 0.253 Angle : 0.686 8.019 9850 Z= 0.352 Chirality : 0.045 0.184 1084 Planarity : 0.005 0.058 1260 Dihedral : 6.207 27.839 985 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.84 % Favored : 82.16 % Rotamer: Outliers : 5.27 % Allowed : 27.38 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -4.27 (0.26), residues: 880 helix: -0.90 (0.31), residues: 244 sheet: -4.20 (0.35), residues: 132 loop : -3.61 (0.25), residues: 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 97 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 22 residues processed: 134 average time/residue: 0.2282 time to fit residues: 40.0520 Evaluate side-chains 107 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1120 time to fit residues: 5.0164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS A 276 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 560 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7293 Z= 0.228 Angle : 0.671 8.104 9850 Z= 0.344 Chirality : 0.045 0.142 1084 Planarity : 0.005 0.059 1260 Dihedral : 6.042 27.237 985 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 3.73 % Allowed : 29.43 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.96 (0.26), residues: 880 helix: -0.65 (0.32), residues: 244 sheet: -3.96 (0.36), residues: 131 loop : -3.43 (0.26), residues: 505 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 115 average time/residue: 0.2356 time to fit residues: 35.3205 Evaluate side-chains 103 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0719 time to fit residues: 3.0117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.0010 chunk 35 optimal weight: 0.0670 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 0.0270 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 0.0770 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 overall best weight: 0.0438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7293 Z= 0.166 Angle : 0.650 10.526 9850 Z= 0.327 Chirality : 0.043 0.142 1084 Planarity : 0.005 0.058 1260 Dihedral : 5.562 25.694 985 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 2.31 % Allowed : 31.36 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.39 (0.27), residues: 880 helix: -0.38 (0.33), residues: 252 sheet: -3.23 (0.42), residues: 112 loop : -3.16 (0.26), residues: 516 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 121 average time/residue: 0.2167 time to fit residues: 34.7478 Evaluate side-chains 93 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0754 time to fit residues: 1.7297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.0270 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 560 GLN ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN A1036 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7293 Z= 0.285 Angle : 0.703 9.577 9850 Z= 0.360 Chirality : 0.046 0.203 1084 Planarity : 0.005 0.067 1260 Dihedral : 5.875 25.907 985 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.61 % Favored : 82.39 % Rotamer: Outliers : 2.96 % Allowed : 31.88 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.65 (0.27), residues: 880 helix: -0.53 (0.33), residues: 249 sheet: -3.67 (0.37), residues: 132 loop : -3.21 (0.26), residues: 499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.789 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 110 average time/residue: 0.2354 time to fit residues: 33.5822 Evaluate side-chains 104 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.791 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0653 time to fit residues: 2.6831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 GLN A 909 HIS A1036 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7293 Z= 0.349 Angle : 0.760 8.462 9850 Z= 0.390 Chirality : 0.047 0.163 1084 Planarity : 0.006 0.066 1260 Dihedral : 6.275 26.607 985 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.66 % Favored : 80.34 % Rotamer: Outliers : 2.44 % Allowed : 33.16 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.90 (0.26), residues: 880 helix: -0.90 (0.31), residues: 257 sheet: -3.83 (0.36), residues: 131 loop : -3.29 (0.26), residues: 492 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 114 average time/residue: 0.2603 time to fit residues: 37.6568 Evaluate side-chains 100 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1791 time to fit residues: 3.3987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 67 optimal weight: 0.0970 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN A 909 HIS A 948 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7293 Z= 0.182 Angle : 0.675 9.245 9850 Z= 0.341 Chirality : 0.044 0.151 1084 Planarity : 0.005 0.063 1260 Dihedral : 5.734 25.156 985 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.57 % Favored : 84.43 % Rotamer: Outliers : 1.80 % Allowed : 33.80 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.35 (0.27), residues: 880 helix: -0.33 (0.33), residues: 250 sheet: -3.41 (0.40), residues: 120 loop : -3.06 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.856 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 118 average time/residue: 0.2327 time to fit residues: 35.6816 Evaluate side-chains 106 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0742 time to fit residues: 2.1068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 617 ASN A 909 HIS A1036 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7293 Z= 0.212 Angle : 0.699 9.037 9850 Z= 0.354 Chirality : 0.045 0.167 1084 Planarity : 0.005 0.077 1260 Dihedral : 5.731 24.936 985 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.05 % Favored : 82.95 % Rotamer: Outliers : 0.90 % Allowed : 35.60 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.35 (0.27), residues: 880 helix: -0.38 (0.33), residues: 249 sheet: -3.25 (0.43), residues: 115 loop : -3.08 (0.26), residues: 516 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 111 average time/residue: 0.2359 time to fit residues: 33.9519 Evaluate side-chains 111 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0701 time to fit residues: 1.7939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 617 ASN A 889 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7293 Z= 0.340 Angle : 0.775 10.865 9850 Z= 0.396 Chirality : 0.047 0.177 1084 Planarity : 0.006 0.073 1260 Dihedral : 6.157 25.869 985 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.32 % Favored : 80.68 % Rotamer: Outliers : 0.64 % Allowed : 35.86 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.72 (0.26), residues: 880 helix: -0.68 (0.32), residues: 249 sheet: -3.62 (0.37), residues: 130 loop : -3.22 (0.26), residues: 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.844 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 104 average time/residue: 0.2479 time to fit residues: 33.3481 Evaluate side-chains 101 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0707 time to fit residues: 1.6613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.0000 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 0.0000 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A1036 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.220707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.189792 restraints weight = 9620.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.190487 restraints weight = 6892.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.191395 restraints weight = 6995.098| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7293 Z= 0.186 Angle : 0.696 9.375 9850 Z= 0.352 Chirality : 0.044 0.156 1084 Planarity : 0.005 0.067 1260 Dihedral : 5.653 24.750 985 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.23 % Favored : 84.77 % Rotamer: Outliers : 0.64 % Allowed : 36.25 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.13 (0.27), residues: 880 helix: -0.17 (0.34), residues: 243 sheet: -2.70 (0.48), residues: 100 loop : -3.05 (0.25), residues: 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1744.88 seconds wall clock time: 32 minutes 21.95 seconds (1941.95 seconds total)