Starting phenix.real_space_refine (version: dev) on Sun May 15 05:43:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp7_11337/05_2022/6zp7_11337_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp7_11337/05_2022/6zp7_11337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp7_11337/05_2022/6zp7_11337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp7_11337/05_2022/6zp7_11337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp7_11337/05_2022/6zp7_11337_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zp7_11337/05_2022/6zp7_11337_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 23615 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7709 Classifications: {'peptide': 988} Link IDs: {'PTRANS': 48, 'TRANS': 939} Chain breaks: 8 Chain: "B" Number of atoms: 7367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7367 Classifications: {'peptide': 943} Link IDs: {'PTRANS': 45, 'TRANS': 897} Chain breaks: 12 Chain: "C" Number of atoms: 7243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7243 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 44, 'TRANS': 885} Chain breaks: 10 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {'BMA': 1, 'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 114 Unusual residues: {'DMS': 3, 'NAG': 6, 'MAN': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'NAG': 4, 'MAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 13.76, per 1000 atoms: 0.58 Number of scatterers: 23615 At special positions: 0 Unit cell: (128.781, 131.922, 196.836, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 4807 8.00 N 3780 7.00 C 14927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 274 " distance=2.05 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 334 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 405 " distance=2.04 Simple disulfide: pdb=" SG CYS A 453 " - pdb=" SG CYS A 461 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 563 " distance=2.01 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 622 " distance=2.02 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 733 " distance=2.02 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 722 " distance=2.01 Simple disulfide: pdb=" SG CYS A1005 " - pdb=" SG CYS A1016 " distance=2.02 Simple disulfide: pdb=" SG CYS A1055 " - pdb=" SG CYS A1099 " distance=2.04 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 197 " distance=2.00 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 257 " distance=2.04 Simple disulfide: pdb=" SG CYS B 275 " - pdb=" SG CYS B 328 " distance=2.05 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 441 " distance=2.00 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 581 " distance=2.02 Simple disulfide: pdb=" SG CYS B 564 " - pdb=" SG CYS B 570 " distance=2.06 Simple disulfide: pdb=" SG CYS B 829 " - pdb=" SG CYS B 840 " distance=2.02 Simple disulfide: pdb=" SG CYS B 879 " - pdb=" SG CYS B 923 " distance=2.03 Simple disulfide: pdb=" SG CYS C 265 " - pdb=" SG CYS C 275 " distance=2.05 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 335 " distance=2.02 Simple disulfide: pdb=" SG CYS C 353 " - pdb=" SG CYS C 406 " distance=2.04 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 499 " distance=2.03 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 564 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 623 " distance=2.03 Simple disulfide: pdb=" SG CYS C 636 " - pdb=" SG CYS C 645 " distance=2.05 Simple disulfide: pdb=" SG CYS C 712 " - pdb=" SG CYS C 734 " distance=2.05 Simple disulfide: pdb=" SG CYS C 717 " - pdb=" SG CYS C 723 " distance=2.04 Simple disulfide: pdb=" SG CYS C1006 " - pdb=" SG CYS C1017 " distance=2.02 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1100 " distance=2.03 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 Atom "HETATM23586 O5 NAG C1322 .*. O " rejected from bonding due to valence issues. Atom "HETATM23178 O5 NAG a 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM23148 O5 NAG Z 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM23556 O5 NAG C1317 .*. O " rejected from bonding due to valence issues. Atom "HETATM22620 O5 NAG L 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM22920 O5 NAG T 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 576 " " NAG A1302 " - " ASN A 589 " " NAG A1319 " - " ASN A 95 " " NAG A1320 " - " ASN A 138 " " NAG A1321 " - " ASN A 207 " " NAG A1331 " - " ASN A 316 " " NAG B1101 " - " ASN B 227 " " NAG B1102 " - " ASN B 467 " " NAG B1103 " - " ASN B 490 " " NAG B1109 " - " ASN B 239 " " NAG B1110 " - " ASN B 97 " " NAG B1114 " - " ASN B 35 " " NAG B1124 " - " ASN B 454 " " NAG B1125 " - " ASN B 81 " " NAG C1317 " - " ASN C 590 " " NAG C1318 " - " ASN C 577 " " NAG C1322 " - " ASN C 305 " " NAG C1329 " - " ASN C 139 " " NAG D 1 " - " ASN A 630 " " NAG E 1 " - " ASN A 690 " " NAG F 1 " - " ASN A 774 " " NAG G 1 " - " ASN A1047 " " NAG H 1 " - " ASN A1071 " " NAG