Starting phenix.real_space_refine (version: dev) on Sat Feb 18 08:13:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/02_2023/6xou_22280.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/02_2023/6xou_22280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/02_2023/6xou_22280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/02_2023/6xou_22280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/02_2023/6xou_22280.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xou_22280/02_2023/6xou_22280.pdb" } resolution = 4.0 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= 0.001 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 Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 901": "OE1" <-> "OE2" Residue "A GLU 1024": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7697 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7697 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 965, 7691 Classifications: {'peptide': 965} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 902} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 965, 7691 Classifications: {'peptide': 965} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 902} Chain breaks: 1 bond proxies already assigned to first conformer: 7875 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 723 " occ=0.42 ... (10 atoms not shown) pdb=" OG BSER A 723 " occ=0.58 Time building chain proxies: 7.46, per 1000 atoms: 0.97 Number of scatterers: 7697 At special positions: 0 Unit cell: (84.744, 98.44, 103.576, 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 39 16.00 O 1457 8.00 N 1304 7.00 C 4897 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: 2.69 Conformation dependent library (CDL) restraints added in 2.0 seconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1824 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 53.6% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 removed outlier: 4.096A pdb=" N ARG A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 101 through 111 removed outlier: 3.927A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.532A pdb=" N MET A 126 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.725A pdb=" N VAL A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.866A pdb=" N GLU A 244 " --> pdb=" O CYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 272 through 284 removed outlier: 3.916A pdb=" N HIS A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.566A pdb=" N ILE A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 457 removed outlier: 4.750A pdb=" N SER A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N CYS A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 481 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 509 through 527 Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 608 through 613 removed outlier: 3.639A pdb=" N ARG A 612 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Proline residue: A 613 - end of helix Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 631 through 642 Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 695 through 713 removed outlier: 3.703A pdb=" N PHE A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 717 through 727 Processing helix chain 'A' and resid 728 through 730 No H-bonds generated for 'chain 'A' and resid 728 through 730' Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.550A pdb=" N VAL A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 763 Processing helix chain 'A' and resid 763 through 773 removed outlier: 4.294A pdb=" N ARG A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 878 through 894 removed outlier: 4.323A pdb=" N SER A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 Processing helix chain 'A' and resid 928 through 945 removed outlier: 3.505A pdb=" N LEU A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 964 Processing helix chain 'A' and resid 968 through 972 removed outlier: 3.566A pdb=" N LYS A 972 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.947A pdb=" N PHE A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 997 through 1008 Processing helix chain 'A' and resid 1025 through 1030 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.798A pdb=" N LYS A 66 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 54 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 64 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 56 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU A 62 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET A 135 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER A 149 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.798A pdb=" N LYS A 66 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 54 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 64 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 56 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU A 62 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313 removed outlier: 5.721A pdb=" N THR A 326 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 387 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 373 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 313 removed outlier: 5.721A pdb=" N THR A 326 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 387 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 579 removed outlier: 3.554A pdb=" N ASP A 575 " --> pdb=" O TYR A 587 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A 782 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN A 586 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA A 784 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 598 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY A 645 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 673 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR A 643 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912 removed outlier: 6.325A pdb=" N THR A 855 " --> pdb=" O ILE A1020 