Starting phenix.real_space_refine on Wed Feb 14 13:52:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrc_21367/02_2024/6vrc_21367.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrc_21367/02_2024/6vrc_21367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrc_21367/02_2024/6vrc_21367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrc_21367/02_2024/6vrc_21367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrc_21367/02_2024/6vrc_21367.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrc_21367/02_2024/6vrc_21367.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 50 5.49 5 S 28 5.16 5 C 5822 2.51 5 N 1603 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A ARG 438": "NH1" <-> "NH2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "A ARG 763": "NH1" <-> "NH2" Residue "A TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 912": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A ASP 933": "OD1" <-> "OD2" Residue "A PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "A ARG 1114": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9429 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 8359 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 983} Chain breaks: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1070 Classifications: {'RNA': 51} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna2p': 18, 'rna3p': 32} Time building chain proxies: 5.80, per 1000 atoms: 0.62 Number of scatterers: 9429 At special positions: 0 Unit cell: (102.6, 92.88, 122.04, 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 28 16.00 P 50 15.00 O 1926 8.00 N 1603 7.00 C 5822 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: 3.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 3 sheets defined 58.1% alpha, 0.8% beta 4 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 67 through 75 removed outlier: 3.795A pdb=" N MET A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 removed outlier: 3.611A pdb=" N ASN A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.681A pdb=" N LEU A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.946A pdb=" N SER A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 179 through 203 removed outlier: 3.613A pdb=" N ASN A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.573A pdb=" N LYS A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 225 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.719A pdb=" N LYS A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.587A pdb=" N LYS A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 278 " --> pdb=" O HIS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 287 through 303 removed outlier: 3.605A pdb=" N LEU A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 302 " --> pdb=" O HIS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 332 removed outlier: 3.764A pdb=" N LYS A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 348 removed outlier: 3.756A pdb=" N GLU A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 388 removed outlier: 3.582A pdb=" N ILE A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.854A pdb=" N ILE A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 4.085A pdb=" N ARG A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 439 " --> pdb=" O TRP A 435 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.242A pdb=" N ASP A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 removed outlier: 4.047A pdb=" N ILE A 507 " --> pdb=" O PRO A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.733A pdb=" N ASP A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 596 removed outlier: 3.525A pdb=" N SER A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 removed outlier: 4.478A pdb=" N GLN A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 606 " --> pdb=" O PRO A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 623 removed outlier: 3.574A pdb=" N PHE A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 658 removed outlier: 4.187A pdb=" N SER A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 removed outlier: 4.007A pdb=" N LYS A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 690 removed outlier: 3.535A pdb=" N ILE A 675 " --> pdb=" O PHE A 671 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 679 " --> pdb=" O ILE A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 removed outlier: 3.864A pdb=" N CYS A 