Starting phenix.real_space_refine (version: dev) on Mon Feb 20 07:02:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrb_21366/02_2023/6vrb_21366.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrb_21366/02_2023/6vrb_21366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrb_21366/02_2023/6vrb_21366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrb_21366/02_2023/6vrb_21366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrb_21366/02_2023/6vrb_21366.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrb_21366/02_2023/6vrb_21366.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A ARG 438": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "A ARG 763": "NH1" <-> "NH2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A ARG 912": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "A ARG 1016": "NH1" <-> "NH2" Residue "A ARG 1114": "NH1" <-> "NH2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11581 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1093 Classifications: {'RNA': 52} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna2p': 21, 'rna3p': 30} Chain: "A" Number of atoms: 8574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8574 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 23, 'TRANS': 1007} Chain breaks: 2 Chain: "C" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1914 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Time building chain proxies: 7.17, per 1000 atoms: 0.62 Number of scatterers: 11581 At special positions: 0 Unit cell: (119.88, 93.96, 106.92, 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 37 16.00 P 51 15.00 O 2335 8.00 N 1948 7.00 C 7210 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: 4.77 Conformation dependent library (CDL) restraints added in 1.7 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 6 sheets defined 59.5% alpha, 2.2% beta 5 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 69 through 75 Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.604A pdb=" N LYS A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.705A pdb=" N VAL A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.688A pdb=" N VAL A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.901A pdb=" N PHE A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 165 Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.711A pdb=" N ASP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 203 removed outlier: 3.719A pdb=" N TRP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.569A pdb=" N ILE A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.659A pdb=" N GLU A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 262 through 278 removed outlier: 3.550A pdb=" N LEU A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 287 through 303 removed outlier: 3.563A pdb=" N LEU A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 302 " --> pdb=" O HIS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.667A pdb=" N ASN A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 333 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYS A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 355 through 388 removed outlier: 3.693A pdb=" N ILE A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.790A pdb=" N LYS A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.784A pdb=" N ILE A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 450 removed outlier: 3.587A pdb=" N ARG A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Proline residue: A 443 - end of helix removed outlier: 3.827A pdb=" N GLU A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 501 through 513 removed outlier: 3.646A pdb=" N ILE A 507 " --> pdb=" O PRO A 503 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.564A pdb=" N LEU A 524 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN A 525 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN A 526 " --> pdb=" O GLN A 523 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 528 " --> pdb=" O ASN A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 583 through 599 removed outlier: 3.589A pdb=" N SER A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 removed outlier: 3.907A pdb=" N GLN A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 623 removed outlier: 3.593A pdb=" N PHE A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 658 removed outlier: 3.673A pdb=" N TYR A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 removed outlier: 3.814A pdb=" N LYS A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 690 removed outlier: 3.726A pdb=" N LYS A 673 " --> pdb=" O ASN A 669 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 729 removed outlier: 3.588A pdb=" N MET A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 748 removed outlier: 3.517A pdb=" N LYS A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 771 removed outlier: 3.825A pdb=" N GLU A 764 " --> pdb=" O THR A 760 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 