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLY A1022 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N PHE A 857 " --> pdb=" O GLY A1022 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS A 854 " --> pdb=" O ILE A1035 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1360 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: 2.74 Time building geometry restraints manager: 2.94 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: 2447 1.34 - 1.46: 1495 1.46 - 1.58: 3885 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 7889 Sorted by residual: bond pdb=" C ILE A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.46e+00 bond pdb=" C ILE A 714 " pdb=" N PRO A 715 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.36e-02 5.41e+03 3.76e+00 bond pdb=" C VAL A 615 " pdb=" N PRO A 616 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.36e-02 5.41e+03 3.71e+00 bond pdb=" CB ASN A 712 " pdb=" CG ASN A 712 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.40e+00 bond pdb=" CG1 ILE A 885 " pdb=" CD1 ILE A 885 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.10e+00 ... (remaining 7884 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.60: 315 106.60 - 113.82: 4252 113.82 - 121.05: 3915 121.05 - 128.27: 2152 128.27 - 135.50: 64 Bond angle restraints: 10698 Sorted by residual: angle pdb=" N ASP A 458 " pdb=" CA ASP A 458 " pdb=" C ASP A 458 " ideal model delta sigma weight residual 111.54 117.53 -5.99 1.36e+00 5.41e-01 1.94e+01 angle pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" C LEU A 131 " ideal model delta sigma weight residual 111.30 106.10 5.20 1.43e+00 4.89e-01 1.32e+01 angle pdb=" C LYS A 893 " pdb=" N PHE A 894 " pdb=" CA PHE A 894 " ideal model delta sigma weight residual 121.54 114.71 6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" CA VAL A 615 " pdb=" C VAL A 615 " pdb=" N PRO A 616 " ideal model delta sigma weight residual 118.88 124.27 -5.39 1.54e+00 4.22e-01 1.23e+01 angle pdb=" CA ASN A 712 " pdb=" CB ASN A 712 " pdb=" CG ASN A 712 " ideal model delta sigma weight residual 112.60 116.10 -3.50 1.00e+00 1.00e+00 1.22e+01 ... (remaining 10693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4386 17.76 - 35.52: 295 35.52 - 53.27: 65 53.27 - 71.03: 15 71.03 - 88.79: 10 Dihedral angle restraints: 4771 sinusoidal: 1952 harmonic: 2819 Sorted by residual: dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N THR A 211 " pdb=" CA THR A 211 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PRO A 170 " pdb=" C PRO A 170 " pdb=" N CYS A 171 " pdb=" CA CYS A 171 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C VAL A 102 " pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" CB VAL A 102 " ideal model delta harmonic sigma weight residual -122.00 -131.21 9.21 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 921 0.070 - 0.140: 213 0.140 - 0.209: 32 0.209 - 0.279: 5 0.279 - 0.349: 1 Chirality restraints: 1172 Sorted by residual: chirality pdb=" CG LEU A 467 " pdb=" CB LEU A 467 " pdb=" CD1 LEU A 467 " pdb=" CD2 LEU A 467 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA VAL A 102 " pdb=" N VAL A 102 " pdb=" C VAL A 102 " pdb=" CB VAL A 102 " both_signs ideal model delta sigma weight residual False 2.44 2.18 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR A 94 " pdb=" CA THR A 94 " pdb=" OG1 THR A 94 " pdb=" CG2 THR A 94 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1169 not shown) Planarity restraints: 1397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 301 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C THR A 301 " -0.040 2.00e-02 2.50e+03 pdb=" O THR A 301 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 302 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 334 " -0.036 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 335 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 793 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C GLU A 793 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU A 793 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 794 " -0.012 2.00e-02 2.50e+03 ... (remaining 1394 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1748 2.79 - 3.32: 6901 3.32 - 3.84: 12652 3.84 - 4.37: 14147 4.37 - 4.90: 24954 Nonbonded interactions: 60402 Sorted by model distance: nonbonded pdb=" ND2 ASN A 783 " pdb=" O PRO A 969 " model vdw 2.261 2.520 nonbonded pdb=" OH TYR A 146 " pdb=" OH TYR A 258 " model vdw 2.270 2.440 nonbonded pdb=" O SER A 351 " pdb=" OG SER A 355 " model vdw 2.285 2.440 nonbonded pdb=" OD1 ASP A 98 " pdb=" OG1 THR A 100 " model vdw 2.302 2.440 nonbonded pdb=" O HIS A 457 " pdb=" OD1 ASP A 458 " model vdw 2.310 3.040 ... (remaining 60397 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 39 5.16 5 C 4897 2.51 5 N 1304 2.21 5 O 1457 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=0.42 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: 0.930 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: 4.170 Check model and map are aligned: 0.100 Process input model: 26.450 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 : 0.005 0.075 7889 Z= 0.332 Angle : 1.063 10.498 10698 Z= 0.562 Chirality : 0.061 0.349 1172 Planarity : 0.007 0.056 1397 Dihedral : 13.628 88.791 2947 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.51 (0.24), residues: 964 helix: -1.05 (0.21), residues: 447 sheet: 0.29 (0.36), residues: 178 loop : -1.42 (0.31), residues: 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2093 time to fit residues: 43.0566 Evaluate side-chains 93 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 151 GLN A 204 ASN ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 HIS A 637 GLN A 638 GLN A 690 ASN ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 7889 Z= 0.320 Angle : 0.797 10.984 10698 Z= 0.400 Chirality : 0.045 0.220 1172 Planarity : 0.005 0.044 1397 Dihedral : 4.509 23.064 1036 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.44 (0.26), residues: 964 helix: 0.87 (0.24), residues: 454 sheet: 0.95 (0.38), residues: 178 loop : -0.79 (0.32), residues: 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 100 average time/residue: 0.1768 time to fit residues: 25.7701 Evaluate side-chains 89 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0773 time to fit residues: 2.7214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7889 Z= 0.214 Angle : 0.726 12.106 10698 Z= 0.356 Chirality : 0.043 0.172 1172 Planarity : 0.005 0.044 1397 Dihedral : 4.267 22.247 1036 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.84 (0.27), residues: 964 helix: 1.23 (0.25), residues: 454 sheet: 1.25 (0.38), residues: 170 loop : -0.68 (0.32), residues: 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.1800 time to fit residues: 22.7500 Evaluate side-chains 75 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 83 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7889 Z= 0.206 Angle : 0.725 13.810 10698 Z= 0.348 Chirality : 0.043 0.151 1172 Planarity : 0.004 0.042 1397 Dihedral : 4.229 24.111 1036 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.09 (0.27), residues: 964 helix: 1.40 (0.25), residues: 454 sheet: 1.32 (0.38), residues: 169 loop : -0.44 (0.33), residues: 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 81 average time/residue: 0.1827 time to fit residues: 21.5127 Evaluate side-chains 78 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0795 time to fit residues: 2.0035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 20.0000 chunk 1 optimal weight: 0.0270 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 HIS ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 7889 Z= 0.297 Angle : 0.749 10.988 10698 Z= 0.368 Chirality : 0.043 0.149 1172 Planarity : 0.004 0.040 1397 Dihedral : 4.500 26.786 1036 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.00 (0.27), residues: 964 helix: 1.39 (0.25), residues: 449 sheet: 1.13 (0.38), residues: 164 loop : -0.46 (0.32), residues: 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 72 average time/residue: 0.1820 time to fit residues: 19.6203 Evaluate side-chains 71 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0783 time to fit residues: 1.8889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7889 Z= 0.201 Angle : 0.731 10.852 10698 Z= 0.350 Chirality : 0.043 0.187 1172 Planarity : 0.004 0.042 1397 Dihedral : 4.284 20.451 1036 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.16 (0.27), residues: 964 helix: 1.47 (0.25), residues: 455 sheet: 0.96 (0.37), residues: 172 loop : -0.21 (0.33), residues: 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 0.1835 time to fit residues: 19.7215 Evaluate side-chains 67 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0898 time to fit residues: 1.5288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.219 Angle : 0.737 13.056 10698 Z= 0.349 Chirality : 0.043 0.158 1172 Planarity : 0.004 0.041 1397 Dihedral : 4.225 17.572 1036 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.17 (0.27), residues: 964 helix: 1.48 (0.25), residues: 454 sheet: 0.87 (0.37), residues: 171 loop : -0.15 (0.34), residues: 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.1678 time to fit residues: 19.1179 Evaluate side-chains 72 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0808 time to fit residues: 1.7204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.190 Angle : 0.756 10.529 10698 Z= 0.357 Chirality : 0.043 0.195 1172 Planarity : 0.004 0.041 1397 Dihedral : 4.130 19.093 1036 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.27 (0.27), residues: 964 helix: 1.56 (0.25), residues: 457 sheet: 0.90 (0.37), residues: 169 loop : -0.07 (0.34), residues: 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.231 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1822 time to fit residues: 22.0646 Evaluate side-chains 73 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 0.0040 chunk 77 optimal weight: 0.0870 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.184 Angle : 0.765 10.164 10698 Z= 0.358 Chirality : 0.043 0.195 1172 Planarity : 0.004 0.041 1397 Dihedral : 4.097 18.895 1036 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.27), residues: 964 helix: 1.54 (0.25), residues: 459 sheet: 0.96 (0.38), residues: 168 loop : 0.02 (0.34), residues: 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1873 time to fit residues: 21.1230 Evaluate side-chains 74 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 63 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 46 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.179 Angle : 0.786 14.827 10698 Z= 0.361 Chirality : 0.044 0.196 1172 Planarity : 0.004 0.042 1397 Dihedral : 4.006 19.503 1036 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.30 (0.27), residues: 964 helix: 1.50 (0.25), residues: 458 sheet: 0.98 (0.38), residues: 168 loop : 0.03 (0.34), residues: 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1841 time to fit residues: 21.0749 Evaluate side-chains 74 residues out of total 855 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.043993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.034928 restraints weight = 48918.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.036394 restraints weight = 27939.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.037439 restraints weight = 18496.340| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.214 Angle : 0.792 18.676 10698 Z= 0.365 Chirality : 0.044 0.193 1172 Planarity : 0.004 0.040 1397 Dihedral : 4.034 16.950 1036 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.27), residues: 964 helix: 1.49 (0.25), residues: 459 sheet: 0.98 (0.38), residues: 168 loop : 0.09 (0.34), residues: 337 =============================================================================== Job complete usr+sys time: 1538.29 seconds wall clock time: 29 minutes 11.18 seconds (1751.18 seconds total)