696 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'A' and resid 733 through 748 removed outlier: 3.727A pdb=" N SER A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 739 " --> pdb=" O GLN A 735 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 763 removed outlier: 3.816A pdb=" N PHE A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 761 " --> pdb=" O SER A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.532A pdb=" N LEU A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN A 772 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 819 through 828 removed outlier: 3.686A pdb=" N LEU A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 826 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 838 Processing helix chain 'A' and resid 847 through 854 removed outlier: 3.935A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 876 removed outlier: 3.857A pdb=" N GLN A 865 " --> pdb=" O GLU A 861 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 874 " --> pdb=" O HIS A 870 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 removed outlier: 3.598A pdb=" N ARG A 881 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 907 removed outlier: 3.697A pdb=" N LYS A 888 " --> pdb=" O ALA A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 944 removed outlier: 3.813A pdb=" N SER A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE A 931 " --> pdb=" O GLY A 927 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A 942 " --> pdb=" O PHE A 938 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1003 Processing helix chain 'A' and resid 1011 through 1021 removed outlier: 3.954A pdb=" N LYS A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A1020 " --> pdb=" O ARG A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1026 removed outlier: 4.006A pdb=" N ASN A1026 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1044 removed outlier: 3.738A pdb=" N ARG A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A1042 " --> pdb=" O ASP A1038 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A1043 " --> pdb=" O ASP A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1052 Processing helix chain 'A' and resid 1055 through 1065 removed outlier: 3.713A pdb=" N LYS A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1060 " --> pdb=" O LYS A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1118 removed outlier: 3.592A pdb=" N CYS A1110 " --> pdb=" O SER A1106 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A1111 " --> pdb=" O ASN A1107 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A1112 " --> pdb=" O GLU A1108 " (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 465 297 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1961 1.33 - 1.45: 2434 1.45 - 1.57: 5169 1.57 - 1.69: 100 1.69 - 1.81: 48 Bond restraints: 9712 Sorted by residual: bond pdb=" N ILE A 112 " pdb=" CA ILE A 112 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.11e-02 8.12e+03 1.27e+01 bond pdb=" N ILE A 515 " pdb=" CA ILE A 515 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" N ILE A 263 " pdb=" CA ILE A 263 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.48e+00 bond pdb=" N ILE A 320 " pdb=" CA ILE A 320 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.22e-02 6.72e+03 9.40e+00 bond pdb=" N LEU A 601 " pdb=" CA LEU A 601 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.04e-02 9.25e+03 9.26e+00 ... (remaining 9707 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.69: 345 105.69 - 112.82: 4950 112.82 - 119.94: 3975 119.94 - 127.07: 3849 127.07 - 134.19: 176 Bond angle restraints: 13295 Sorted by residual: angle pdb=" C3' A B 34 " pdb=" C2' A B 34 " pdb=" O2' A B 34 " ideal model delta sigma weight residual 114.60 124.79 -10.19 1.50e+00 4.44e-01 4.62e+01 angle pdb=" N GLU A 287 " pdb=" CA GLU A 287 " pdb=" C GLU A 287 " ideal model delta sigma weight residual 113.88 105.87 8.01 1.23e+00 6.61e-01 4.24e+01 angle pdb=" O3' A B 34 " pdb=" C3' A B 34 " pdb=" C2' A B 34 " ideal model delta sigma weight residual 109.50 118.71 -9.21 1.50e+00 4.44e-01 3.77e+01 angle pdb=" C CYS A 89 " pdb=" N ARG A 90 " pdb=" CA ARG A 90 " ideal model delta sigma weight residual 120.09 127.70 -7.61 1.25e+00 6.40e-01 3.70e+01 angle pdb=" N SER A 247 " pdb=" CA SER A 247 " pdb=" C SER A 247 " ideal model delta sigma weight residual 113.41 106.22 7.19 1.22e+00 6.72e-01 3.48e+01 ... (remaining 13290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 5769 35.61 - 71.22: 199 71.22 - 106.82: 20 106.82 - 142.43: 2 142.43 - 178.04: 4 Dihedral angle restraints: 5994 sinusoidal: 2982 harmonic: 3012 Sorted by residual: 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 49.68 -177.68 1 1.70e+01 3.46e-03 6.64e+01 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 -128.00 46.87 -174.87 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U B 33 " pdb=" C1' U B 33 " pdb=" N1 U B 33 " pdb=" C2 U B 33 " ideal model delta sinusoidal sigma weight residual -160.00 -44.75 -115.25 1 1.50e+01 4.44e-03 6.09e+01 ... (remaining 5991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1310 0.112 - 0.224: 174 0.224 - 0.335: 10 0.335 - 0.447: 3 0.447 - 0.559: 3 Chirality restraints: 1500 Sorted by residual: chirality pdb=" C3' G B 1 " pdb=" C4' G B 1 " pdb=" O3' G B 1 " pdb=" C2' G B 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.19 -0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" C3' A B 34 " pdb=" C4' A B 34 " pdb=" O3' A B 34 " pdb=" C2' A B 34 " both_signs ideal model delta sigma weight residual False -2.74 -2.20 -0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" C2' A B 34 " pdb=" C3' A B 34 " pdb=" O2' A B 34 " pdb=" C1' A B 34 " both_signs ideal model delta sigma weight residual False -2.52 -2.04 -0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 1497 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 103 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C LEU A 103 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU A 103 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 104 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 822 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE A 822 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE A 822 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP A 823 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 607 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C ASN A 607 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN A 607 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 608 " 0.018 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 605 2.72 - 3.26: 8559 3.26 - 3.81: 14041 3.81 - 4.35: 18699 4.35 - 4.90: 30108 Nonbonded interactions: 72012 Sorted by model distance: nonbonded pdb=" O2' C B 7 " pdb=" O5' U B 8 " model vdw 2.170 2.440 nonbonded pdb=" OE2 GLU A 498 " pdb=" ND2 ASN A 772 " model vdw 2.209 2.520 nonbonded pdb=" OE2 GLU A 139 " pdb=" NZ LYS A 195 " model vdw 2.247 2.520 nonbonded pdb=" O ASN A 309 " pdb=" O6 G B 1 " model vdw 2.265 3.040 nonbonded pdb=" O GLN A 523 " pdb=" OH TYR A 694 " model vdw 2.274 2.440 ... (remaining 72007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.030 Extract box with map and model: 2.170 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.510 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.010 0.097 9712 Z= 0.622 Angle : 1.272 10.365 13295 Z= 0.794 Chirality : 0.079 0.559 1500 Planarity : 0.007 0.065 1503 Dihedral : 17.403 178.042 4028 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.70 % Allowed : 8.99 % Favored : 87.30 % Cbeta Deviations : 0.20 % 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: -4.83 (0.21), residues: 997 helix: -3.25 (0.17), residues: 550 sheet: -3.36 (0.60), residues: 38 loop : -2.92 (0.25), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 417 HIS 0.013 0.002 HIS A1093 PHE 0.034 0.003 PHE A1071 TYR 0.025 0.003 TYR A 486 ARG 0.024 0.002 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 245 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 128 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.7242 (m-70) REVERT: A 218 ASP cc_start: 0.7939 (t70) cc_final: 0.7592 (t0) REVERT: A 250 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7939 (mtmm) REVERT: A 338 ARG cc_start: 0.8151 (tpt-90) cc_final: 0.7937 (mtp85) REVERT: A 586 GLN cc_start: 0.7422 (tt0) cc_final: 0.7202 (mt0) outliers start: 35 outliers final: 9 residues processed: 266 average time/residue: 0.2523 time to fit residues: 88.8638 Evaluate side-chains 133 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 938 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN A 121 ASN A 124 ASN A 165 GLN A 259 ASN A 285 ASN A 289 ASN A 292 ASN A 328 ASN A 333 ASN A 360 GLN A 508 ASN A 532 ASN A 576 