Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 19:12:47 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/12_2021/7rpi_24615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/12_2021/7rpi_24615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/12_2021/7rpi_24615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/12_2021/7rpi_24615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/12_2021/7rpi_24615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/12_2021/7rpi_24615_updated.pdb" } resolution = 2.5 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= 0.005 sd= 0.579 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 258": "OE1" <-> "OE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A ARG 754": "NH1" <-> "NH2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A GLU 859": "OE1" <-> "OE2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A GLU 936": "OE1" <-> "OE2" Residue "A GLU 952": "OE1" <-> "OE2" Residue "A GLU 958": "OE1" <-> "OE2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A GLU 1036": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 8526 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8526 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 8521 Unusual residues: {' NA': 2, 'Y01': 26, 'AV0': 2, 'NAG': 5} Classifications: {'undetermined': 35, 'water': 43, 'peptide': 926} Link IDs: {'PTRANS': 39, 'TRANS': 885, None: 78, 'PCIS': 1} Not linked: pdbres="PHE A1143 " pdbres="Y01 A2101 " Not linked: pdbres="Y01 A2101 " pdbres="Y01 A2102 " Not linked: pdbres="Y01 A2102 " pdbres="Y01 A2103 " Not linked: pdbres="Y01 A2103 " pdbres="Y01 A2104 " Not linked: pdbres="Y01 A2104 " pdbres="Y01 A2105 " ... (remaining 73 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Conformer: "B" Number of residues, atoms: 1004, 8521 Unusual residues: {' NA': 2, 'Y01': 26, 'AV0': 2, 'NAG': 5} Classifications: {'undetermined': 35, 'water': 43, 'peptide': 926} Link IDs: {'PTRANS': 39, 'TRANS': 885, None: 78, 'PCIS': 1} Not linked: pdbres="PHE A1143 " pdbres="Y01 A2101 " Not linked: pdbres="Y01 A2101 " pdbres="Y01 A2102 " Not linked: pdbres="Y01 A2102 " pdbres="Y01 A2103 " Not linked: pdbres="Y01 A2103 " pdbres="Y01 A2104 " Not linked: pdbres="Y01 A2104 " pdbres="Y01 A2105 " ... (remaining 73 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 bond proxies already assigned to first conformer: 8752 Time building chain proxies: 8.96, per 1000 atoms: 1.05 Number of scatterers: 8526 At special positions: 0 Unit cell: (86.005, 87.675, 127.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Na 2 11.00 O 1534 8.00 N 1184 7.00 C 5741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 366 " distance=2.05 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 829 " - pdb=" SG CYS A 849 " distance=2.05 Simple disulfide: pdb=" SG CYS A 863 " - pdb=" SG CYS A 872 " distance=2.04 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 887 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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 Links applied NAG-ASN " NAG A2129 " - " ASN A 915 " " NAG A2130 " - " ASN A 834 " " NAG A2131 " - " ASN A 475 " " NAG A2132 " - " ASN A 390 " " NAG A2133 " - " ASN A 362 " Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 2.2 seconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 2 sheets defined 59.5% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 188 through 208 Processing helix chain 'A' and resid 228 through 241 Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.827A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.564A pdb=" N CYS A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 338 No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 371 through 389 removed outlier: 5.239A pdb=" N LYS A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 429 Processing helix chain 'A' and resid 461 through 470 removed outlier: 4.361A pdb=" N ASN A 465 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A 469 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 521 removed outlier: 3.827A pdb=" N GLN A 496 " --> pdb=" O HIS A 492 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TYR A 505 " --> pdb=" O MET A 501 " (cutoff:3.500A) Proline residue: A 506 - end of helix Processing helix chain 'A' and resid 524 through 547 removed outlier: 3.761A pdb=" N LEU A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.521A pdb=" N ILE A 564 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 565 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 568 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 586 removed outlier: 3.764A pdb=" N PHE A 574 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS A 577 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 623 removed outlier: 5.557A pdb=" N LEU A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N SER A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR A 622 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 623 " --> pdb=" O TYR A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 648 Processing helix chain 'A' and resid 650 through 660 Processing helix chain 'A' and resid 662 through 665 No H-bonds generated for 'chain 'A' and resid 662 through 665' Processing helix chain 'A' and resid 682 through 705 removed outlier: 4.586A pdb=" N GLN A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 716 through 735 Processing helix chain 'A' and resid 