783 removed outlier: 3.845A pdb=" N GLU A 782 " --> pdb=" O ASP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 795 removed outlier: 3.549A pdb=" N TRP A 790 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 804 removed outlier: 4.115A pdb=" N LEU A 803 " --> pdb=" O GLU A 800 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN A 804 " --> pdb=" O GLU A 801 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 800 through 804' Processing helix chain 'A' and resid 823 through 828 removed outlier: 3.789A pdb=" N TYR A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 839 removed outlier: 3.523A pdb=" N GLU A 835 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 836 " --> pdb=" O THR A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.996A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 876 removed outlier: 3.710A pdb=" N ILE A 874 " --> pdb=" O HIS A 870 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 882 through 907 Processing helix chain 'A' and resid 909 through 946 removed outlier: 3.618A pdb=" N ARG A 924 " --> pdb=" O ASP A 920 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 931 " --> pdb=" O GLY A 927 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR A 942 " --> pdb=" O PHE A 938 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 946 " --> pdb=" O TYR A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.639A pdb=" N ARG A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 3.651A pdb=" N LYS A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A1020 " --> pdb=" O ARG A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1044 removed outlier: 3.609A pdb=" N ARG A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A1042 " --> pdb=" O ASP A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1053 removed outlier: 3.719A pdb=" N ALA A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1065 removed outlier: 3.740A pdb=" N LYS A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1118 removed outlier: 3.718A pdb=" N CYS A1110 " --> pdb=" O SER A1106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A1111 " --> pdb=" O ASN A1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 34 removed outlier: 3.571A pdb=" N PHE C 30 " --> pdb=" O GLY C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 54 removed outlier: 4.029A pdb=" N LYS C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU C 52 " --> pdb=" O ASN C 48 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP C 54 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.536A pdb=" N CYS C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 161 removed outlier: 3.826A pdb=" N LYS C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 176 removed outlier: 3.556A pdb=" N THR C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 200 removed outlier: 3.605A pdb=" N SER C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 removed outlier: 4.415A pdb=" N ILE C 204 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 229 removed outlier: 3.654A pdb=" N GLN C 225 " --> pdb=" O GLN C 221 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA4, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 124 through 126 removed outlier: 3.800A pdb=" N THR C 125 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 141 " --> pdb=" O THR C 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 432 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1871 1.32 - 1.44: 3397 1.44 - 1.56: 6486 1.56 - 1.69: 102 1.69 - 1.81: 61 Bond restraints: 11917 Sorted by residual: bond pdb=" N VAL A 859 " pdb=" CA VAL A 859 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.36e+01 bond pdb=" N ILE A 448 " pdb=" CA ILE A 448 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 1.01e+01 bond pdb=" N ILE A 320 " pdb=" CA ILE A 320 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.79e+00 bond pdb=" N ILE A 170 " pdb=" CA ILE A 170 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.56e+00 bond pdb=" N GLU C 133 " pdb=" CA GLU C 133 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.51e+00 ... (remaining 11912 not shown) Histogram of bond angle deviations from ideal: 97.57 - 104.91: 323 104.91 - 112.25: 5613 112.25 - 119.59: 4961 119.59 - 126.93: 5158 126.93 - 134.27: 217 Bond angle restraints: 16272 Sorted by residual: angle pdb=" N GLU A 431 " pdb=" CA GLU A 431 " pdb=" C GLU A 431 " ideal model delta sigma weight residual 114.62 105.17 9.45 1.14e+00 7.69e-01 6.87e+01 angle pdb=" N VAL A 595 " pdb=" CA VAL A 595 " pdb=" C VAL A 595 " ideal model delta sigma weight residual 110.72 104.95 5.77 1.01e+00 9.80e-01 3.27e+01 angle pdb=" N LYS C 65 " pdb=" CA LYS C 65 " pdb=" C LYS C 65 " ideal model delta sigma weight residual 111.02 117.58 -6.56 1.22e+00 6.72e-01 2.89e+01 angle pdb=" C ARG A 316 " pdb=" N ASN A 317 " pdb=" CA ASN A 317 " ideal model delta sigma weight residual 120.28 127.07 -6.79 1.34e+00 5.57e-01 2.57e+01 angle pdb=" C THR A 308 " pdb=" N