I 1 " - " ASN A1107 " " NAG J 1 " - " ASN A 255 " " NAG K 1 " - " ASN A 304 " " NAG L 1 " - " ASN A 682 " " NAG M 1 " - " ASN B 530 " " NAG N 1 " - " ASN B 931 " " NAG O 1 " - " ASN B 871 " " NAG P 1 " - " ASN B 895 " " NAG Q 1 " - " ASN B 622 " " NAG R 1 " - " ASN B 538 " " NAG S 1 " - " ASN B 178 " " NAG T 1 " - " ASN B 151 " " NAG U 1 " - " ASN C1108 " " NAG V 1 " - " ASN C1072 " " NAG W 1 " - " ASN C1048 " " NAG X 1 " - " ASN C 775 " " NAG Y 1 " - " ASN C 691 " " NAG Z 1 " - " ASN C 683 " " NAG a 1 " - " ASN C 256 " " NAG b 1 " - " ASN C 317 " " NAG c 1 " - " ASN C 96 " Time building additional restraints: 10.91 Conformation dependent library (CDL) restraints added in 3.0 seconds 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 42 sheets defined 23.7% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 312 through 315 No H-bonds generated for 'chain 'A' and resid 312 through 315' Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 377 through 382 removed outlier: 4.386A pdb=" N ARG A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 382' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.683A pdb=" N LEU A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 755 removed outlier: 3.711A pdb=" N ASP A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 840 through 856 Processing helix chain 'A' and resid 860 through 863 No H-bonds generated for 'chain 'A' and resid 860 through 863' Processing helix chain 'A' and resid 871 through 882 removed outlier: 3.750A pdb=" N ILE A 882 " --> pdb=" O ARG A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 893 through 912 Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.124A pdb=" N LEU A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER A 940 " --> pdb=" O VAL A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 955 Processing helix chain 'A' and resid 959 through 1004 removed outlier: 4.109A pdb=" N VAL A 964 " --> pdb=" O PRO A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1119 removed outlier: 4.172A pdb=" N GLU A1117 " --> pdb=" O PRO A1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 313 through 316 No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.920A pdb=" N GLN B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 603 removed outlier: 3.502A pdb=" N ASP B 596 " --> pdb=" O ALA B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 684 through 687 No H-bonds generated for 'chain 'B' and resid 684 through 687' Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 710 through 715 removed outlier: 3.886A pdb=" N GLU B 715 " --> pdb=" O VAL B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 737 Processing helix chain 'B' and resid 743 through 764 removed outlier: 4.200A pdb=" N LEU B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER B 764 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 783 through 829 removed outlier: 3.947A pdb=" N VAL B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 793 " --> pdb=" O GLN B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 942 removed outlier: 3.687A pdb=" N GLU B 941 " --> pdb=" O PRO B 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'C' and resid 313 through 316 No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 358 through 362 removed outlier: 4.126A pdb=" N ASN C 362 " --> pdb=" O THR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 removed outlier: 4.372A pdb=" N ARG C 382 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 395 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 712 through 717 Processing helix chain 'C' and resid 721 through 728 Processing helix chain 'C' and resid 733 through 756 removed outlier: 3.547A pdb=" N ASP C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 799 Processing helix chain 'C' and resid 841 through 858 Processing helix chain 'C' and resid 861 through 864 No H-bonds generated for 'chain 'C' and resid 861 through 864' Processing helix chain 'C' and resid 872 through 883 Processing helix chain 'C' and resid 887 through 892 removed outlier: 3.938A pdb=" N GLU C 892 " --> pdb=" O VAL C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 914 removed outlier: 3.597A pdb=" N GLN C 909 " --> pdb=" O ILE C 905 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 910 " --> pdb=" O GLY C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 941 removed outlier: 4.132A pdb=" N LEU C 940 " --> pdb=" O LEU C 936 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER C 941 " --> pdb=" O VAL C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 956 Processing helix chain 'C' and resid 960 through 1006 removed outlier: 4.256A pdb=" N VAL C 965 " --> pdb=" O PRO C 961 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1120 removed outlier: 4.172A pdb=" N GLU C1118 " --> pdb=" O PRO C1114 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 removed outlier: 3.759A pdb=" N SER A 33 " --> pdb=" O SER A 4 