ASN A 598 GLN A 607 ASN A 654 GLN A 659 GLN A 772 ASN A 894 ASN A 915 HIS A1023 ASN A1052 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9712 Z= 0.173 Angle : 0.658 10.663 13295 Z= 0.347 Chirality : 0.041 0.259 1500 Planarity : 0.005 0.056 1503 Dihedral : 17.562 175.430 1853 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.70 % Allowed : 13.33 % Favored : 82.96 % 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: -3.31 (0.23), residues: 997 helix: -1.77 (0.20), residues: 563 sheet: -3.50 (0.62), residues: 19 loop : -2.63 (0.26), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 185 HIS 0.003 0.001 HIS A 913 PHE 0.026 0.002 PHE A 459 TYR 0.016 0.001 TYR A 889 ARG 0.004 0.001 ARG A 763 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7424 (m-70) REVERT: A 218 ASP cc_start: 0.7804 (t70) cc_final: 0.7595 (t0) REVERT: A 820 ARG cc_start: 0.7591 (ttp-110) cc_final: 0.7340 (ttp80) REVERT: A 1086 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8575 (tt) outliers start: 35 outliers final: 10 residues processed: 174 average time/residue: 0.2910 time to fit residues: 65.6927 Evaluate side-chains 113 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 850 ASP Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 165 GLN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN A 461 ASN A 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9712 Z= 0.208 Angle : 0.595 8.315 13295 Z= 0.312 Chirality : 0.040 0.184 1500 Planarity : 0.004 0.048 1503 Dihedral : 16.729 179.800 1830 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.60 % Allowed : 15.13 % Favored : 81.27 % 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: -2.44 (0.25), residues: 997 helix: -0.95 (0.22), residues: 569 sheet: -2.84 (0.78), residues: 31 loop : -2.43 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 185 HIS 0.004 0.001 HIS A 913 PHE 0.026 0.002 PHE A 459 TYR 0.013 0.001 TYR A 889 ARG 0.006 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.7885 (t70) cc_final: 0.7622 (t0) REVERT: A 820 ARG cc_start: 0.7559 (ttp-110) cc_final: 0.7343 (ttp80) REVERT: A 1086 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8682 (tt) outliers start: 34 outliers final: 19 residues processed: 144 average time/residue: 0.2810 time to fit residues: 53.5093 Evaluate side-chains 124 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 124 ASN A 165 GLN A 184 ASN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9712 Z= 0.193 Angle : 0.561 7.604 13295 Z= 0.294 Chirality : 0.039 0.167 1500 Planarity : 0.003 0.047 1503 Dihedral : 16.476 178.352 1828 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.23 % Allowed : 15.24 % Favored : 80.53 % 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: -1.88 (0.25), residues: 997 helix: -0.43 (0.22), residues: 577 sheet: -2.71 (0.77), residues: 31 loop : -2.31 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 417 HIS 0.004 0.001 HIS A 913 PHE 0.028 0.001 PHE A 459 TYR 0.011 0.001 TYR A 889 ARG 0.005 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 118 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.7832 (t70) cc_final: 0.7599 (t0) REVERT: A 415 ARG cc_start: 0.7971 (ttp-110) cc_final: 0.7541 (mtt90) REVERT: A 876 LYS cc_start: 0.7662 (mmtm) cc_final: 0.7409 (tptm) REVERT: A 920 ASP cc_start: 0.8150 (m-30) cc_final: 0.7736 (m-30) REVERT: A 1086 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8743 (tt) outliers start: 40 outliers final: 20 residues processed: 147 average time/residue: 0.2484 time to fit residues: 49.5846 Evaluate side-chains 128 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1046 TYR Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 165 GLN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9712 Z= 0.162 Angle : 0.527 6.644 13295 Z= 0.276 Chirality : 0.038 0.154 1500 Planarity : 0.003 0.045 1503 Dihedral : 16.275 178.142 1826 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.70 % Allowed : 16.51 % Favored : 79.79 % 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: -1.44 (0.26), residues: 997 helix: 0.01 (0.22), residues: 580 sheet: -2.60 (0.79), residues: 29 loop : -2.29 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 456 HIS 0.003 0.001 HIS A 915 PHE 0.013 0.001 PHE A 459 TYR 0.010 0.001 TYR A 889 ARG 0.004 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.7826 (t70) cc_final: 0.7585 (t0) REVERT: A 