747 through 749 No H-bonds generated for 'chain 'A' and resid 747 through 749' Processing helix chain 'A' and resid 758 through 764 removed outlier: 3.689A pdb=" N ASP A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 768 No H-bonds generated for 'chain 'A' and resid 766 through 768' Processing helix chain 'A' and resid 771 through 774 No H-bonds generated for 'chain 'A' and resid 771 through 774' Processing helix chain 'A' and resid 819 through 834 removed outlier: 3.854A pdb=" N ASN A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 860 Processing helix chain 'A' and resid 866 through 868 No H-bonds generated for 'chain 'A' and resid 866 through 868' Processing helix chain 'A' and resid 881 through 898 removed outlier: 3.978A pdb=" N LYS A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP A 896 " --> pdb=" O ILE A 892 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG A 897 " --> pdb=" O MET A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 955 removed outlier: 3.945A pdb=" N SER A 955 " --> pdb=" O HIS A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1001 Processing helix chain 'A' and resid 1004 through 1027 Processing helix chain 'A' and resid 1036 through 1060 removed outlier: 3.590A pdb=" N ILE A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASP A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1095 removed outlier: 5.434A pdb=" N SER A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1122 Processing helix chain 'A' and resid 1124 through 1132 Processing sheet with id= A, first strand: chain 'A' and resid 450 through 454 removed outlier: 6.543A pdb=" N ALA A 305 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL A 483 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 964 through 966 removed outlier: 6.868A pdb=" N ARG A 911 " --> pdb=" O ARG A 919 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 921 " --> pdb=" O GLY A 909 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 909 " --> pdb=" O VAL A 921 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1080 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: 2.31 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1340 1.32 - 1.45: 2192 1.45 - 1.58: 5065 1.58 - 1.70: 69 1.70 - 1.83: 98 Bond restraints: 8764 Sorted by residual: bond pdb=" N MET A 557 " pdb=" CA BMET A 557 " ideal model delta sigma weight residual 1.458 1.357 0.102 1.27e-02 6.20e+03 6.43e+01 bond pdb=" C5 NAG A2130 " pdb=" O5 NAG A2130 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.10e-02 8.26e+03 2.09e+01 bond pdb=" C5 NAG A2131 " pdb=" O5 NAG A2131 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.10e-02 8.26e+03 2.08e+01 bond pdb=" C5 NAG A2132 " pdb=" O5 NAG A2132 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.10e-02 8.26e+03 2.02e+01 bond pdb=" C5 NAG A2133 " pdb=" O5 NAG A2133 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.10e-02 8.26e+03 1.87e+01 ... (remaining 8759 not shown) Histogram of bond angle deviations from ideal: 93.37 - 101.77: 49 101.77 - 110.16: 2060 110.16 - 118.55: 4927 118.55 - 126.95: 4923 126.95 - 135.34: 103 Bond angle restraints: 12062 Sorted by residual: angle pdb=" N ARG A 341 " pdb=" CA ARG A 341 " pdb=" C ARG A 341 " ideal model delta sigma weight residual 108.76 122.02 -13.26 1.69e+00 3.50e-01 6.16e+01 angle pdb=" N MET A 557 " pdb=" CA BMET A 557 " pdb=" C MET A 557 " ideal model delta sigma weight residual 111.75 120.36 -8.61 1.28e+00 6.10e-01 4.52e+01 angle pdb=" CA PHE A 759 " pdb=" CB PHE A 759 " pdb=" CG PHE A 759 " ideal model delta sigma weight residual 113.80 120.40 -6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" CA PHE A 549 " pdb=" CB PHE A 549 " pdb=" CG PHE A 549 " ideal model delta sigma weight residual 113.80 120.17 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" CA ASP A 293 " pdb=" CB ASP A 293 " pdb=" CG ASP A 293 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 ... (remaining 12057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.89: 4684 26.89 - 53.79: 156 53.79 - 80.68: 16 80.68 - 107.57: 6 107.57 - 134.47: 2 Dihedral angle restraints: 4864 sinusoidal: 2136 harmonic: 2728 Sorted by residual: dihedral pdb=" CA VAL A1048 " pdb=" C VAL A1048 " pdb=" N ASP A1049 " pdb=" CA ASP A1049 " ideal model delta harmonic sigma weight residual 180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA TYR A 420 " pdb=" C TYR A 420 " pdb=" N ASN A 421 " pdb=" CA ASN A 421 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA TYR A 443 " pdb=" C TYR A 443 " pdb=" N ALA A 444 " pdb=" CA ALA A 444 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 4861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 924 0.095 - 0.191: 433 0.191 - 0.286: 66 0.286 - 0.381: 15 0.381 - 0.477: 3 Chirality restraints: 1441 Sorted by residual: chirality pdb=" CA GLU A1031 " pdb=" N GLU A1031 " pdb=" C GLU A1031 " pdb=" CB GLU A1031 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA BMET A 557 " pdb=" N MET A 557 " pdb=" C MET A 557 " pdb=" CB BMET A 557 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA ASP A 916 " pdb=" N ASP A 916 " pdb=" C ASP A 916 " pdb=" CB ASP A 916 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 1438 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 834 " -0.102 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" CG ASN A 834 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 834 