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 21 through 24 removed outlier: 3.765A pdb=" N ASP A 260 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 36 through 38 removed outlier: 3.538A pdb=" N ILE A 176 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 200 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER A 178 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 77 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= F, first strand: chain 'A' and resid 299 through 301 Processing sheet with id= G, first strand: chain 'A' and resid 327 through 331 removed outlier: 4.040A pdb=" N VAL A 368 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 425 through 427 Processing sheet with id= I, first strand: chain 'A' and resid 524 through 527 removed outlier: 3.872A pdb=" N GLU A 556 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP A 547 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY A 539 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 615 through 618 removed outlier: 4.981A pdb=" N GLY A 567 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 570 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN A 287 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR A 572 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE A 285 " --> pdb=" O THR A 572 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 644 through 648 Processing sheet with id= L, first strand: chain 'A' and resid 684 through 688 removed outlier: 3.746A pdb=" N ALA A1051 " --> pdb=" O PHE A1068 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A1068 " --> pdb=" O ALA A1051 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 690 through 701 removed outlier: 6.029A pdb=" N TYR A1040 " --> pdb=" O HIS A1021 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS A1021 " --> pdb=" O TYR A1040 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 706 through 709 removed outlier: 4.442A pdb=" N LYS A 706 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1053 through 1056 Processing sheet with id= P, first strand: chain 'B' and resid 2 through 4 removed outlier: 7.137A pdb=" N ASN B 35 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N TYR B 165 " --> pdb=" O ASN B 35 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.769A pdb=" N ASP B 183 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 62 through 65 removed outlier: 3.502A pdb=" N PHE B 65 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 86 through 88 Processing sheet with id= T, first strand: chain 'B' and resid 222 through 224 removed outlier: 5.309A pdb=" N ASP B 425 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY B 417 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 250 through 254 removed outlier: 4.271A pdb=" N ASN B 290 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 367 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 475 through 477 removed outlier: 4.282A pdb=" N GLY B 445 " --> pdb=" O GLN B 464 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 212 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 448 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLN B 210 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR B 450 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE B 208 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 513 through 517 removed outlier: 6.475A pdb=" N ALA B 505 " --> pdb=" O PRO B 498 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 532 through 536 Processing sheet with id= Y, first strand: chain 'B' and resid 538 through 549 removed outlier: 6.183A pdb=" N TYR B 864 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N HIS B 845 " --> pdb=" O TYR B 864 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 555 through 557 Processing sheet with id= AA, first strand: chain 'B' and resid 885 through 887 Processing sheet with id= AB, first strand: chain 'B' and resid 891 through 894 Processing sheet with id= AC, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= AD, first strand: chain 'C' and resid 22 through 25 removed outlier: 3.682A pdb=" N ASP C 261 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 28 through 30 Processing sheet with id= AF, first strand: chain 'C' and resid 238 through 243 removed outlier: 4.368A pdb=" N ALA C 238 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR C 69 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 68 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 100 through 103 Processing sheet with id= AH, first strand: chain 'C' and resid 300 through 302 removed outlier: 3.822A pdb=" N ILE C 300 " --> pdb=" O ASN C 514 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 328 through 332 removed outlier: 4.766A pdb=" N ASN C 368 " --> pdb=" O GLU C 490 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 490 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 622 through 625 removed outlier: 4.802A pdb=" N GLY C 