Starting phenix.real_space_refine (version: dev) on Mon Dec 12 13:48:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2022/6k7g_9931_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2022/6k7g_9931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2022/6k7g_9931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2022/6k7g_9931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2022/6k7g_9931_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7g_9931/12_2022/6k7g_9931_updated.pdb" } resolution = 3.3 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 205": "OD1" <-> "OD2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ASP 482": "OD1" <-> "OD2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 513": "OD1" <-> "OD2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 786": "OD1" <-> "OD2" Residue "A ASP 816": "OD1" <-> "OD2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 961": "OD1" <-> "OD2" Residue "A TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1022": "OD1" <-> "OD2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C ASP 248": "OD1" <-> "OD2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10569 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7852 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 957} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.30, per 1000 atoms: 0.60 Number of scatterers: 10569 At special positions: 0 Unit cell: (66.4, 111.22, 164.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1914 8.00 N 1747 7.00 C 6852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.02 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 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 4.58 Conformation dependent library (CDL) restraints added in 1.5 seconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 9 sheets defined 40.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 64 through 73 Processing helix chain 'A' and resid 76 through 89 removed outlier: 4.480A pdb=" N GLN A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 131 removed outlier: 4.257A pdb=" N LYS A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 289 through 322 Processing helix chain 'A' and resid 340 through 354 removed outlier: 5.464A pdb=" N ASN A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 376 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 459 through 471 removed outlier: 4.935A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 Processing helix chain 'A' and resid 560 through 566 removed outlier: 4.076A pdb=" N ASP A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 removed outlier: 4.310A pdb=" N GLU A 575 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 579 " --> pdb=" O ILE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 743 through 750 Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'A' and resid 788 through 796 removed outlier: 4.390A pdb=" N SER A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N MET A 793 " --> pdb=" O ASN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.911A pdb=" N LYS A 826 " --> pdb=" O LYS A 823 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 829 " --> pdb=" O LYS A 826 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET A 830 " --> pdb=" O ASN A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 855 Processing helix chain 'A' and resid 857 through 860 No H-bonds generated for 'chain 'A' and resid 857 through 860' Processing helix chain 'A' and resid 862 through 865 No H-bonds generated for 'chain 'A' and resid 862 through 865' Processing helix chain 'A' and resid 876 through 879 No H-bonds generated for 'chain 'A' and resid 876 through 879' Processing helix chain 'A' and resid 888 through 895 Processing helix chain 'A' and resid 902 through 907 Processing helix chain 'A' and resid 909 through 917 removed outlier: 3.616A pdb=" N THR A 914 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A 915 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 916 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 962 through 984 Processing helix chain 'A' and resid 990 through 1012 removed outlier: 4.074A pdb=" N VAL A1004 " --> pdb=" O ILE A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1032 Processing helix chain 'A' and resid 1035 through 1060 removed outlier: 3.947A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 4.992A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 73 Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.884A pdb=" N HIS C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 134 through 137 removed outlier: 3.709A pdb=" N VAL A 146 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 155 through 160 removed outlier: 3.971A pdb=" N ASP A 155 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 173 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE A 266 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU A 171 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 180 through 183 Processing sheet with id= E, first strand: chain 'A' and resid 726 through 728 removed outlier: 6.754A pdb=" N ALA A 755 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL A 780 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE A 406 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 782 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N SER A 408 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 784 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 799 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLY A 785 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 801 " --> pdb=" O GLY A 785 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 506 through 508 removed outlier: 3.510A pdb=" N VAL A 515 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 543 through 545 removed outlier: 3.759A pdb=" N ARG A 553 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 592 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU A 645 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N PHE A 421 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 77 through 81 Processing sheet with