ASN A 309 " pdb=" CA ASN A 309 " ideal model delta sigma weight residual 121.19 128.99 -7.80 1.59e+00 3.96e-01 2.41e+01 ... (remaining 16267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 7024 35.54 - 71.09: 155 71.09 - 106.63: 7 106.63 - 142.17: 0 142.17 - 177.71: 4 Dihedral angle restraints: 7190 sinusoidal: 3415 harmonic: 3775 Sorted by residual: dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 232.00 54.29 177.71 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 37 " pdb=" C1' U B 37 " pdb=" N1 U B 37 " pdb=" C2 U B 37 " ideal model delta sinusoidal sigma weight residual -128.00 49.39 -177.39 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 51 " pdb=" C1' U B 51 " pdb=" N1 U B 51 " pdb=" C2 U B 51 " ideal model delta sinusoidal sigma weight residual 232.00 58.11 173.89 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 7187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1486 0.095 - 0.191: 289 0.191 - 0.286: 43 0.286 - 0.381: 1 0.381 - 0.477: 1 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CA LYS C 11 " pdb=" N LYS C 11 " pdb=" C LYS C 11 " pdb=" CB LYS C 11 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA ASN A 532 " pdb=" N ASN A 532 " pdb=" C ASN A 532 " pdb=" CB ASN A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL A 527 " pdb=" CA VAL A 527 " pdb=" CG1 VAL A 527 " pdb=" CG2 VAL A 527 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1817 not shown) Planarity restraints: 1873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 5 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ILE C 5 " 0.063 2.00e-02 2.50e+03 pdb=" O ILE C 5 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 6 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 508 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASN A 508 " 0.061 2.00e-02 2.50e+03 pdb=" O ASN A 508 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS A 509 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 594 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C MET A 594 " -0.052 2.00e-02 2.50e+03 pdb=" O MET A 594 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A 595 " 0.018 2.00e-02 2.50e+03 ... (remaining 1870 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 60 2.48 - 3.09: 7248 3.09 - 3.69: 17273 3.69 - 4.30: 26170 4.30 - 4.90: 41661 Nonbonded interactions: 92412 Sorted by model distance: nonbonded pdb=" O ARG A 212 " pdb=" OG SER A 213 " model vdw 1.877 2.440 nonbonded pdb=" OH TYR C 197 " pdb=" OH TYR C 213 " model vdw 2.166 2.440 nonbonded pdb=" O TYR C 197 " pdb=" O SER C 200 " model vdw 2.178 3.040 nonbonded pdb=" O6 G B 1 " pdb=" O ASN A 309 " model vdw 2.216 3.040 nonbonded pdb=" O2' G B 15 " pdb=" NH1 ARG A 129 " model vdw 2.231 2.520 ... (remaining 92407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 51 5.49 5 S 37 5.16 5 C 7210 2.51 5 N 1948 2.21 5 O 2335 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 2.750 Check model and map are aligned: 0.170 Process input model: 35.380 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.009 0.089 11917 Z= 0.574 Angle : 1.205 10.467 16272 Z= 0.768 Chirality : 0.076 0.477 1820 Planarity : 0.006 0.067 1873 Dihedral : 14.698 177.714 4730 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % 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: -4.13 (0.21), residues: 1252 helix: -2.70 (0.17), residues: 725 sheet: -3.03 (0.56), residues: 75 loop : -2.40 (0.26), residues: 452 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 274 time to evaluate : 1.376 Fit side-chains outliers start: 37 outliers final: 3 residues processed: 298 average time/residue: 1.3159 time to fit residues: 421.8103 Evaluate side-chains 133 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.3183 time to fit residues: 2.3406 ------------------------------------------------------------------------------- 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: 4.9990 chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 121 ASN A 127 ASN A 153 ASN A 165 GLN A 285 ASN A 289 ASN A 329 HIS A 333 ASN A 410 HIS A 416 GLN A 532 ASN A 576 ASN A 598 GLN A 654 GLN A 714 HIS A 751 GLN A 866 GLN A 915 HIS ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN A1111 GLN C 129 HIS C 180 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 11917 Z= 0.197 Angle : 0.643 9.708 16272 Z= 0.349 Chirality : 0.041 0.196 1820 Planarity : 0.005 0.058 1873 Dihedral : 13.045 177.464 1977 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 5.