568 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 571 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLN C 288 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR C 573 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE C 286 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY C 575 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS C 284 " --> pdb=" O GLY C 575 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 665 through 670 removed outlier: 6.447A pdb=" N ALA C 646 " --> pdb=" O PRO C 639 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 685 through 689 Processing sheet with id= AM, first strand: chain 'C' and resid 691 through 702 removed outlier: 6.076A pdb=" N TYR C1041 " --> pdb=" O HIS C1022 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N HIS C1022 " --> pdb=" O TYR C1041 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 707 through 710 removed outlier: 4.304A pdb=" N LYS C 707 " --> pdb=" O LEU C 835 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 1055 through 1057 Processing sheet with id= AP, first strand: chain 'C' and resid 1068 through 1071 816 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.68 Time building geometry restraints manager: 11.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 23707 1.54 - 1.86: 379 1.86 - 2.18: 1 2.18 - 2.50: 0 2.50 - 2.83: 1 Bond restraints: 24088 Sorted by residual: bond pdb=" C CYS A 498 " pdb=" N GLY A 499 " ideal model delta sigma weight residual 1.330 2.827 -1.497 1.49e-02 4.50e+03 1.01e+04 bond pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 1.331 1.992 -0.661 2.07e-02 2.33e+03 1.02e+03 bond pdb=" C1 NAG G 2 " pdb=" O1 NAG G 2 " ideal model delta sigma weight residual 1.390 1.431 -0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" C1 NAG E 1 " pdb=" O1 NAG E 1 " ideal model delta sigma weight residual 1.390 1.431 -0.041 1.00e-02 1.00e+04 1.69e+01 bond pdb=" C1 NAG Z 2 " pdb=" O1 NAG Z 2 " ideal model delta sigma weight residual 1.390 1.431 -0.041 1.00e-02 1.00e+04 1.66e+01 ... (remaining 24083 not shown) Histogram of bond angle deviations from ideal: 88.14 - 98.52: 6 98.52 - 108.91: 1700 108.91 - 119.30: 18543 119.30 - 129.69: 12489 129.69 - 140.08: 80 Bond angle restraints: 32818 Sorted by residual: angle pdb=" O LEU A 308 " pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 122.81 90.95 31.86 1.42e+00 4.96e-01 5.03e+02 angle pdb=" C CYS A 498 " pdb=" N GLY A 499 " pdb=" CA GLY A 499 " ideal model delta sigma weight residual 121.87 88.14 33.73 1.57e+00 4.06e-01 4.62e+02 angle pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N CYS A 309 " ideal model delta sigma weight residual 115.54 140.08 -24.54 1.52e+00 4.33e-01 2.61e+02 angle pdb=" O CYS A 498 " pdb=" C CYS A 498 " pdb=" N GLY A 499 " ideal model delta sigma weight residual 123.24 108.40 14.84 1.23e+00 6.61e-01 1.46e+02 angle pdb=" O1 NAG W 2 " pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 110.25 134.98 -24.73 2.76e+00 1.32e-01 8.04e+01 ... (remaining 32813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 13374 22.34 - 44.68: 758 44.68 - 67.03: 81 67.03 - 89.37: 28 89.37 - 111.71: 4 Dihedral angle restraints: 14245 sinusoidal: 5915 harmonic: 8330 Sorted by residual: dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 563 " pdb=" CB CYS A 563 " ideal model delta sinusoidal sigma weight residual -86.00 -11.43 -74.57 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CB CYS C 636 " pdb=" SG CYS C 636 " pdb=" SG CYS C 645 " pdb=" CB CYS C 645 " ideal model delta sinusoidal sigma weight residual -86.00 -13.39 -72.61 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS C 512 " pdb=" SG CYS C 512 " pdb=" SG CYS C 564 " pdb=" CB CYS C 564 " ideal model delta sinusoidal sigma weight residual -86.00 -154.61 68.61 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 14242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.031: 4054 1.031 - 2.061: 12 2.061 - 3.092: 1 3.092 - 4.123: 1 4.123 - 5.154: 2 Chirality restraints: 4070 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 2.75 -5.15 2.00e-02 2.50e+03 6.64e+04 chirality pdb=" C1 NAG C1318 " pdb=" C2 NAG C1318 " pdb=" O1 NAG C1318 " pdb=" O5 NAG C1318 " both_signs ideal model delta sigma weight residual False 2.30 -2.42 4.73 2.00e-01 2.50e+01 5.59e+02 chirality pdb=" C1 NAG W 2 " pdb=" C2 NAG W 2 " pdb=" O1 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False 2.30 -1.09 3.40 2.00e-01 2.50e+01 2.89e+02 ... (remaining 4067 not shown) Planarity restraints: 4122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O DMS A1329 " -0.204 2.00e-02 2.50e+03 2.78e-01 7.71e+02 pdb=" C1 DMS A1329 " -0.137 2.00e-02 2.50e+03 pdb=" C2 DMS A1329 " -0.137 2.00e-02 2.50e+03 pdb=" S DMS A1329 " 0.479 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O DMS A1330 " 0.201 2.00e-02 2.50e+03 2.76e-01 7.60e+02 pdb=" C1 DMS A1330 " 0.137 2.00e-02 2.50e+03 pdb=" C2 DMS A1330 " 0.137 2.00e-02 2.50e+03 pdb=" S DMS A1330 " -0.475 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 139 " 0.287 2.00e-02 2.50e+03 2.30e-01 6.61e+02 pdb=" CG ASN C 139 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN C 139 " -0.233 2.00e-02 2.50e+03 pdb=" ND2 ASN C 139 " -0.231 2.00e-02 2.50e+03 pdb=" C1 NAG C1329 " 0.260 2.00e-02 2.50e+03 ... (remaining 4119 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.99: 44 0.99 - 1.96: 140 1.96 - 2.94: 11798 2.94 - 3.92: 61474 3.92 - 4.90: 114190 Warning: very small nonbonded interaction distances. Nonbonded interactions: 187646 Sorted by model distance: nonbonded pdb=" O4 NAG I 1 " pdb=" O1 NAG I 2 " model vdw 0.008 2.440 nonbonded pdb=" O4 NAG c 1 " pdb=" O1 NAG c 2 " model vdw 0.020 2.440 nonbonded pdb=" O4 NAG Z 1 " pdb=" O1 NAG Z 2 " model vdw 0.024 2.440 nonbonded pdb=" O4 NAG D 1 " pdb=" O1 NAG D 2 " model vdw 0.031 2.440 nonbonded pdb=" O4 NAG Y 1 " pdb=" O1 NAG Y 2 " model vdw 0.037 2.440 ... (remaining 187641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 39 or resid 55 through 104 or resid 138 through \ 145 or resid 162 through 214 or resid 238 through 415 or resid 433 through 443 o \ r resid 483 through 593 or resid 614 through 801 or resid 827 through 1119)) selection = (chain 'B' and (resid 2 through 90 or resid 97 through 104 or resid 106 through \ 158 or resid 161 through 338 or resid 345 through 355 or resid 361 through 471 o \ r resid 474 through 649 or resid 651 through 943)) selection = (chain 'C' and (resid 2 through 105 or resid 139 through 146 or resid 163 throug \ h 215 or resid 239 through 416 or resid 434 through 1120)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'R' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 14927 2.51 5 N 3780 2.21 5 O 4807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 19.490 Check model and map are aligned: 0.410 Convert atoms to be neutral: 0.220 Process input model: 63.640 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.497 24088 Z= 0.828 Angle : 0.833 33.734 32818 Z= 0.470 Chirality : 0.164 5.154 4070 Planarity : 0.009 0.278 4078 Dihedral : 13.519 111.712 8756 Min Nonbonded Distance : 0.008 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.52 % 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: -0.93 (0.14), residues: 2793 helix: 0.56 (0.19), residues: 660 sheet: -0.21 (0.19), residues: 631 loop : -1.35 (0.14), residues: 1502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5586 Ramachandran restraints generated. 2793 Oldfield, 0 Emsley, 2793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 431 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 442 average time/residue: 0.3764 time to fit residues: 257.3803 Evaluate side-chains 203 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 198 time to evaluate : 3.090 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2204 time to fit residues: 6.1923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 166 optimal weight: 0.6980 chunk 258 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN A 617 GLN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN A 874 GLN A 887 ASN A 938 GLN A1009 GLN A1061 HIS A1079 GLN A1108 ASN B 128 ASN B 333 ASN B 391 ASN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN B 723 GLN B 751 GLN B 752 ASN B 807 GLN B 898 HIS B 916 ASN C 288 GLN C 537 GLN ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN C 927 ASN C 929 ASN C 985 GLN C1045 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.150 24088 Z= 0.292 Angle : 0.816 21.604 32818 Z= 0.417 Chirality : 0.117 4.811 4070 Planarity : 0.004 0.040 4078 Dihedral : 7.494 105.489 3658 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 1.91 % 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: -0.46 (0.15), residues: 2795 helix: 1.36 (0.20), residues: 649 sheet: -0.06 (0.20), residues: 624 loop : -1.18 (0.15), residues: 1522 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 220 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 23 residues processed: 254 average time/residue: 0.3215 time to fit residues: 133.2539 Evaluate side-chains 201 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 2.535 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.2108 time to fit residues: 12.9111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 259 optimal weight: 0.1980 chunk 280 optimal weight: 0.8980 chunk 230 optimal weight: 0.4980 chunk 257 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 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 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN A 777 GLN ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN B 752 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 758 GLN C 761 GLN C 909 GLN C 966 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.139 24088 Z= 0.225 Angle : 0.742 20.904 32818 Z= 0.361 Chirality : 0.115 4.777 4070 Planarity : 0.004 