342 GLU cc_start: 0.8011 (pp20) cc_final: 0.7803 (pp20) REVERT: A 415 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7514 (mtt90) REVERT: A 507 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8794 (mt) REVERT: A 727 MET cc_start: 0.8150 (ttp) cc_final: 0.7843 (ttp) REVERT: A 768 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8984 (tp) REVERT: A 820 ARG cc_start: 0.7561 (ttp-110) cc_final: 0.7264 (ttp80) REVERT: A 920 ASP cc_start: 0.8105 (m-30) cc_final: 0.7712 (m-30) REVERT: A 1086 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8730 (tt) outliers start: 35 outliers final: 21 residues processed: 145 average time/residue: 0.2601 time to fit residues: 50.6978 Evaluate side-chains 127 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9712 Z= 0.158 Angle : 0.519 6.643 13295 Z= 0.271 Chirality : 0.038 0.143 1500 Planarity : 0.003 0.047 1503 Dihedral : 16.153 178.072 1826 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.49 % Allowed : 17.67 % Favored : 78.84 % 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: -1.12 (0.26), residues: 997 helix: 0.30 (0.23), residues: 582 sheet: -2.80 (0.79), residues: 19 loop : -2.23 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 456 HIS 0.003 0.001 HIS A 915 PHE 0.011 0.001 PHE A 548 TYR 0.009 0.001 TYR A 889 ARG 0.003 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.7826 (t70) cc_final: 0.7581 (t0) REVERT: A 415 ARG cc_start: 0.7983 (ttp-110) cc_final: 0.7558 (mtt90) REVERT: A 507 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8791 (mt) REVERT: A 727 MET cc_start: 0.8153 (ttp) cc_final: 0.7826 (ttp) REVERT: A 768 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8987 (tp) REVERT: A 820 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.7316 (ttp80) REVERT: A 920 ASP cc_start: 0.8082 (m-30) cc_final: 0.7671 (m-30) REVERT: A 1086 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8715 (tt) outliers start: 33 outliers final: 22 residues processed: 137 average time/residue: 0.2548 time to fit residues: 47.3141 Evaluate side-chains 131 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.0170 chunk 11 optimal weight: 0.0470 chunk 57 optimal weight: 0.2980 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 124 ASN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9712 Z= 0.117 Angle : 0.486 6.588 13295 Z= 0.254 Chirality : 0.036 0.136 1500 Planarity : 0.003 0.050 1503 Dihedral : 16.000 178.013 1826 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.65 % Allowed : 18.41 % Favored : 78.94 % 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: -0.70 (0.27), residues: 997 helix: 0.72 (0.23), residues: 576 sheet: -2.41 (0.87), residues: 19 loop : -2.17 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 780 HIS 0.002 0.000 HIS A 913 PHE 0.040 0.001 PHE A 459 TYR 0.009 0.001 TYR A1109 ARG 0.003 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7214 (mmm) cc_final: 0.6992 (mmm) REVERT: A 218 ASP cc_start: 0.7803 (t70) cc_final: 0.7550 (t0) REVERT: A 415 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7541 (mtt90) REVERT: A 483 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6514 (mm-30) REVERT: A 507 ILE cc_start: 0.9113 (tp) cc_final: 0.8784 (mt) REVERT: A 727 MET cc_start: 0.8118 (ttp) cc_final: 0.7791 (ttp) REVERT: A 768 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8968 (tp) REVERT: A 820 ARG cc_start: 0.7526 (ttp-110) cc_final: 0.7283 (ttp80) REVERT: A 920 ASP cc_start: 0.7969 (m-30) cc_final: 0.7520 (m-30) REVERT: A 1086 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8625 (tt) outliers start: 25 outliers final: 12 residues processed: 140 average time/residue: 0.2663 time to fit residues: 50.0943 Evaluate side-chains 123 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 79 optimal weight: 0.0030 chunk 92 optimal weight: 0.0980 chunk 96 optimal weight: 0.9980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN A 581 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9712 Z= 0.120 Angle : 0.492 7.529 13295 Z= 0.254 Chirality : 0.037 0.134 1500 Planarity : 0.003 0.051 1503 Dihedral : 15.932 177.847 1826 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.90 % Allowed : 19.26 % Favored : 78.84 % 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: -0.56 (0.27), residues: 997 helix: 0.81 (0.23), residues: 582 sheet: -2.24 (0.91), residues: 19 loop : -2.13 