Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 10:43:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gud_34273/04_2023/8gud_34273_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gud_34273/04_2023/8gud_34273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gud_34273/04_2023/8gud_34273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gud_34273/04_2023/8gud_34273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gud_34273/04_2023/8gud_34273_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gud_34273/04_2023/8gud_34273_updated.pdb" } resolution = 2.62 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 62 5.16 5 C 4360 2.51 5 N 1159 2.21 5 O 1230 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6814 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6814 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 836, 6814 Unusual residues: {'1LT': 1} Classifications: {'peptide': 835, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 794, None: 1} Not linked: pdbres="GLY A1050 " pdbres="1LT A1101 " Chain breaks: 8 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AILE A 932 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE A 932 " occ=0.50 residue: pdb=" N AASP A 933 " occ=0.50 ... (6 atoms not shown) pdb=" OD2AASP A 933 " occ=0.50 residue: pdb=" N APHE A 934 " occ=0.50 ... (9 atoms not shown) pdb=" CZ APHE A 934 " occ=0.50 residue: pdb=" N AGLY A 935 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY A 935 " occ=0.50 Time building chain proxies: 4.10, per 1000 atoms: 0.60 Number of scatterers: 6814 At special positions: 0 Unit cell: (74.97, 87.822, 101.745, 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 62 16.00 F 3 9.00 O 1230 8.00 N 1159 7.00 C 4360 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: 2.96 Conformation dependent library (CDL) restraints added in 989.9 milliseconds 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1594 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 5 sheets defined 41.2% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.996A pdb=" N ASP A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N PHE A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 154 removed outlier: 5.323A pdb=" N CYS A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LYS A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 151 " --> pdb=" O CYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.753A pdb=" N TYR A 294 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 529 through 535 Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.632A pdb=" N PHE A 550 " --> pdb=" O GLN A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 558 No H-bonds generated for 'chain 'A' and resid 555 through 558' Processing helix chain 'A' and resid 562 through 571 Proline residue: A 566 - end of helix removed outlier: 4.471A pdb=" N LEU A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 570 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 585 removed outlier: 3.529A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 598 No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'A' and resid 609 through 621 removed outlier: 3.580A pdb=" N LYS A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 5.041A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 678 through 692 removed outlier: 4.422A pdb=" N GLN A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 686 " --> pdb=" O GLN A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 719 removed outlier: 3.882A pdb=" N GLU A 707 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 711 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 713 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 716 " --> pdb=" O ILE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 740 Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.514A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (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 808 through 824 Processing helix chain 'A' and resid 858 through 861 No H-bonds generated for 'chain 'A' and resid 858 through 861' Processing helix chain 'A' and resid 876 through 883 Processing helix chain 'A' and resid 888 through 905 removed outlier: 3.816A pdb=" N ASP A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 892 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA A 893 " --> pdb=" O TYR A 890 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU A 896 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 898 " --> pdb=" O ASP A 895 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 899 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA A 902 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLY A 903 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR A 904 " --> pdb=" O CYS A 901 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS A 905 " --> pdb=" O ALA A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 959 through 964 removed outlier: 3.930A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 964 " --> pdb=" O PHE A 960 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 959 through 964' Processing helix chain 'A' and resid 975 through 991 removed outlier: 3.674A pdb=" N LYS A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 988 " --> pdb=" O CYS A 984 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1005 removed outlier: 3.865A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1026 removed outlier: 4.676A pdb=" N TYR A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1046 removed outlier: 3.704A pdb=" N TYR A1038 " --> pdb=" O GLU A1034 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A1042 " --> pdb=" O TYR A1038 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 204 through 212 removed outlier: 7.251A pdb=" N TRP A 195 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 285 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE A 197 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 287 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 385 through 388 removed outlier: 6.691A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 355 through 357 Processing sheet with id= D, first strand: chain 'A' and resid 779 through 784 Processing sheet with id= E, first strand: chain 'A' and resid 921 through 923 removed outlier: 3.535A pdb=" N MET A 922 " --> pdb=" O PHE A 930 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 930 " --> pdb=" O MET A 922 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 191 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1128 1.30 - 1.43: 1781 1.43 - 1.56: 3957 1.56 - 1.69: 6 1.69 - 1.81: 94 Bond