0.056 4078 Dihedral : 6.582 110.206 3658 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.87 % 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 (0.15), residues: 2795 helix: 1.65 (0.20), residues: 653 sheet: 0.02 (0.20), residues: 610 loop : -1.03 (0.15), residues: 1532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 190 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 17 residues processed: 230 average time/residue: 0.3024 time to fit residues: 117.6371 Evaluate side-chains 182 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 2.859 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.2369 time to fit residues: 11.0568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 28 optimal weight: 0.3980 chunk 123 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 246 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN A 757 GLN ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 799 GLN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 GLN B 932 ASN ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 887 GLN C 923 GLN C 927 ASN C1075 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.146 24088 Z= 0.252 Angle : 0.739 20.162 32818 Z= 0.359 Chirality : 0.114 4.745 4070 Planarity : 0.004 0.061 4078 Dihedral : 6.433 109.407 3658 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 2.03 % 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: -0.13 (0.15), residues: 2795 helix: 1.79 (0.20), residues: 656 sheet: 0.03 (0.20), residues: 592 loop : -0.98 (0.15), residues: 1547 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 177 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 18 residues processed: 219 average time/residue: 0.3198 time to fit residues: 116.6871 Evaluate side-chains 175 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 2.987 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 18 average time/residue: 0.2192 time to fit residues: 11.1185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 235 optimal weight: 8.9990 chunk 190 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 247 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN C 758 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.144 24088 Z= 0.231 Angle : 0.712 20.493 32818 Z= 0.346 Chirality : 0.114 4.768 4070 Planarity : 0.004 0.067 4078 Dihedral : 6.327 108.244 3658 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.55 % 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: -0.10 (0.15), residues: 2795 helix: 1.83 (0.20), residues: 648 sheet: 0.11 (0.20), residues: 587 loop : -0.98 (0.15), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 18 residues processed: 210 average time/residue: 0.3227 time to fit residues: 113.7933 Evaluate side-chains 173 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 2.996 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 18 average time/residue: 0.2023 time to fit residues: 10.3311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.146 24088 Z= 0.236 Angle : 0.710 20.389 32818 Z= 0.346 Chirality : 0.113 4.757 4070 Planarity : 0.004 0.061 4078 Dihedral : 6.259 107.110 3658 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.67 % 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: -0.10 (0.15), residues: 2795 helix: 1.88 (0.20), residues: 644 sheet: 0.10 (0.20), residues: 608 loop : -1.00 (0.15), residues: 1543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 18 residues processed: 199 average time/residue: 0.3207 time to fit residues: 107.9524 Evaluate side-chains 169 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 2.911 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 18 average time/residue: 0.2268 time to fit residues: 11.5014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 232 optimal weight: 0.0870 chunk 153 optimal weight: 3.9990 chunk 274 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN C 554 GLN ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.144 24088 Z= 0.288 Angle : 0.727 20.654 32818 Z= 0.356 Chirality : 0.113 4.780 4070 Planarity : 0.004 0.058 4078 Dihedral : 6.276 106.283 3658 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 1.00 % 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: -0.09 (0.16), residues: 2795 helix: 1.77 (0.21), residues: 651 sheet: 0.09 (0.20), residues: 604 loop : -0.94 (0.15), residues: 1540 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 177 average time/residue: 0.3537 time to fit residues: 104.4917 Evaluate side-chains 151 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 2.885 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.2144 time to fit residues: 7.8861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 82 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 187 optimal weight: 0.0980 chunk 135 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 215 optimal weight: 0.0000 chunk 249 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN A 880 ASN A 930 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN B 752 ASN ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN C1057 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.145 24088 Z= 0.198 Angle : 0.704 20.680 32818 Z= 0.343 Chirality : 0.113 4.774 4070 Planarity : 0.004 0.092 4078 Dihedral : 6.170 106.106 3658 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.72 % 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: -0.05 (0.16), residues: 2795 helix: 1.93 (0.21), residues: 642 sheet: 0.10 (0.20), residues: 622 loop : -0.97 (0.15), residues: 1531 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 172 average time/residue: 0.3162 time to fit residues: 91.3102 Evaluate side-chains 150 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 2.764 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.2503 time to fit residues: 6.4780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 2.9990 chunk 240 optimal weight: 0.0670 chunk 255 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 242 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 270 optimal weight: 3.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 GLN ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.143 24088 Z= 0.257 Angle : 0.719 20.870 32818 Z= 0.351 Chirality : 0.113 4.784 4070 Planarity : 0.004 0.062 4078 Dihedral : 6.189 105.781 3658 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.44 % 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: -0.05 (0.16), residues: 2795 helix: 1.87 (0.21), residues: 647 sheet: 0.04 (0.20), residues: 630 loop : -0.93 (0.15), residues: 1518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 159 average time/residue: 0.3536 time to fit residues: 93.8510 Evaluate side-chains 147 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 2.692 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.2229 time to fit residues: 6.0945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 283 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 226 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 240 optimal weight: 0.0770 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.146 24088 Z= 0.217 Angle : 0.709 20.762 32818 Z= 0.346 Chirality : 0.113 4.771 4070 Planarity : 0.004 0.055 4078 Dihedral : 6.143 105.505 3658 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.32 % 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: -0.01 (0.16), residues: 2795 helix: 1.95 (0.21), residues: 645 sheet: 0.11 (0.20), residues: 625 loop : -0.94 (0.15), residues: 1525 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5590 Ramachandran restraints generated. 2795 Oldfield, 0 Emsley, 2795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 153 average time/residue: 0.3295 time to fit residues: 85.5302 Evaluate side-chains 149 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 3.076 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.2269 time to fit residues: 6.2944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 226 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 232 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 41 optimal weight: 0.0030 chunk 198 optimal weight: 7.9990 chunk 12 optimal weight: 0.0970 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN B 213 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.094978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064109 restraints weight = 79401.894| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.22 r_work: 0.3145 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work: 0.3127 rms_B_bonded: 3.95 restraints_weight: 0.1250 r_work: 0.3119 rms_B_bonded: 3.97 restraints_weight: 0.0625 r_work: 0.3110 rms_B_bonded: 4.01 restraints_weight: 0.0312 r_work: 0.3100 rms_B_bonded: 4.06 restraints_weight: 0.0156 r_work: 0.3091 rms_B_bonded: 4.13 restraints_weight: 0.0078 r_work: 0.3081 rms_B_bonded: 4.21 restraints_weight: 0.0039 r_work: 0.3072 rms_B_bonded: 4.30 restraints_weight: 0.0020 r_work: 0.3062 rms_B_bonded: 4.41 restraints_weight: 0.0010 r_work: 0.3052 rms_B_bonded: 4.52 restraints_weight: 0.0005 r_work: 0.3041 rms_B_bonded: 4.65 restraints_weight: 0.0002 r_work: 0.3031 rms_B_bonded: 4.80 restraints_weight: 0.0001 r_work: 0.3020 rms_B_bonded: 4.96 restraints_weight: 0.0001 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.146 24088 Z= 0.186 Angle : 0.700 20.782 32818 Z= 0.340 Chirality : 0.113 4.771 4070 Planarity : 0.004 0.049 4078 Dihedral : 6.082 105.483 3658 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.32 % 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 (0.16), residues: 2795 helix: 2.04 (0.21), residues: 647 sheet: 0.16 (0.20), residues: 622 loop : -0.91 (0.15), residues: 1526 =============================================================================== Job complete usr+sys time: 4188.32 seconds wall clock time: 79 minutes 5.67 seconds (4745.67 seconds total)