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.22), residues: 1252 helix: -1.26 (0.18), residues: 732 sheet: -2.59 (0.63), residues: 73 loop : -2.05 (0.26), residues: 447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 180 time to evaluate : 1.435 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 16 residues processed: 223 average time/residue: 1.3362 time to fit residues: 321.4099 Evaluate side-chains 147 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.384 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 6 average time/residue: 0.3861 time to fit residues: 4.8066 ------------------------------------------------------------------------------- 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: 0.9990 chunk 36 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 165 GLN A 333 ASN A 357 ASN A 462 ASN A 714 HIS A 751 GLN C 142 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 11917 Z= 0.160 Angle : 0.547 10.081 16272 Z= 0.296 Chirality : 0.039 0.204 1820 Planarity : 0.004 0.057 1873 Dihedral : 12.797 177.333 1977 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 6.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.23), residues: 1252 helix: -0.26 (0.19), residues: 738 sheet: -2.43 (0.65), residues: 70 loop : -1.87 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 164 time to evaluate : 1.697 Fit side-chains outliers start: 72 outliers final: 22 residues processed: 214 average time/residue: 1.4362 time to fit residues: 330.8611 Evaluate side-chains 137 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 3 average time/residue: 0.7203 time to fit residues: 4.4456 ------------------------------------------------------------------------------- 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: 0.6980 chunk 88 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 410 HIS A 462 ASN A 735 GLN A 751 GLN A 772 ASN A 793 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 11917 Z= 0.200 Angle : 0.587 11.144 16272 Z= 0.315 Chirality : 0.041 0.203 1820 Planarity : 0.004 0.055 1873 Dihedral : 12.762 178.383 1977 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 6.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.24), residues: 1252 helix: 0.26 (0.20), residues: 739 sheet: -2.06 (0.67), residues: 68 loop : -1.79 (0.27), residues: 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 142 time to evaluate : 1.438 Fit side-chains revert: symmetry clash outliers start: 73 outliers final: 28 residues processed: 199 average time/residue: 1.2969 time to fit residues: 279.8771 Evaluate side-chains 146 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 23 residues processed: 5 average time/residue: 0.9032 time to fit residues: 6.8833 ------------------------------------------------------------------------------- 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: 4.9990 chunk 71 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 360 GLN A 385 ASN A 410 HIS A 462 ASN A 751 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 11917 Z= 0.294 Angle : 0.637 11.866 16272 Z= 0.340 Chirality : 0.043 0.188 1820 Planarity : 0.004 0.056 1873 Dihedral : 12.792 179.341 1977 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 6.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.24), residues: 1252 helix: 0.37 (0.19), residues: 746 sheet: -2.11 (0.65), residues: 73 loop : -1.90 (0.27), residues: 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 131 time to evaluate : 1.399 Fit side-chains revert: symmetry clash outliers start: 73 outliers final: 32 residues processed: 183 average time/residue: 1.3759 time to fit residues: 273.8323 Evaluate side-chains 148 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 22 residues processed: 10 average time/residue: 0.5736 time to fit residues: 8.7971 ------------------------------------------------------------------------------- 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: 4.9990 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 410 HIS A 462 ASN A 751 GLN A1017 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11917 Z= 0.228 Angle : 0.585 11.354 16272 Z= 0.313 Chirality : 0.041 0.192 1820 Planarity : 0.004 0.054 1873 Dihedral : 12.730 178.732 1977 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 5.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.24), residues: 1252 helix: 0.59 (0.20), residues: 746 sheet: -2.00 (0.65), residues: 73 loop : -1.84 (0.27), residues: 433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 128 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 39 residues processed: 175 average time/residue: 1.2977 time to fit residues: 246.6967 Evaluate side-chains 150 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 111 time to evaluate : 1.367 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 33 residues processed: 6 average time/residue: 0.5692 time to fit residues: 5.8730 ------------------------------------------------------------------------------- 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: 10.0000 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 70 optimal weight: 0.0670 chunk 125 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 77 optimal weight: 0.4980 overall best weight: 0.7132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 462 ASN A 751 GLN A 819 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 11917 Z= 0.147 Angle : 0.518 10.234 16272 Z= 0.280 Chirality : 0.039 0.190 1820 Planarity : 0.003 0.054 1873 Dihedral : 12.644 178.306 1977 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 4.