restraints: 6966 Sorted by residual: bond pdb=" C9 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.738 1.530 0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 1.734 1.529 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.569 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C5 1LT A1101 " pdb=" C6 1LT A1101 " ideal model delta sigma weight residual 1.525 1.352 0.173 2.00e-02 2.50e+03 7.51e+01 bond pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " ideal model delta sigma weight residual 1.291 1.416 -0.125 2.00e-02 2.50e+03 3.89e+01 ... (remaining 6961 not shown) Histogram of bond angle deviations from ideal: 98.39 - 106.21: 203 106.21 - 114.04: 3973 114.04 - 121.86: 3799 121.86 - 129.68: 1389 129.68 - 137.50: 57 Bond angle restraints: 9421 Sorted by residual: angle pdb=" N1 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " ideal model delta sigma weight residual 118.47 137.50 -19.03 3.00e+00 1.11e-01 4.02e+01 angle pdb=" C2 1LT A1101 " pdb=" S 1LT A1101 " pdb=" C9 1LT A1101 " ideal model delta sigma weight residual 88.90 107.71 -18.81 3.00e+00 1.11e-01 3.93e+01 angle pdb=" N 1LT A1101 " pdb=" C2 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 126.74 114.54 12.20 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CA TYR A 392 " pdb=" CB TYR A 392 " pdb=" CG TYR A 392 " ideal model delta sigma weight residual 113.90 119.10 -5.20 1.80e+00 3.09e-01 8.35e+00 angle pdb=" CB MET A 583 " pdb=" CG MET A 583 " pdb=" SD MET A 583 " ideal model delta sigma weight residual 112.70 104.36 8.34 3.00e+00 1.11e-01 7.72e+00 ... (remaining 9416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3755 17.55 - 35.11: 373 35.11 - 52.66: 69 52.66 - 70.21: 8 70.21 - 87.77: 11 Dihedral angle restraints: 4216 sinusoidal: 1763 harmonic: 2453 Sorted by residual: dihedral pdb=" CA GLU A 642 " pdb=" C GLU A 642 " pdb=" N GLN A 643 " pdb=" CA GLN A 643 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ASN A 647 " pdb=" C ASN A 647 " pdb=" N LEU A 648 " pdb=" CA LEU A 648 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASN A 145 " pdb=" C ASN A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 162.49 17.51 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 822 0.055 - 0.110: 179 0.110 - 0.165: 22 0.165 - 0.220: 3 0.220 - 0.276: 1 Chirality restraints: 1027 Sorted by residual: chirality pdb=" CG LEU A 404 " pdb=" CB LEU A 404 " pdb=" CD1 LEU A 404 " pdb=" CD2 LEU A 404 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CG LEU A 719 " pdb=" CB LEU A 719 " pdb=" CD1 LEU A 719 " pdb=" CD2 LEU A 719 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA ILE A 848 " pdb=" N ILE A 848 " pdb=" C ILE A 848 " pdb=" CB ILE A 848 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 1024 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA AGLY A 935 " 0.036 2.00e-02 2.50e+03 7.39e-02 5.46e+01 pdb=" C AGLY A 935 " -0.128 2.00e-02 2.50e+03 pdb=" O AGLY A 935 " 0.048 2.00e-02 2.50e+03 pdb=" N HIS A 936 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 383 " -0.023 2.00e-02 2.50e+03 2.08e-02 1.09e+01 pdb=" CG TRP A 383 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP A 383 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 383 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 383 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 383 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 383 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 383 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 383 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 383 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 216 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO A 217 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.032 5.00e-02 4.00e+02 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 177 2.67 - 3.23: 6740 3.23 - 3.79: 10877 3.79 - 4.34: 15565 4.34 - 4.90: 24113 Nonbonded interactions: 57472 Sorted by model distance: nonbonded pdb=" NH1 ARG A 398 " pdb=" OH TYR A 644 " model vdw 2.116 2.520 nonbonded pdb=" O ILE A 633 " pdb=" NE2 GLN A 637 " model vdw 2.138 2.520 nonbonded pdb=" O ASP A 603 " pdb=" NH2 ARG A 612 " model vdw 2.143 2.520 nonbonded pdb=" OH TYR A 165 " pdb=" O CYS A 695 " model vdw 2.172 2.440 nonbonded pdb=" O LYS A1024 " pdb=" OH TYR A1038 " model vdw 2.197 2.440 ... (remaining 57467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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 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: 0.980 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: 4.150 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.080 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 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 : 0.008 0.208 6966 Z= 0.524 Angle : 0.788 19.031 9421 Z= 0.373 Chirality : 0.047 0.276 1027 Planarity : 0.006 0.074 1203 Dihedral : 14.797 87.766 2622 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 0.00 % 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: -2.12 (0.29), residues: 817 helix: -1.47 (0.26), residues: 364 sheet: -1.93 (0.54), residues: 85 loop : -1.00 (0.34), residues: 368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.846 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 1.1647 time to fit residues: 117.2018 Evaluate side-chains 75 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5450 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6966 Z= 0.225 Angle : 0.603 8.066 9421 Z= 0.297 Chirality : 0.042 0.143 1027 Planarity : 0.005 0.056 1203 Dihedral : 5.488 44.447 903 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 2.37 % 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: -1.73 (0.29), residues: 817 helix: -1.14 (0.27), residues: 359 sheet: -1.63 (0.54), residues: 86 loop : -0.84 (0.34), residues: 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.801 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 94 average time/residue: 1.1612 time to fit residues: 115.6688 Evaluate side-chains 86 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.7344 time to fit residues: 3.5506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 0.0050 chunk 60 optimal weight: 0.5980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN A 370 ASN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 6966 Z= 0.250 Angle : 0.619 8.409 9421 Z= 0.307 Chirality : 0.043 0.169 1027 Planarity : 0.005 0.056 1203 Dihedral : 5.432 43.550 903 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 2.90 % 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 (0.30), residues: 817 helix: -1.03 (0.27), residues: 