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 834 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG A2130 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 313 " 0.145 2.00e-02 2.50e+03 7.20e-02 1.30e+02 pdb=" CG TRP A 313 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 313 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP A 313 " -0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP A 313 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 313 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 313 " -0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 313 " 0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 313 " -0.043 2.00e-02 2.50e+03 pdb=" CH2 TRP A 313 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 915 " -0.091 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" CG ASN A 915 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 915 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 915 " 0.164 2.00e-02 2.50e+03 pdb=" C1 NAG A2129 " -0.119 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 140 2.72 - 3.26: 8334 3.26 - 3.81: 12764 3.81 - 4.35: 18587 4.35 - 4.90: 29525 Nonbonded interactions: 69350 Sorted by model distance: nonbonded pdb=" OD1 ASP A1049 " pdb="NA NA A2134 " model vdw 2.170 2.470 nonbonded pdb=" O GLY A1045 " pdb="NA NA A2134 " model vdw 2.205 2.470 nonbonded pdb=" OD1 ASP A 572 " pdb="NA NA A2135 " model vdw 2.213 2.470 nonbonded pdb=" OD2 ASP A 572 " pdb="NA NA A2135 " model vdw 2.245 2.470 nonbonded pdb="NA NA A2135 " pdb=" O HOH A2231 " model vdw 2.261 2.470 ... (remaining 69345 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: 5 Type Number sf(0) Gaussians S 65 5.16 5 Na 2 4.78 5 C 5741 2.51 5 N 1184 2.21 5 O 1534 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Write .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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.450 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.080 Process input model: 30.180 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 50.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 : 0.016 0.102 8764 Z= 0.956 Angle : 1.816 13.262 12062 Z= 1.188 Chirality : 0.105 0.477 1441 Planarity : 0.014 0.100 1339 Dihedral : 13.768 134.467 3074 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.23 % 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: -0.69 (0.25), residues: 919 helix: -0.43 (0.19), residues: 558 sheet: 0.48 (0.94), residues: 29 loop : -0.29 (0.35), residues: 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 1.1745 time to fit residues: 162.4045 Evaluate side-chains 85 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 421 ASN A 465 ASN A 470 ASN A 856 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 8764 Z= 0.193 Angle : 0.668 8.453 12062 Z= 0.323 Chirality : 0.042 0.227 1441 Planarity : 0.005 0.094 1339 Dihedral : 11.275 145.198 1403 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.41 (0.27), residues: 919 helix: 1.40 (0.21), residues: 560 sheet: 0.76 (0.92), residues: 29 loop : 0.30 (0.35), residues: 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.962 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 102 average time/residue: 1.1002 time to fit residues: 121.0069 Evaluate side-chains 88 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 1.1478 time to fit residues: 4.8996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 50.0000 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 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 340 GLN A 856 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 8764 Z= 0.228 Angle : 0.673 7.214 12062 Z= 0.316 Chirality : 0.043 0.390 1441 Planarity : 0.005 0.105 1339 Dihedral : 11.303 142.979 1403 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer Outliers : 2.33 % 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: 1.47 (0.28), residues: 919 helix: 1.56 (0.22), residues: 560 sheet: 0.90 (0.94), residues: 29 loop : 0.07 (0.35), residues: 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 105 average time/residue: 1.0661 time to fit residues: 120.8530 Evaluate side-chains 95 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.6857 time to fit residues: 5.0054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 50.0000 chunk 86 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.7212 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 8764 Z= 0.199 Angle : 0.635 8.173 12062 Z= 0.294 Chirality : 0.042 0.407 1441 Planarity : 0.005 0.110 1339 Dihedral : 10.962 141.278 1403 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 1.72 % 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: 1.48 (0.28), residues: 919 helix: 1.63 (0.22), residues: 561 sheet: 1.02 (0.93), residues: 29 loop : -0.06 (0.34), residues: 329 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 98 average time/residue: 1.0699 time to fit residues: 113.4454 Evaluate side-chains 93 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 1.1235 time to fit residues: 4.7703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 8764 Z= 0.150 Angle : 0.584 8.354 12062 Z= 0.270 Chirality : 0.040 0.365 1441 Planarity : 0.005 0.109 1339 Dihedral : 10.491 139.821 1403 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 1.11 % 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: 1.63 (0.28), residues: 919 helix: 1.78 (0.22), residues: 565 sheet: 1.13 (0.93), residues: 29 loop : -0.10 (0.34), residues: 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 0.9984 time to fit residues: 99.9775 Evaluate side-chains 89 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 3 average time/residue: 0.4922 time to fit residues: 2.9558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 96 optimal weight: 50.0000 chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 8764 Z= 0.180 Angle : 0.606 8.621 12062 Z= 0.279 Chirality : 0.041 0.364 1441 Planarity : 0.005 0.092 1339 Dihedral : 10.632 140.085 1403 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 0.86 % 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: 1.54 (0.28), residues: 919 helix: 1.73 (0.22), residues: 566 sheet: 1.01 (0.91), residues: 29 loop : -0.17 (0.34), residues: 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.9890 time to fit residues: 98.9525 Evaluate side-chains 88 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.9969 time to fit residues: 3.2827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 50.0000 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 57 optimal weight: 0.0770 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 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 8764 Z= 0.147 Angle : 0.573 9.097 12062 Z= 0.261 Chirality : 0.039 0.353 1441 Planarity : 0.004 0.083 1339 Dihedral : 10.452 139.357 1403 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 0.74 % 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: 1.63 (0.28), residues: 919 helix: 1.83 (0.22), residues: 566 sheet: 1.01 (0.92), residues: 29 loop : -0.20 (0.34), residues: 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.972 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 1.0321 time to fit residues: 107.6493 Evaluate side-chains 86 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.2074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8764 Z= 0.216 Angle : 0.638 8.885 12062 Z= 0.293 Chirality : 0.042 0.356 1441 Planarity : 0.005 0.079 1339 Dihedral : 10.793 140.051 1403 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 1.23 % 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: 1.43 (0.28), residues: 919 helix: 1.68 (0.22), residues: 565 sheet: 0.98 (0.92), residues: 29 loop : -0.30 (0.33), residues: 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 1.0441 time to fit residues: 107.5749 Evaluate side-chains 92 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 2.5832 time to fit residues: 3.9583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8764 Z= 0.165 Angle : 0.601 9.247 12062 Z= 0.274 Chirality : 0.040 0.357 1441 Planarity : 0.004 0.076 1339 Dihedral : 10.660 139.011 1403 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.74 % 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: 1.50 (0.28), residues: 919 helix: 1.75 (0.22), residues: 565 sheet: 1.03 (0.92), residues: 29 loop : -0.31 (0.33), residues: 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 92 average time/residue: 1.0318 time to fit residues: 102.9519 Evaluate side-chains 88 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.2657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 50.0000 chunk 91 optimal weight: 0.0040 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 8764 Z= 0.148 Angle : 0.586 9.492 12062 Z= 0.266 Chirality : 0.039 0.355 1441 Planarity : 0.004 0.075 1339 Dihedral : 10.502 139.010 1403 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 0.61 % 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: 1.62 (0.28), residues: 919 helix: 1.85 (0.22), residues: 564 sheet: 1.08 (0.92), residues: 29 loop : -0.25 (0.33), residues: 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 88 average time/residue: 1.0022 time to fit residues: 96.5877 Evaluate side-chains 89 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.2894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 69 optimal weight: 0.0070 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.187811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134728 restraints weight = 10823.301| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.04 r_work: 0.3590 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3549 rms_B_bonded: 1.99 restraints_weight: 0.1250 r_work: 0.3528 rms_B_bonded: 2.18 restraints_weight: 0.0625 r_work: 0.3504 rms_B_bonded: 2.45 restraints_weight: 0.0312 r_work: 0.3478 rms_B_bonded: 2.80 restraints_weight: 0.0156 r_work: 0.3449 rms_B_bonded: 3.24 restraints_weight: 0.0078 r_work: 0.3416 rms_B_bonded: 3.79 restraints_weight: 0.0039 r_work: 0.3378 rms_B_bonded: 4.49 restraints_weight: 0.0020 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4188 r_free = 0.4188 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4188 r_free = 0.4188 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 8764 Z= 0.147 Angle : 0.582 10.918 12062 Z= 0.264 Chirality : 0.039 0.343 1441 Planarity : 0.004 0.074 1339 Dihedral : 10.384 139.202 1403 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.61 % 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: 1.66 (0.28), residues: 919 helix: 1.87 (0.22), residues: 565 sheet: 1.04 (0.91), residues: 29 loop : -0.23 (0.34), residues: 325 =============================================================================== Job complete usr+sys time: 2655.35 seconds wall clock time: 48 minutes 21.30 seconds (2901.30 seconds total)