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.24), residues: 1252 helix: 0.92 (0.20), residues: 742 sheet: -1.77 (0.67), residues: 66 loop : -1.82 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 128 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 33 residues processed: 170 average time/residue: 1.3207 time to fit residues: 243.8954 Evaluate side-chains 147 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 28 residues processed: 5 average time/residue: 0.4227 time to fit residues: 4.5047 ------------------------------------------------------------------------------- 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: 6.9990 chunk 74 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 113 optimal weight: 0.0870 chunk 120 optimal weight: 0.0970 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN A 633 GLN A 751 GLN A1023 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 11917 Z= 0.134 Angle : 0.502 10.551 16272 Z= 0.268 Chirality : 0.038 0.195 1820 Planarity : 0.003 0.054 1873 Dihedral : 12.571 179.867 1977 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 3.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.25), residues: 1252 helix: 1.24 (0.21), residues: 728 sheet: -1.74 (0.66), residues: 66 loop : -1.66 (0.27), residues: 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 129 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 31 residues processed: 161 average time/residue: 1.3225 time to fit residues: 231.0510 Evaluate side-chains 146 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.375 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 3 average time/residue: 0.7912 time to fit residues: 4.5750 ------------------------------------------------------------------------------- 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: 1.9990 chunk 120 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.0370 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 462 ASN A 586 GLN A 751 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 11917 Z= 0.133 Angle : 0.502 9.469 16272 Z= 0.267 Chirality : 0.038 0.199 1820 Planarity : 0.003 0.054 1873 Dihedral : 12.551 179.641 1977 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.25), residues: 1252 helix: 1.34 (0.21), residues: 734 sheet: -1.66 (0.66), residues: 66 loop : -1.65 (0.27), residues: 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 128 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 31 residues processed: 159 average time/residue: 1.3472 time to fit residues: 232.6265 Evaluate side-chains 149 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 3 average time/residue: 0.5265 time to fit residues: 3.8318 ------------------------------------------------------------------------------- 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: 0.8980 chunk 58 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN A 586 GLN A 751 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 11917 Z= 0.147 Angle : 0.511 9.431 16272 Z= 0.271 Chirality : 0.038 0.196 1820 Planarity : 0.003 0.054 1873 Dihedral : 12.543 179.284 1977 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.25), residues: 1252 helix: 1.37 (0.21), residues: 735 sheet: -1.54 (0.72), residues: 56 loop : -1.69 (0.27), residues: 461 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 30 residues processed: 152 average time/residue: 1.3658 time to fit residues: 225.7792 Evaluate side-chains 147 residues out of total 1184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.458 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 0.1585 time to fit residues: 2.4184 ------------------------------------------------------------------------------- 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: 2.9990 chunk 95 optimal weight: 0.0020 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 0.0170 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 5 optimal weight: 0.0030 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN A 586 GLN A 751 GLN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.161483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133599 restraints weight = 13467.601| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.36 r_work: 0.2966 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 11917 Z= 0.122 Angle : 0.477 8.970 16272 Z= 0.253 Chirality : 0.037 0.200 1820 Planarity : 0.003 0.054 1873 Dihedral : 12.472 178.774 1977 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.25), residues: 1252 helix: 1.59 (0.21), residues: 725 sheet: -1.55 (0.72), residues: 56 loop : -1.62 (0.27), residues: 471 =============================================================================== Job complete usr+sys time: 4493.28 seconds wall clock time: 81 minutes 8.98 seconds (4868.98 seconds total)