355 sheet: -1.62 (0.54), residues: 86 loop : -0.82 (0.34), residues: 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 0.816 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 97 average time/residue: 1.1966 time to fit residues: 122.7654 Evaluate side-chains 87 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0631 time to fit residues: 1.3010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5435 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6966 Z= 0.202 Angle : 0.581 7.840 9421 Z= 0.286 Chirality : 0.041 0.153 1027 Planarity : 0.004 0.057 1203 Dihedral : 5.227 42.994 903 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 3.03 % 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: -1.57 (0.30), residues: 817 helix: -1.02 (0.27), residues: 374 sheet: -1.53 (0.54), residues: 86 loop : -0.72 (0.36), residues: 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.821 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 99 average time/residue: 1.1447 time to fit residues: 120.1175 Evaluate side-chains 85 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0644 time to fit residues: 1.3028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6966 Z= 0.206 Angle : 0.589 8.157 9421 Z= 0.290 Chirality : 0.041 0.146 1027 Planarity : 0.004 0.057 1203 Dihedral : 5.162 42.468 903 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.30), residues: 817 helix: -0.92 (0.27), residues: 373 sheet: -1.45 (0.54), residues: 86 loop : -0.69 (0.36), residues: 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 95 average time/residue: 1.1495 time to fit residues: 115.7368 Evaluate side-chains 88 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.3430 time to fit residues: 2.7155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 0.0070 chunk 37 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 77 optimal weight: 0.0970 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5384 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6966 Z= 0.172 Angle : 0.557 8.095 9421 Z= 0.273 Chirality : 0.040 0.148 1027 Planarity : 0.004 0.057 1203 Dihedral : 4.956 41.377 903 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.19 (0.31), residues: 817 helix: -0.68 (0.27), residues: 375 sheet: -1.34 (0.54), residues: 86 loop : -0.55 (0.36), residues: 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 100 average time/residue: 1.1123 time to fit residues: 118.2056 Evaluate side-chains 87 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1195 time to fit residues: 1.3820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 6966 Z= 0.231 Angle : 0.607 8.173 9421 Z= 0.297 Chirality : 0.042 0.147 1027 Planarity : 0.004 0.059 1203 Dihedral : 5.121 41.675 903 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.33 (0.30), residues: 817 helix: -0.80 (0.27), residues: 372 sheet: -1.36 (0.54), residues: 86 loop : -0.63 (0.36), residues: 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 79 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 98 average time/residue: 1.1188 time to fit residues: 116.4377 Evaluate side-chains 88 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1341 time to fit residues: 1.5083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6966 Z= 0.204 Angle : 0.592 8.029 9421 Z= 0.290 Chirality : 0.041 0.146 1027 Planarity : 0.004 0.058 1203 Dihedral : 5.052 41.992 903 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.24 (0.30), residues: 817 helix: -0.68 (0.28), residues: 368 sheet: -1.25 (0.55), residues: 86 loop : -0.67 (0.35), residues: 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 93 average time/residue: 1.0638 time to fit residues: 105.3660 Evaluate side-chains 88 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.743 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 1.0045 time to fit residues: 2.1616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 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 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 6966 Z= 0.208 Angle : 0.607 9.302 9421 Z= 0.296 Chirality : 0.042 0.145 1027 Planarity : 0.004 0.058 1203 Dihedral : 5.040 42.196 903 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 2.77 % 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: -1.24 (0.30), residues: 817 helix: -0.63 (0.28), residues: 361 sheet: -1.22 (0.55), residues: 86 loop : -0.74 (0.35), residues: 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 93 average time/residue: 1.0955 time to fit residues: 108.5178 Evaluate side-chains 89 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.0649 time to fit residues: 1.3566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5447 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 6966 Z= 0.232 Angle : 0.644 15.368 9421 Z= 0.309 Chirality : 0.042 0.145 1027 Planarity : 0.004 0.058 1203 Dihedral : 5.146 42.053 903 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 2.24 % 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: -1.34 (0.30), residues: 817 helix: -0.72 (0.28), residues: 360 sheet: -1.25 (0.55), residues: 86 loop : -0.79 (0.35), residues: 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 89 average time/residue: 1.0905 time to fit residues: 103.3643 Evaluate side-chains 89 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 1.0470 time to fit residues: 3.4406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 67 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 0.0000 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.261768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.228208 restraints weight = 6658.829| |-----------------------------------------------------------------------------| r_work (start): 0.4724 rms_B_bonded: 2.03 r_work: 0.4607 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4617 r_free = 0.4617 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4616 r_free = 0.4616 target_work(ls_wunit_k1) = 0.217 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5434 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6966 Z= 0.196 Angle : 0.628 14.994 9421 Z= 0.298 Chirality : 0.041 0.143 1027 Planarity : 0.004 0.058 1203 Dihedral : 4.971 41.505 903 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 1.98 % 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: -1.16 (0.30), residues: 817 helix: -0.56 (0.28), residues: 361 sheet: -1.14 (0.55), residues: 86 loop : -0.72 (0.35), residues: 370 =============================================================================== Job complete usr+sys time: 2587.17 seconds wall clock time: 46 minutes 47.63 seconds (2807.63 seconds total)