id= I, first strand: chain 'C' and resid 291 through 293 removed outlier: 3.695A pdb=" N PHE C 186 " --> pdb=" O SER C 292 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1071 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: 3.03 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1899 1.32 - 1.45: 2821 1.45 - 1.57: 6013 1.57 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 10818 Sorted by residual: bond pdb=" C SER A 223 " pdb=" N PRO A 224 " ideal model delta sigma weight residual 1.330 1.370 -0.040 1.19e-02 7.06e+03 1.13e+01 bond pdb=" C VAL C 99 " pdb=" N THR C 100 " ideal model delta sigma weight residual 1.331 1.269 0.062 2.07e-02 2.33e+03 9.10e+00 bond pdb=" CG GLN A 870 " pdb=" CD GLN A 870 " ideal model delta sigma weight residual 1.516 1.450 0.066 2.50e-02 1.60e+03 7.04e+00 bond pdb=" C4 NAG B 2 " pdb=" O4 NAG B 2 " ideal model delta sigma weight residual 1.423 1.449 -0.026 1.00e-02 1.00e+04 6.88e+00 bond pdb=" CB VAL A 853 " pdb=" CG2 VAL A 853 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.61e+00 ... (remaining 10813 not shown) Histogram of bond angle deviations from ideal: 93.63 - 102.33: 41 102.33 - 111.04: 3910 111.04 - 119.74: 5689 119.74 - 128.45: 4948 128.45 - 137.15: 101 Bond angle restraints: 14689 Sorted by residual: angle pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" O4 NAG B 2 " ideal model delta sigma weight residual 110.01 119.54 -9.53 1.87e+00 2.86e-01 2.60e+01 angle pdb=" C HIS A 227 " pdb=" N LEU A 228 " pdb=" CA LEU A 228 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C2 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" O3 NAG B 2 " ideal model delta sigma weight residual 109.47 100.67 8.80 1.96e+00 2.61e-01 2.02e+01 angle pdb=" C GLU A 633 " pdb=" N LYS A 634 " pdb=" CA LYS A 634 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C2 NAG C 401 " pdb=" C3 NAG C 401 " pdb=" C4 NAG C 401 " ideal model delta sigma weight residual 110.39 115.46 -5.07 1.16e+00 7.50e-01 1.93e+01 ... (remaining 14684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5640 17.70 - 35.40: 622 35.40 - 53.10: 126 53.10 - 70.80: 22 70.80 - 88.50: 12 Dihedral angle restraints: 6422 sinusoidal: 2590 harmonic: 3832 Sorted by residual: dihedral pdb=" CB CYS C 91 " pdb=" SG CYS C 91 " pdb=" SG CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.87 -62.87 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CA ALA C 169 " pdb=" C ALA C 169 " pdb=" N PRO C 170 " pdb=" CA PRO C 170 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLU C 111 " pdb=" C GLU C 111 " pdb=" N LYS C 112 " pdb=" CA LYS C 112 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 6419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1274 0.074 - 0.147: 360 0.147 - 0.221: 39 0.221 - 0.295: 8 0.295 - 0.369: 2 Chirality restraints: 1683 Sorted by residual: chirality pdb=" CB VAL A 103 " pdb=" CA VAL A 103 " pdb=" CG1 VAL A 103 " pdb=" CG2 VAL A 103 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CB ILE A 784 " pdb=" CA ILE A 784 " pdb=" CG1 ILE A 784 " pdb=" CG2 ILE A 784 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1680 not shown) Planarity restraints: 1839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.323 2.00e-02 2.50e+03 2.81e-01 9.89e+02 pdb=" C7 NAG B 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.052 2.00e-02 2.50e+03 4.27e-02 2.28e+01 pdb=" C7 NAG C 401 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.067 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 255 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLU C 255 " -0.066 2.00e-02 2.50e+03 pdb=" O GLU C 255 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP C 256 " 0.023 2.00e-02 2.50e+03 ... (remaining 1836 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2620 2.79 - 3.32: 9619 3.32 - 3.84: 17918 3.84 - 4.37: 21087 4.37 - 4.90: 36252 Nonbonded interactions: 87496 Sorted by model distance: nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.262 2.440 nonbonded pdb=" OG SER A 94 " pdb=" O GLY A 97 " model vdw 2.275 2.440 nonbonded pdb=" O MET A1038 " pdb=" OH TYR C 329 " model vdw 2.313 2.440 nonbonded pdb=" NE2 GLN A 795 " pdb=" OG SER A 814 " model vdw 2.314 2.520 nonbonded pdb=" OH TYR A 611 " pdb=" OE1 GLU A 626 " model vdw 2.329 2.440 ... (remaining 87491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6852 2.51 5 N 1747 2.21 5 O 1914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.630 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: 4.730 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 30.000 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.012 0.108 10818 Z= 0.809 Angle : 1.178 13.907 14689 Z= 0.633 Chirality : 0.067 0.369 1683 Planarity : 0.011 0.281 1836 Dihedral : 15.551 88.497 3941 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.13 % Favored : 90.71 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.18), residues: 1303 helix: -2.64 (0.15), residues: 589 sheet: -1.36 (0.37), residues: 171 loop : -3.20 (0.22), residues: 543 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 129 average time/residue: 0.3234 time to fit residues: 54.9379 Evaluate side-chains 88 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0955 time to fit residues: 2.3086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 147 HIS A 187 ASN A 264 HIS ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 451 ASN A 456 HIS A 530 ASN A 679 ASN A 993 HIS C 92 ASN C 131 HIS C 254 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 10818 Z= 0.192 Angle : 0.633 10.947 14689 Z= 0.326 Chirality : 0.043 0.139 1683 Planarity : 0.005 0.059 1836 Dihedral : 6.138 52.723 1462 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -2.62 (0.21), residues: 1303 helix: -1.02 (0.19), residues: 578 sheet: -1.24 (0.36), residues: 175 loop : -2.65 (0.23), residues: 550 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 114 average time/residue: 0.2543 time to fit residues: 41.7979 Evaluate side-chains 102 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1124 time to fit residues: 4.1004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 