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 780 HIS 0.003 0.001 HIS A 128 PHE 0.038 0.001 PHE A 459 TYR 0.008 0.001 TYR A1075 ARG 0.002 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.7807 (t70) cc_final: 0.7543 (t0) REVERT: A 415 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7550 (mtt90) REVERT: A 483 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6524 (mm-30) REVERT: A 507 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8763 (mt) REVERT: A 768 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8992 (tp) REVERT: A 820 ARG cc_start: 0.7605 (ttp-110) cc_final: 0.7344 (ttp80) REVERT: A 920 ASP cc_start: 0.7982 (m-30) cc_final: 0.7537 (m-30) REVERT: A 1086 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8601 (tt) outliers start: 18 outliers final: 10 residues processed: 124 average time/residue: 0.2675 time to fit residues: 44.4632 Evaluate side-chains 121 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9712 Z= 0.236 Angle : 0.570 7.654 13295 Z= 0.296 Chirality : 0.041 0.131 1500 Planarity : 0.004 0.050 1503 Dihedral : 16.022 178.066 1826 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.22 % Allowed : 19.15 % Favored : 78.62 % 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: -0.68 (0.27), residues: 997 helix: 0.66 (0.23), residues: 589 sheet: -1.21 (0.82), residues: 29 loop : -2.21 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 780 HIS 0.005 0.001 HIS A 101 PHE 0.041 0.002 PHE A 459 TYR 0.014 0.002 TYR A1046 ARG 0.006 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 218 ASP cc_start: 0.7832 (t70) cc_final: 0.7575 (t0) REVERT: A 507 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8810 (mt) REVERT: A 768 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9023 (tp) REVERT: A 820 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7412 (ttp80) REVERT: A 920 ASP cc_start: 0.8162 (m-30) cc_final: 0.7924 (m-30) outliers start: 21 outliers final: 12 residues processed: 116 average time/residue: 0.2694 time to fit residues: 42.1923 Evaluate side-chains 112 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 998 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9712 Z= 0.275 Angle : 0.592 7.964 13295 Z= 0.307 Chirality : 0.042 0.149 1500 Planarity : 0.004 0.047 1503 Dihedral : 16.122 177.959 1826 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.01 % Allowed : 19.37 % Favored : 78.62 % 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: -0.92 (0.27), residues: 997 helix: 0.48 (0.22), residues: 588 sheet: -2.14 (0.65), residues: 49 loop : -2.22 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 780 HIS 0.004 0.001 HIS A 670 PHE 0.041 0.002 PHE A 459 TYR 0.017 0.002 TYR A1046 ARG 0.008 0.001 ARG A 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 218 ASP cc_start: 0.7826 (t70) cc_final: 0.7546 (t0) REVERT: A 507 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8830 (mt) REVERT: A 753 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7446 (p) REVERT: A 768 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9002 (tp) REVERT: A 820 ARG cc_start: 0.7702 (ttp-110) cc_final: 0.7400 (ttp80) outliers start: 19 outliers final: 13 residues processed: 120 average time/residue: 0.2679 time to fit residues: 43.0757 Evaluate side-chains 117 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 780 TRP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 818 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 8.9990 chunk 25 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113335 restraints weight = 13191.722| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.84 r_work: 0.2987 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9712 Z= 0.232 Angle : 0.574 8.472 13295 Z= 0.297 Chirality : 0.040 0.146 1500 Planarity : 0.004 0.047 1503 Dihedral : 15.975 178.104 1826 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.01 % Allowed : 19.47 % Favored : 78.52 % 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: -0.84 (0.27), residues: 997 helix: 0.54 (0.23), residues: 589 sheet: -1.24 (0.83), residues: 29 loop : -2.32 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 780 HIS 0.003 0.001 HIS A 915 PHE 0.041 0.001 PHE A 459 TYR 0.022 0.001 TYR A1046 ARG 0.006 0.000 ARG A 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.00 seconds wall clock time: 38 minutes 49.23 seconds (2329.23 seconds total)