94 optimal weight: 0.0000 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 0.054 10818 Z= 0.166 Angle : 0.591 11.547 14689 Z= 0.300 Chirality : 0.042 0.141 1683 Planarity : 0.004 0.060 1836 Dihedral : 5.577 47.114 1462 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.21 % Favored : 92.71 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.88 (0.22), residues: 1303 helix: -0.33 (0.21), residues: 577 sheet: -0.82 (0.40), residues: 168 loop : -2.37 (0.24), residues: 558 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 115 average time/residue: 0.2712 time to fit residues: 43.4851 Evaluate side-chains 95 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1047 time to fit residues: 3.1112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 125 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 GLN C 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 10818 Z= 0.311 Angle : 0.631 12.002 14689 Z= 0.321 Chirality : 0.044 0.160 1683 Planarity : 0.004 0.058 1836 Dihedral : 5.625 37.803 1462 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.77 (0.22), residues: 1303 helix: -0.21 (0.21), residues: 579 sheet: -0.91 (0.39), residues: 179 loop : -2.31 (0.24), residues: 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 97 average time/residue: 0.2728 time to fit residues: 37.1755 Evaluate side-chains 91 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1075 time to fit residues: 2.7714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.0370 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 0.0770 chunk 112 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 10818 Z= 0.144 Angle : 0.565 12.423 14689 Z= 0.283 Chirality : 0.041 0.143 1683 Planarity : 0.004 0.056 1836 Dihedral : 5.208 34.265 1462 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.35 (0.23), residues: 1303 helix: 0.13 (0.22), residues: 582 sheet: -0.68 (0.39), residues: 179 loop : -2.11 (0.25), residues: 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 103 average time/residue: 0.2707 time to fit residues: 39.3646 Evaluate side-chains 100 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0990 time to fit residues: 2.9053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 0.0170 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 10818 Z= 0.149 Angle : 0.549 12.836 14689 Z= 0.276 Chirality : 0.041 0.134 1683 Planarity : 0.004 0.054 1836 Dihedral : 5.017 31.193 1462 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.13 (0.23), residues: 1303 helix: 0.34 (0.22), residues: 579 sheet: -0.56 (0.40), residues: 179 loop : -2.02 (0.26), residues: 545 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.2561 time to fit residues: 39.8113 Evaluate side-chains 100 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1347 time to fit residues: 3.3287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS A 279 ASN ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 10818 Z= 0.170 Angle : 0.553 12.947 14689 Z= 0.277 Chirality : 0.042 0.146 1683 Planarity : 0.004 0.056 1836 Dihedral : 4.954 30.994 1462 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.03 (0.23), residues: 1303 helix: 0.35 (0.22), residues: 582 sheet: -0.45 (0.40), residues: 179 loop : -1.90 (0.26), residues: 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 107 average time/residue: 0.2634 time to fit residues: 40.4799 Evaluate side-chains 99 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1045 time to fit residues: 2.6698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 10818 Z= 0.272 Angle : 0.602 13.049 14689 Z= 0.301 Chirality : 0.044 0.147 1683 Planarity : 0.004 0.054 1836 Dihedral : 5.144 31.930 1462 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.12 (0.23), residues: 1303 helix: 0.24 (0.22), residues: 577 sheet: -0.47 (0.41), residues: 175 loop : -1.88 (0.26), residues: 551 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 100 average time/residue: 0.2451 time to fit residues: 35.2908 Evaluate side-chains 93 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0982 time to fit residues: 2.2435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 10818 Z= 0.228 Angle : 0.583 13.380 14689 Z= 0.292 Chirality : 0.043 0.135 1683 Planarity : 0.004 0.055 1836 Dihedral : 5.119 34.405 1462 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.08 (0.23), residues: 1303 helix: 0.24 (0.22), residues: 578 sheet: -0.30 (0.42), residues: 168 loop : -1.87 (0.26), residues: 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 93 average time/residue: 0.2836 time to fit residues: 38.2239 Evaluate side-chains 90 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1276 time to fit residues: 2.5404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 10818 Z= 0.179 Angle : 0.563 13.713 14689 Z= 0.282 Chirality : 0.042 0.134 1683 Planarity : 0.004 0.054 1836 Dihedral : 5.013 33.465 1462 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.96 (0.23), residues: 1303 helix: 0.35 (0.22), residues: 582 sheet: -0.22 (0.42), residues: 168 loop : -1.83 (0.26), residues: 553 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 93 average time/residue: 0.2709 time to fit residues: 35.7840 Evaluate side-chains 90 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 HIS ** 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 = 0.3979 r_free = 0.3979 target = 0.183681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.139927 restraints weight = 11127.636| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.42 r_work: 0.2955 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 10818 Z= 0.245 Angle : 0.592 13.572 14689 Z= 0.297 Chirality : 0.043 0.136 1683 Planarity : 0.004 0.054 1836 Dihedral : 5.093 34.956 1462 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.02 (0.23), residues: 1303 helix: 0.24 (0.22), residues: 579 sheet: -0.19 (0.43), residues: 160 loop : -1.79 (0.26), residues: 564 =============================================================================== Job complete usr+sys time: 1997.51 seconds wall clock time: 37 minutes 22.66 seconds (2242.66 seconds total)